ARBA00027164 RNA catabolic process (GO:0006401)

id: ARBA00027164
description: >-
  Assigns GO:0006401 (RNA catabolic process) through 52 alternative condition sets built from InterPro,
  PANTHER and CATH FunFam signatures of RNA decay factors, most of them with a taxon condition.
status: COMPLETE
rule_type: ARBA
rule:
  rule_id: ARBA00027164
  condition_sets:
  - number: 1
    conditions:
    - condition_type: INTERPRO
      value: IPR000086
      curie: InterPro:IPR000086
      label: NUDIX hydrolase domain
      interpro_type: DOMAIN
      negated: false
    - condition_type: PANTHER
      value: PTHR23114:SF17
      curie: PANTHER:PTHR23114:SF17
      negated: false
    - condition_type: TAXON
      value: Eukaryota
      curie: NCBITaxon:2759
      label: Eukaryota
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 10 (UniProtKB query, 2026-11-10); unreviewed
      entries: 4009. Swiss-Prot matches: Q8IU60 (DCP2), Q8GW31 (DCP2), P53550 (DCP2), O62255 (dcap-2),
      Q9CYC6 (Dcp2), O13828 (dcp2), Q583R7 (NH4), Q5REQ8 (DCP2), and 2 more. Experimental annotation to
      GO:0006401 RNA catabolic process or an is_a/part_of descendant (QuickGO): O13828 dcp2 GO:0000290
      deadenylation-dependent decapping of nuclear-transcribed mRNA IDA PMID:27183195 (ComplexPortal);
      O62255 dcap-2 GO:0000290 deadenylation-dependent decapping of nuclear-transcribed mRNA IDA PMID:16199859
      (WB); P53550 DCP2 GO:0000290 deadenylation-dependent decapping of nuclear-transcribed mRNA IDA PMID:10508173
      (SGD); Q583R7 NH4 GO:0031087 deadenylation-independent decapping of nuclear-transcribed mRNA IDA
      PMID:26038549 (GeneDB); Q8GW31 DCP2 GO:0006402 mRNA catabolic process IMP PMID:17513503 (TAIR).
  - number: 2
    conditions:
    - condition_type: INTERPRO
      value: IPR001247
      curie: InterPro:IPR001247
      label: Exoribonuclease, phosphorolytic domain 1
      interpro_type: DOMAIN
      negated: false
    - condition_type: INTERPRO
      value: IPR020568
      curie: InterPro:IPR020568
      label: Ribosomal protein uS5 domain 2-type superfamily
      interpro_type: HOMOLOGOUS_SUPERFAMILY
      negated: false
    - condition_type: TAXON
      value: Primates
      curie: NCBITaxon:9443
      label: Primates
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 8 (UniProtKB query, 2026-11-10); unreviewed entries:
      417. Swiss-Prot matches: Q15024 (EXOSC7), Q8TCS8 (PNPT1), Q96B26 (EXOSC8), Q9NQT4 (EXOSC5), Q5RKV6
      (EXOSC6), Q9NPD3 (EXOSC4), Q06265 (EXOSC9), Q5RCW2 (PNPT1). Experimental annotation to GO:0006401
      RNA catabolic process or an is_a/part_of descendant (QuickGO): Q06265 EXOSC9 GO:0000956 nuclear-transcribed
      mRNA catabolic process IMP PMID:17545563 (UniProt); Q15024 EXOSC7 GO:0006401 RNA catabolic process
      IDA PMID:17174896 (ComplexPortal); Q5RKV6 EXOSC6 GO:0006401 RNA catabolic process IDA PMID:17174896
      (ComplexPortal); Q8TCS8 PNPT1 GO:0000957 mitochondrial RNA catabolic process IDA PMID:18501193 (UniProt);
      Q96B26 EXOSC8 GO:0006401 RNA catabolic process IDA PMID:17174896 (ComplexPortal).
  - number: 3
    conditions:
    - condition_type: INTERPRO
      value: IPR007282
      curie: InterPro:IPR007282
      label: NOT2/NOT3/NOT5, C-terminal
      interpro_type: DOMAIN
      negated: false
    - condition_type: INTERPRO
      value: IPR038635
      curie: InterPro:IPR038635
      label: CCR4-NOT complex subunit 2/3/5, C-terminal domain superfamily
      interpro_type: HOMOLOGOUS_SUPERFAMILY
      negated: false
    - condition_type: TAXON
      value: Fungi
      curie: NCBITaxon:4751
      label: Fungi
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 5 (UniProtKB query, 2026-11-10); unreviewed entries:
      3255. Swiss-Prot matches: Q12514 (NOT5), P06102 (NOT3), P06100 (CDC36), O13870 (not3), P87240 (not2).
      Experimental annotation to GO:0006401 RNA catabolic process or an is_a/part_of descendant (QuickGO):
      O13870 not3 GO:0000289 nuclear-transcribed mRNA poly(A) tail shortening IDA PMID:26804377 (PomBase);
      P06100 CDC36 GO:0000288 nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
      IDA PMID:11889048 (SGD); P06102 NOT3 GO:0000289 nuclear-transcribed mRNA poly(A) tail shortening
      IDA PMID:11889048 (SGD); P87240 not2 GO:0000289 nuclear-transcribed mRNA poly(A) tail shortening
      IDA PMID:26804377 (PomBase); Q12514 NOT5 GO:0000289 nuclear-transcribed mRNA poly(A) tail shortening
      IDA PMID:11889048 (SGD).
  - number: 4
    conditions:
    - condition_type: INTERPRO
      value: IPR028322
      curie: InterPro:IPR028322
      label: Proline-rich nuclear receptor coactivator-like, proline rich region
      interpro_type: CONSERVED_SITE
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 19 (UniProtKB query, 2026-11-10); unreviewed
      entries: 5074. Swiss-Prot matches: Q9NPJ4 (PNRC2), Q12796 (PNRC1), P40023 (EDC2), P53080 (EDC1),
      Q9CR73 (Pnrc2), Q10108 (no gene name), Q0VCW6 (PNRC2), B7TWP7 (pnrc2), and 11 more. Experimental
      annotation to GO:0006401 RNA catabolic process or an is_a/part_of descendant (QuickGO): B7TWP7 pnrc2
      GO:0000956 nuclear-transcribed mRNA catabolic process IGI PMID:28648842 (ZFIN); P40023 EDC2 GO:0000290
      deadenylation-dependent decapping of nuclear-transcribed mRNA IDA PMID:12554867 (SGD); P53080 EDC1
      GO:0000290 deadenylation-dependent decapping of nuclear-transcribed mRNA IDA PMID:12554867 (SGD);
      Q10108 SPAC18G6.09c GO:0000290 deadenylation-dependent decapping of nuclear-transcribed mRNA IDA
      PMID:27183195 (ComplexPortal); Q9NPJ4 PNRC2 GO:0000184 nuclear-transcribed mRNA catabolic process,
      nonsense-mediated decay IDA PMID:19150429 (UniProt).
  - number: 5
    conditions:
    - condition_type: FUNFAM
      value: 1.10.1410.10:FF:000003
      curie: CATH.FunFam:1.10.1410.10:FF:000003
      label: non-canonical poly(A) RNA polymerase PAPD7
      negated: false
    - condition_type: TAXON
      value: Eukaryota
      curie: NCBITaxon:2759
      label: Eukaryota
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 8 (UniProtKB query, 2026-11-10); unreviewed entries:
      2182. Swiss-Prot matches: Q5XG87 (TENT4A), P53632 (PAP2), P48561 (TRF5), Q6PB75 (Tent4a), Q7KVS9
      (Trf4-1), Q9UTN3 (cid14), Q9HFW3 (TRF5), Q5K9E2 (CID14). Experimental annotation to GO:0006401 RNA
      catabolic process or an is_a/part_of descendant (QuickGO): P48561 TRF5 GO:0071035 nuclear polyadenylation-dependent
      rRNA catabolic process IGI PMID:15935758 (SGD); P53632 PAP2 GO:0071031 nuclear mRNA surveillance
      of mRNA 3'-end processing IGI PMID:17410208 (SGD); Q7KVS9 Trf4-1 GO:0043634 polyadenylation-dependent
      ncRNA catabolic process IMP PMID:18765642 (FlyBase); Q9UTN3 cid14 GO:0043634 polyadenylation-dependent
      ncRNA catabolic process IMP PMID:16478992 (PomBase).
  - number: 6
    conditions:
    - condition_type: FUNFAM
      value: 3.90.79.10:FF:000003
      curie: CATH.FunFam:3.90.79.10:FF:000003
      label: M7GpppN-mRNA hydrolase isoform 2
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 6 (UniProtKB query, 2026-11-10); unreviewed entries:
      3628. Swiss-Prot matches: Q8IU60 (DCP2), Q8GW31 (DCP2), Q9CYC6 (Dcp2), O62255 (dcap-2), O13828 (dcp2),
      Q5REQ8 (DCP2). Experimental annotation to GO:0006401 RNA catabolic process or an is_a/part_of descendant
      (QuickGO): O13828 dcp2 GO:0000290 deadenylation-dependent decapping of nuclear-transcribed mRNA
      IDA PMID:27183195 (ComplexPortal); O62255 dcap-2 GO:0000290 deadenylation-dependent decapping of
      nuclear-transcribed mRNA IDA PMID:16199859 (WB); Q8GW31 DCP2 GO:0006402 mRNA catabolic process IMP
      PMID:17513503 (TAIR); Q8IU60 DCP2 GO:0006402 mRNA catabolic process IDA PMID:21070968 (UniProt);
      Q9CYC6 Dcp2 GO:0006402 mRNA catabolic process IMP PMID:21070968 (UniProt).
  - number: 7
    conditions:
    - condition_type: FUNFAM
      value: 4.10.1000.10:FF:000001
      curie: CATH.FunFam:4.10.1000.10:FF:000001
      label: zinc finger CCCH domain-containing protein 15-like
      negated: false
    - condition_type: FUNFAM
      value: 4.10.1000.10:FF:000002
      curie: CATH.FunFam:4.10.1000.10:FF:000002
      label: Zinc finger protein 36, C3H1 type-like 1
      negated: false
    - condition_type: TAXON
      value: Mus
      curie: NCBITaxon:10088
      label: Mus
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 4 (UniProtKB query, 2026-11-10); unreviewed entries:
      14. Swiss-Prot matches: P22893 (Zfp36), P23949 (Zfp36l2), P23950 (Zfp36l1), Q5ISE2 (Zfp36l3). Experimental
      annotation to GO:0006401 RNA catabolic process or an is_a/part_of descendant (QuickGO): P22893 Zfp36
      GO:0000288 nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay IDA PMID:15814898
      (MGI); P23949 Zfp36l2 GO:0000288 nuclear-transcribed mRNA catabolic process, deadenylation-dependent
      decay IDA PMID:15814898 (MGI); P23950 Zfp36l1 GO:0000288 nuclear-transcribed mRNA catabolic process,
      deadenylation-dependent decay IDA PMID:15814898 (MGI); Q5ISE2 Zfp36l3 GO:0000288 nuclear-transcribed
      mRNA catabolic process, deadenylation-dependent decay IDA PMID:15814898 (MGI).
  - number: 8
    conditions:
    - condition_type: FUNFAM
      value: 1.10.3380.30:FF:000001
      curie: CATH.FunFam:1.10.3380.30:FF:000001
      label: Ski2 ATP-dependent RNA helicase
      negated: false
    - condition_type: FUNFAM
      value: 3.40.50.300:FF:000354
      curie: CATH.FunFam:3.40.50.300:FF:000354
      label: ATP-dependent RNA helicase SKI2
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 5 (UniProtKB query, 2026-11-10); unreviewed entries:
      2814. Swiss-Prot matches: Q15477 (SKIC2), F4JAA5 (SKI2), P35207 (SKI2), Q6NZR5 (Skic2), O59801 (no
      gene name). Experimental annotation to GO:0006401 RNA catabolic process or an is_a/part_of descendant
      (QuickGO): F4JAA5 SKI2 GO:0000292 RNA fragment catabolic process IMP PMID:26464441 (TAIR); O59801
      SPCC550.03c GO:1990074 polyuridylation-dependent mRNA catabolic process IGI PMID:39333464 (PomBase);
      P35207 SKI2 GO:0000956 nuclear-transcribed mRNA catabolic process IDA PMID:23953113 (ComplexPortal);
      Q15477 SKIC2 GO:0000956 nuclear-transcribed mRNA catabolic process IPI PMID:35120588 (ComplexPortal).
  - number: 9
    conditions:
    - condition_type: FUNFAM
      value: 1.10.3380.30:FF:000002
      curie: CATH.FunFam:1.10.3380.30:FF:000002
      label: superkiller viralicidic activity 2-like 2
      negated: false
    - condition_type: FUNFAM
      value: 2.40.30.300:FF:000001
      curie: CATH.FunFam:2.40.30.300:FF:000001
      label: Mtr4 exosome RNA helicase
      negated: false
    - condition_type: FUNFAM
      value: 3.40.50.300:FF:000083
      curie: CATH.FunFam:3.40.50.300:FF:000083
      label: ATP-dependent RNA helicase DOB1
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 4 (UniProtKB query, 2026-11-10); unreviewed entries:
      1545. Swiss-Prot matches: P42285 (MTREX), P47047 (MTR4), Q9CZU3 (Mtrex), O14232 (mtr4). Experimental
      annotation to GO:0006401 RNA catabolic process or an is_a/part_of descendant (QuickGO): O14232 mtr4
      GO:0006401 RNA catabolic process IDA PMID:29906447 (PomBase); P42285 MTREX GO:0006401 RNA catabolic
      process IDA PMID:29906447 (UniProt); P47047 MTR4 GO:0000292 RNA fragment catabolic process IMP PMID:26317469
      (CACAO).
  - number: 10
    conditions:
    - condition_type: FUNFAM
      value: 2.40.50.140:FF:000087
      curie: CATH.FunFam:2.40.50.140:FF:000087
      label: Protein lin-28 homolog B
      negated: false
    - condition_type: FUNFAM
      value: 4.10.60.10:FF:000007
      curie: CATH.FunFam:4.10.60.10:FF:000007
      label: Protein lin-28 homolog A
      negated: false
    - condition_type: TAXON
      value: Mammalia
      curie: NCBITaxon:40674
      label: Mammalia
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 4 (UniProtKB query, 2026-11-10); unreviewed entries:
      455. Swiss-Prot matches: Q6ZN17 (LIN28B), Q9H9Z2 (LIN28A), Q45KJ6 (Lin28b), Q8K3Y3 (Lin28a). Experimental
      annotation to GO:0006401 RNA catabolic process or an is_a/part_of descendant (QuickGO): Q6ZN17 LIN28B
      GO:0010587 miRNA catabolic process IMP PMID:19703396 (UniProt); Q8K3Y3 Lin28a GO:0010587 miRNA catabolic
      process IDA PMID:21962509 (BHF-UCL); Q9H9Z2 LIN28A GO:0010587 miRNA catabolic process IMP PMID:19703396
      (UniProt).
  - number: 11
    conditions:
    - condition_type: FUNFAM
      value: 3.40.50.12390:FF:000001
      curie: CATH.FunFam:3.40.50.12390:FF:000001
      label: 5'-3' exoribonuclease
      negated: false
    - condition_type: FUNFAM
      value: 3.40.50.12390:FF:000003
      curie: CATH.FunFam:3.40.50.12390:FF:000003
      label: 5'-3' exoribonuclease
      negated: false
    - condition_type: TAXON
      value: Viridiplantae
      curie: NCBITaxon:33090
      label: Viridiplantae
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 3 (UniProtKB query, 2026-11-10); unreviewed entries:
      1240. Swiss-Prot matches: Q9FQ02 (XRN2), Q9FQ03 (XRN3), Q9FQ04 (XRN4). Experimental annotation to
      GO:0006401 RNA catabolic process or an is_a/part_of descendant (QuickGO): Q9FQ02 XRN2 GO:0010587
      miRNA catabolic process IMP PMID:17993620 (TAIR); Q9FQ03 XRN3 GO:0010587 miRNA catabolic process
      IMP PMID:17993620 (TAIR); Q9FQ04 XRN4 GO:0000956 nuclear-transcribed mRNA catabolic process IMP
      PMID:15528448 (TAIR).
  - number: 12
    conditions:
    - condition_type: FUNFAM
      value: 2.130.10.10:FF:000065
      curie: CATH.FunFam:2.130.10.10:FF:000065
      label: WD repeat-containing protein 82
      negated: false
    - condition_type: TAXON
      value: Metazoa
      curie: NCBITaxon:33208
      label: Metazoa
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 8 (UniProtKB query, 2026-11-10); unreviewed entries:
      1499. Swiss-Prot matches: Q6UXN9 (WDR82), Q8BFQ4 (Wdr82), Q9VLN1 (Wdr82), Q6NV31 (wdr82), Q58E77
      (wdr82-b), Q640J6 (wdr82-a), Q6GL39 (wdr82), Q5ZMV7 (WDR82). Experimental annotation to GO:0006401
      RNA catabolic process or an is_a/part_of descendant (QuickGO): Q6UXN9 WDR82 GO:0071027 nuclear RNA
      surveillance IDA PMID:33913806 (UniProt); Q8BFQ4 Wdr82 GO:0071027 nuclear RNA surveillance IDA PMID:33767452
      (UniProt); Q9VLN1 Wdr82 GO:0071027 nuclear RNA surveillance IDA PMID:26577379 (UniProt).
  - number: 13
    conditions:
    - condition_type: FUNFAM
      value: 1.25.40.180:FF:000012
      curie: CATH.FunFam:1.25.40.180:FF:000012
      label: Ccr4-Not transcription complex subunit
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 3 (UniProtKB query, 2026-11-10); unreviewed entries:
      2550. Swiss-Prot matches: P25655 (CDC39), Q20937 (let-711), P87112 (not1). Experimental annotation
      to GO:0006401 RNA catabolic process or an is_a/part_of descendant (QuickGO): P25655 CDC39 GO:0000288
      nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay IDA PMID:11889048 (SGD);
      P87112 not1 GO:0000289 nuclear-transcribed mRNA poly(A) tail shortening IDA PMID:26804377 (PomBase);
      Q20937 let-711 GO:0000289 nuclear-transcribed mRNA poly(A) tail shortening IMP PMID:23843623 (WB).
  - number: 14
    conditions:
    - condition_type: FUNFAM
      value: 2.40.50.700:FF:000001
      curie: CATH.FunFam:2.40.50.700:FF:000001
      label: Exosome complex exonuclease exoribonuclease (Rrp44)
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 5 (UniProtKB query, 2026-11-10); unreviewed entries:
      3577. Swiss-Prot matches: Q9Y2L1 (DIS3), Q08162 (DIS3), Q9CSH3 (Dis3), P37202 (dis3), Q17632 (dis-3).
      Experimental annotation to GO:0006401 RNA catabolic process or an is_a/part_of descendant (QuickGO):
      P37202 dis3 GO:0006401 RNA catabolic process IDA PMID:29906447 (PomBase); Q08162 DIS3 GO:0000957
      mitochondrial RNA catabolic process IMP PMID:24143261 (SGD); Q9Y2L1 DIS3 GO:0006401 RNA catabolic
      process IDA PMID:17174896 (ComplexPortal).
  - number: 15
    conditions:
    - condition_type: FUNFAM
      value: 2.40.50.700:FF:000003
      curie: CATH.FunFam:2.40.50.700:FF:000003
      label: DIS3-like exonuclease 2
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 4 (UniProtKB query, 2026-11-10); unreviewed entries:
      1376. Swiss-Prot matches: Q8IYB7 (DIS3L2), Q8CI75 (Dis3l2), O14040 (dis32), Q0V9R3 (dis3l2). Experimental
      annotation to GO:0006401 RNA catabolic process or an is_a/part_of descendant (QuickGO): O14040 dis32
      GO:0000956 nuclear-transcribed mRNA catabolic process IMP PMID:23503588 (UniProt); Q8CI75 Dis3l2
      GO:0010587 miRNA catabolic process IDA PMID:25119025 (UniProt); Q8IYB7 DIS3L2 GO:0000956 nuclear-transcribed
      mRNA catabolic process IMP PMID:23756462 (UniProt).
  - number: 16
    conditions:
    - condition_type: FUNFAM
      value: 3.30.460.10:FF:000006
      curie: CATH.FunFam:3.30.460.10:FF:000006
      label: non-canonical poly(A) RNA polymerase PAPD5
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 5 (UniProtKB query, 2026-11-10); unreviewed entries:
      2281. Swiss-Prot matches: Q8NDF8 (TENT4B), Q7KVS9 (Trf4-1), Q68ED3 (Tent4b), Q9UTN3 (cid14), Q5K9E2
      (CID14). Experimental annotation to GO:0006401 RNA catabolic process or an is_a/part_of descendant
      (QuickGO): Q7KVS9 Trf4-1 GO:0043634 polyadenylation-dependent ncRNA catabolic process IMP PMID:18765642
      (FlyBase); Q8NDF8 TENT4B GO:0010587 miRNA catabolic process IDA PMID:25049417 (UniProt); Q9UTN3
      cid14 GO:0043634 polyadenylation-dependent ncRNA catabolic process IMP PMID:16478992 (PomBase).
  - number: 17
    conditions:
    - condition_type: FUNFAM
      value: 3.30.460.10:FF:000067
      curie: CATH.FunFam:3.30.460.10:FF:000067
      label: Terminal uridylyltransferase cid1
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 3 (UniProtKB query, 2026-11-10); unreviewed entries:
      632. Swiss-Prot matches: O64642 (URT1), O13833 (cid1), O13798 (cid16). Experimental annotation to
      GO:0006401 RNA catabolic process or an is_a/part_of descendant (QuickGO): O13798 cid16 GO:0000957
      mitochondrial RNA catabolic process IMP PMID:39333464 (PomBase); O13833 cid1 GO:0036450 polyuridylation-dependent
      decapping of nuclear-transcribed mRNA IGI PMID:39333464 (PomBase); O64642 URT1 GO:0000289 nuclear-transcribed
      mRNA poly(A) tail shortening IDA PMID:33637717 (TAIR).
  - number: 18
    conditions:
    - condition_type: FUNFAM
      value: 1.10.10.400:FF:000001
      curie: CATH.FunFam:1.10.10.400:FF:000001
      label: Polyribonucleotide nucleotidyltransferase 1, mitochondrial
      negated: false
    - condition_type: FUNFAM
      value: 2.40.50.140:FF:000113
      curie: CATH.FunFam:2.40.50.140:FF:000113
      label: polyribonucleotide nucleotidyltransferase 1, mitochondrial
      negated: false
    - condition_type: FUNFAM
      value: 3.30.1370.10:FF:000044
      curie: CATH.FunFam:3.30.1370.10:FF:000044
      label: Polyribonucleotide nucleotidyltransferase 1, mitochondrial
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 3 (UniProtKB query, 2026-11-10); unreviewed entries:
      753. Swiss-Prot matches: Q8TCS8 (PNPT1), Q8K1R3 (Pnpt1), Q5RCW2 (PNPT1). Experimental annotation
      to GO:0006401 RNA catabolic process or an is_a/part_of descendant (QuickGO): Q8K1R3 Pnpt1 GO:0000958
      mitochondrial mRNA catabolic process IMP PMID:20691904 (UniProt); Q8TCS8 PNPT1 GO:0000957 mitochondrial
      RNA catabolic process IDA PMID:18501193 (UniProt).
  - number: 19
    conditions:
    - condition_type: FUNFAM
      value: 1.10.10.460:FF:000001
      curie: CATH.FunFam:1.10.10.460:FF:000001
      label: Ribonuclease
      negated: false
    - condition_type: FUNFAM
      value: 3.30.420.10:FF:000016
      curie: CATH.FunFam:3.30.420.10:FF:000016
      label: Ribonuclease
      negated: false
    - condition_type: TAXON
      value: Fungi
      curie: NCBITaxon:4751
      label: Fungi
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 3 (UniProtKB query, 2026-11-10); unreviewed entries:
      1359. Swiss-Prot matches: P53942 (RNH201), Q10236 (rnh201), Q9P5X8 (rnh-201). Experimental annotation
      to GO:0006401 RNA catabolic process or an is_a/part_of descendant (QuickGO): P53942 RNH201 GO:0043137
      DNA replication, removal of RNA primer IDA PMID:10567561 (SGD); Q10236 rnh201 GO:0006401 RNA catabolic
      process IMP PMID:29622660 (PomBase).
  - number: 20
    conditions:
    - condition_type: FUNFAM
      value: 1.10.1410.10:FF:000002
      curie: CATH.FunFam:1.10.1410.10:FF:000002
      label: terminal uridylyltransferase 4 isoform X1
      negated: false
    - condition_type: FUNFAM
      value: 1.10.1410.10:FF:000004
      curie: CATH.FunFam:1.10.1410.10:FF:000004
      label: terminal uridylyltransferase 4 isoform X2
      negated: false
    - condition_type: TAXON
      value: Glires
      curie: NCBITaxon:314147
      label: Glires
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 2 (UniProtKB query, 2026-11-10); unreviewed entries:
      141. Swiss-Prot matches: B2RX14 (Tut4), Q5BLK4 (Tut7). Experimental annotation to GO:0006401 RNA
      catabolic process or an is_a/part_of descendant (QuickGO): B2RX14 Tut4 GO:1990074 polyuridylation-dependent
      mRNA catabolic process IMP PMID:28792939 (MGI); Q5BLK4 Tut7 GO:1990074 polyuridylation-dependent
      mRNA catabolic process IMP PMID:28792939 (UniProt).
  - number: 21
    conditions:
    - condition_type: FUNFAM
      value: 1.10.287.3700:FF:000001
      curie: CATH.FunFam:1.10.287.3700:FF:000001
      label: PAN2-PAN3 deadenylation complex subunit PAN3
      negated: false
    - condition_type: FUNFAM
      value: 1.10.510.10:FF:000168
      curie: CATH.FunFam:1.10.510.10:FF:000168
      label: PAN2-PAN3 deadenylation complex subunit PAN3
      negated: false
    - condition_type: FUNFAM
      value: 1.20.5.5160:FF:000001
      curie: CATH.FunFam:1.20.5.5160:FF:000001
      label: PAN2-PAN3 deadenylation complex subunit PAN3
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 3 (UniProtKB query, 2026-11-10); unreviewed entries:
      1187. Swiss-Prot matches: Q58A45 (PAN3), Q640Q5 (Pan3), A1L1C7 (pan3). Experimental annotation to
      GO:0006401 RNA catabolic process or an is_a/part_of descendant (QuickGO): Q640Q5 Pan3 GO:0000289
      nuclear-transcribed mRNA poly(A) tail shortening IGI PMID:41714623 (MGI).
  - number: 22
    conditions:
    - condition_type: FUNFAM
      value: 1.10.510.10:FF:000215
      curie: CATH.FunFam:1.10.510.10:FF:000215
      label: serine/threonine-protein kinase/endoribonuclease IRE1 isoform X1
      negated: false
    - condition_type: FUNFAM
      value: 1.20.1440.180:FF:000001
      curie: CATH.FunFam:1.20.1440.180:FF:000001
      label: Serine/threonine-protein kinase/endoribonuclease IRE1
      negated: false
    - condition_type: TAXON
      value: Primates
      curie: NCBITaxon:9443
      label: Primates
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 2 (UniProtKB query, 2026-11-10); unreviewed entries:
      112. Swiss-Prot matches: Q76MJ5 (ERN2), O75460 (ERN1). Experimental annotation to GO:0006401 RNA
      catabolic process or an is_a/part_of descendant (QuickGO): Q76MJ5 ERN2 GO:0016075 rRNA catabolic
      process IDA PMID:11175748 (UniProt).
  - number: 23
    conditions:
    - condition_type: FUNFAM
      value: 1.20.1270.10:FF:000003
      curie: CATH.FunFam:1.20.1270.10:FF:000003
      label: heat shock cognate 71 kDa protein-like
      negated: false
    - condition_type: FUNFAM
      value: 3.30.30.30:FF:000001
      curie: CATH.FunFam:3.30.30.30:FF:000001
      label: heat shock 70 kDa protein-like
      negated: false
    - condition_type: TAXON
      value: Haplorrhini
      curie: NCBITaxon:376913
      label: Haplorrhini
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 4 (UniProtKB query, 2026-11-10); unreviewed entries:
      61. Swiss-Prot matches: P0DMV8 (HSPA1A), P0DMV9 (HSPA1B), Q5R7D3 (HSPA1A), Q28222 (HSPA1). Experimental
      annotation to GO:0006401 RNA catabolic process or an is_a/part_of descendant (QuickGO): P0DMV8 HSPA1A
      GO:0006402 mRNA catabolic process IDA PMID:10205060 (UniProt); P0DMV9 HSPA1B GO:0006402 mRNA catabolic
      process IDA PMID:10205060 (UniProt).
  - number: 24
    conditions:
    - condition_type: FUNFAM
      value: 1.25.10.10:FF:000167
      curie: CATH.FunFam:1.25.10.10:FF:000167
      label: RNA binding protein Jsn1
      negated: false
    - condition_type: FUNFAM
      value: 3.30.70.330:FF:000617
      curie: CATH.FunFam:3.30.70.330:FF:000617
      label: Puf family protein
      negated: false
    - condition_type: TAXON
      value: Dikarya
      curie: NCBITaxon:451864
      label: Dikarya
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 2 (UniProtKB query, 2026-11-10); unreviewed entries:
      58. Swiss-Prot matches: P47135 (JSN1), Q12221 (PUF2). Experimental annotation to GO:0006401 RNA
      catabolic process or an is_a/part_of descendant (QuickGO): P47135 JSN1 GO:0000288 nuclear-transcribed
      mRNA catabolic process, deadenylation-dependent decay IGI PMID:11101532 (SGD); Q12221 PUF2 GO:0000288
      nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay IMP PMID:11101532 (SGD).
  - number: 25
    conditions:
    - condition_type: FUNFAM
      value: 1.25.40.1050:FF:000001
      curie: CATH.FunFam:1.25.40.1050:FF:000001
      label: 5'-3' exoribonuclease 1
      negated: false
    - condition_type: FUNFAM
      value: 3.40.50.12390:FF:000002
      curie: CATH.FunFam:3.40.50.12390:FF:000002
      label: 5'-3' exoribonuclease 1
      negated: false
    - condition_type: TAXON
      value: Ascomycota
      curie: NCBITaxon:4890
      label: Ascomycota
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 2 (UniProtKB query, 2026-11-10); unreviewed entries:
      34. Swiss-Prot matches: P22147 (XRN1), P40383 (exo2). Experimental annotation to GO:0006401 RNA
      catabolic process or an is_a/part_of descendant (QuickGO): P22147 XRN1 GO:0000184 nuclear-transcribed
      mRNA catabolic process, nonsense-mediated decay IMP PMID:10848586 (SGD).
  - number: 26
    conditions:
    - condition_type: FUNFAM
      value: 1.25.40.10:FF:000094
      curie: CATH.FunFam:1.25.40.10:FF:000094
      label: telomerase-binding protein EST1A isoform X1
      negated: false
    - condition_type: FUNFAM
      value: 3.40.50.1010:FF:000014
      curie: CATH.FunFam:3.40.50.1010:FF:000014
      label: telomerase-binding protein EST1A isoform X1
      negated: false
    - condition_type: TAXON
      value: Chordata
      curie: NCBITaxon:7711
      label: Chordata
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 4 (UniProtKB query, 2026-11-10); unreviewed entries:
      784. Swiss-Prot matches: Q86US8 (SMG6), A0A0R4IZ84 (smg6), P61406 (Smg6), Q5RAK6 (SMG6). Experimental
      annotation to GO:0006401 RNA catabolic process or an is_a/part_of descendant (QuickGO): A0A0R4IZ84
      smg6 GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IDA PMID:19414594
      (ZFIN); Q86US8 SMG6 GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
      IMP PMID:18974281 (UniProt).
  - number: 27
    conditions:
    - condition_type: FUNFAM
      value: 2.30.30.140:FF:000018
      curie: CATH.FunFam:2.30.30.140:FF:000018
      label: Serine/threonine-protein kinase 31
      negated: false
    - condition_type: FUNFAM
      value: 2.40.50.90:FF:000010
      curie: CATH.FunFam:2.40.50.90:FF:000010
      label: Ribonuclease
      negated: false
    - condition_type: FUNFAM
      value: 2.40.50.90:FF:000011
      curie: CATH.FunFam:2.40.50.90:FF:000011
      label: Ribonuclease
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 2 (UniProtKB query, 2026-11-10); unreviewed entries:
      677. Swiss-Prot matches: Q9FLT0 (TSN2), Q8VZG7 (TSN1). Experimental annotation to GO:0006401 RNA
      catabolic process or an is_a/part_of descendant (QuickGO): Q8VZG7 TSN1 GO:0006402 mRNA catabolic
      process IGI PMID:25736060 (TAIR); Q9FLT0 TSN2 GO:0006402 mRNA catabolic process IGI PMID:25736060
      (TAIR).
  - number: 28
    conditions:
    - condition_type: FUNFAM
      value: 2.30.30.870:FF:000002
      curie: CATH.FunFam:2.30.30.870:FF:000002
      label: Protein pelota homolog
      negated: false
    - condition_type: FUNFAM
      value: 3.30.1330.30:FF:000008
      curie: CATH.FunFam:3.30.1330.30:FF:000008
      label: Protein pelota homolog
      negated: false
    - condition_type: FUNFAM
      value: 3.30.420.60:FF:000002
      curie: CATH.FunFam:3.30.420.60:FF:000002
      label: Protein pelota homolog
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 2 (UniProtKB query, 2026-11-10); unreviewed entries:
      447. Swiss-Prot matches: Q9ZT87 (PEL1), Q9M2H7 (PEL2). No experimental annotation; curated non-experimental
      annotation (QuickGO): Q9M2H7 PEL2 GO:0070481 nuclear-transcribed mRNA catabolic process, non-stop
      decay IEP PMID:30107878 (TAIR); Q9ZT87 PEL1 GO:0070481 nuclear-transcribed mRNA catabolic process,
      non-stop decay IEP PMID:30107878 (TAIR).
  - number: 29
    conditions:
    - condition_type: FUNFAM
      value: 3.30.1370.10:FF:000001
      curie: CATH.FunFam:3.30.1370.10:FF:000001
      label: Polyribonucleotide nucleotidyltransferase
      negated: false
    - condition_type: FUNFAM
      value: 3.30.230.70:FF:000001
      curie: CATH.FunFam:3.30.230.70:FF:000001
      label: Polyribonucleotide nucleotidyltransferase
      negated: false
    - condition_type: TAXON
      value: Streptophyta
      curie: NCBITaxon:35493
      label: Streptophyta
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 3 (UniProtKB query, 2026-11-10); unreviewed entries:
      793. Swiss-Prot matches: Q8GZQ3 (PNP1), Q9S7G6 (PNP2), Q69LE7 (PNP1). Experimental annotation to
      GO:0006401 RNA catabolic process or an is_a/part_of descendant (QuickGO): Q8GZQ3 PNP1 GO:0006401
      RNA catabolic process IMP PMID:12486011 (UniProt); Q9S7G6 PNP2 GO:0000957 mitochondrial RNA catabolic
      process IMP PMID:16537927 (UniProt).
  - number: 30
    conditions:
    - condition_type: FUNFAM
      value: 3.30.200.40:FF:000002
      curie: CATH.FunFam:3.30.200.40:FF:000002
      label: m7GpppX diphosphatase
      negated: false
    - condition_type: FUNFAM
      value: 3.30.428.10:FF:000015
      curie: CATH.FunFam:3.30.428.10:FF:000015
      label: m7GpppX diphosphatase
      negated: false
    - condition_type: TAXON
      value: Saccharomycotina
      curie: NCBITaxon:147537
      label: Saccharomycotina
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 2 (UniProtKB query, 2026-11-10); unreviewed entries:
      62. Swiss-Prot matches: Q12123 (DCS2), Q06151 (DCS1). Experimental annotation to GO:0006401 RNA
      catabolic process or an is_a/part_of descendant (QuickGO): Q06151 DCS1 GO:0000288 nuclear-transcribed
      mRNA catabolic process, deadenylation-dependent decay IMP PMID:12198172 (UniProt); Q12123 DCS2 GO:0000290
      deadenylation-dependent decapping of nuclear-transcribed mRNA IDA PMID:16963086 (SGD).
  - number: 31
    conditions:
    - condition_type: FUNFAM
      value: 3.30.200.40:FF:000003
      curie: CATH.FunFam:3.30.200.40:FF:000003
      label: m7GpppX diphosphatase
      negated: false
    - condition_type: FUNFAM
      value: 3.30.428.10:FF:000006
      curie: CATH.FunFam:3.30.428.10:FF:000006
      label: m7GpppX diphosphatase
      negated: false
    - condition_type: TAXON
      value: Ecdysozoa
      curie: NCBITaxon:1206794
      label: Ecdysozoa
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 2 (UniProtKB query, 2026-11-10); unreviewed entries:
      47. Swiss-Prot matches: G5EFS4 (dcs-1), D3K0N9 (no gene name). Experimental annotation to GO:0006401
      RNA catabolic process or an is_a/part_of descendant (QuickGO): G5EFS4 dcs-1 GO:0006401 RNA catabolic
      process IDA PMID:12871939 (WB).
  - number: 32
    conditions:
    - condition_type: FUNFAM
      value: 3.30.420.10:FF:000035
      curie: CATH.FunFam:3.30.420.10:FF:000035
      label: Poly(A)-specific ribonuclease PARN
      negated: false
    - condition_type: FUNFAM
      value: 3.30.420.10:FF:000042
      curie: CATH.FunFam:3.30.420.10:FF:000042
      label: poly(A)-specific ribonuclease PARN
      negated: false
    - condition_type: FUNFAM
      value: 3.30.70.330:FF:000196
      curie: CATH.FunFam:3.30.70.330:FF:000196
      label: Poly(A)-specific ribonuclease PARN
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 4 (UniProtKB query, 2026-11-10); unreviewed entries:
      503. Swiss-Prot matches: O95453 (PARN), Q8VDG3 (Parn), P69341 (PARN), Q5RC51 (PARN). Experimental
      annotation to GO:0006401 RNA catabolic process or an is_a/part_of descendant (QuickGO): O95453 PARN
      GO:0010587 miRNA catabolic process IDA PMID:25049417 (UniProt); Q8VDG3 Parn GO:0000289 nuclear-transcribed
      mRNA poly(A) tail shortening IDA PMID:18337750 (MGI).
  - number: 33
    conditions:
    - condition_type: FUNFAM
      value: 3.30.420.10:FF:000058
      curie: CATH.FunFam:3.30.420.10:FF:000058
      label: PARN like, ribonuclease domain containing 1
      negated: false
    - condition_type: FUNFAM
      value: 3.30.420.10:FF:000061
      curie: CATH.FunFam:3.30.420.10:FF:000061
      label: PARN like, ribonuclease domain containing 1
      negated: false
    - condition_type: TAXON
      value: Euteleostomi
      curie: NCBITaxon:117571
      label: Euteleostomi
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 3 (UniProtKB query, 2026-11-10); unreviewed entries:
      281. Swiss-Prot matches: Q8NA58 (PNLDC1), B2RXZ1 (Pnldc1), Q5R6R6 (PNLDC1). Experimental annotation
      to GO:0006401 RNA catabolic process or an is_a/part_of descendant (QuickGO): B2RXZ1 Pnldc1 GO:0000289
      nuclear-transcribed mRNA poly(A) tail shortening IDA PMID:27515512 (UniProt); Q8NA58 PNLDC1 GO:0000289
      nuclear-transcribed mRNA poly(A) tail shortening IDA PMID:27515512 (UniProt).
  - number: 34
    conditions:
    - condition_type: FUNFAM
      value: 3.30.70.330:FF:000216
      curie: CATH.FunFam:3.30.70.330:FF:000216
      label: RNA-binding protein BRN1 isoform X1
      negated: false
    - condition_type: FUNFAM
      value: 3.30.70.330:FF:000302
      curie: CATH.FunFam:3.30.70.330:FF:000302
      label: RNA-binding protein BRN1
      negated: false
    - condition_type: TAXON
      value: Embryophyta
      curie: NCBITaxon:3193
      label: Embryophyta
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 2 (UniProtKB query, 2026-11-10); unreviewed entries:
      735. Swiss-Prot matches: Q8LFS6 (BRN1), Q8GZ26 (BRN2). Experimental annotation to GO:0006401 RNA
      catabolic process or an is_a/part_of descendant (QuickGO): Q8GZ26 BRN2 GO:0006402 mRNA catabolic
      process IDA PMID:23437850 (UniProt); Q8LFS6 BRN1 GO:0006402 mRNA catabolic process IDA PMID:23437850
      (UniProt).
  - number: 35
    conditions:
    - condition_type: FUNFAM
      value: 3.30.1560.10:FF:000001
      curie: CATH.FunFam:3.30.1560.10:FF:000001
      label: Protein mago nashi homolog
      negated: false
    - condition_type: TAXON
      value: Hominidae
      curie: NCBITaxon:9604
      label: Hominidae
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 2 (UniProtKB query, 2026-11-10); unreviewed entries:
      17. Swiss-Prot matches: P61326 (MAGOH), Q96A72 (MAGOHB). Experimental annotation to GO:0006401 RNA
      catabolic process or an is_a/part_of descendant (QuickGO): P61326 MAGOH GO:0000184 nuclear-transcribed
      mRNA catabolic process, nonsense-mediated decay IGI PMID:23917022 (HGNC); Q96A72 MAGOHB GO:0000184
      nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IGI PMID:23917022 (HGNC).
  - number: 36
    conditions:
    - condition_type: FUNFAM
      value: 3.30.230.70:FF:000012
      curie: CATH.FunFam:3.30.230.70:FF:000012
      label: exosome complex component RRP46
      negated: false
    - condition_type: TAXON
      value: Euarchontoglires
      curie: NCBITaxon:314146
      label: Euarchontoglires
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 2 (UniProtKB query, 2026-11-10); unreviewed entries:
      81. Swiss-Prot matches: Q9NQT4 (EXOSC5), Q9CRA8 (Exosc5). Experimental annotation to GO:0006401
      RNA catabolic process or an is_a/part_of descendant (QuickGO): Q9CRA8 Exosc5 GO:0006401 RNA catabolic
      process IMP PMID:21670248 (MGI); Q9NQT4 EXOSC5 GO:0006401 RNA catabolic process IDA PMID:17174896
      (ComplexPortal).
  - number: 37
    conditions:
    - condition_type: FUNFAM
      value: 3.30.2310.20:FF:000004
      curie: CATH.FunFam:3.30.2310.20:FF:000004
      label: Toxin RelE
      negated: false
    - condition_type: TAXON
      value: Bacteria
      curie: NCBITaxon:2
      label: Bacteria
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 2 (UniProtKB query, 2026-11-10); unreviewed entries:
      11. Swiss-Prot matches: O33348 (relG), O50461 (relE). Experimental annotation to GO:0006401 RNA
      catabolic process or an is_a/part_of descendant (QuickGO): O33348 relG GO:0006401 RNA catabolic
      process IDA PMID:19114484 (MTBBASE); O50461 relE GO:0006401 RNA catabolic process IDA PMID:19114484
      (MTBBASE).
  - number: 38
    conditions:
    - condition_type: FUNFAM
      value: 3.30.40.10:FF:000006
      curie: CATH.FunFam:3.30.40.10:FF:000006
      label: CCR4-NOT transcription complex subunit 4
      negated: false
    - condition_type: FUNFAM
      value: 3.30.70.330:FF:000257
      curie: CATH.FunFam:3.30.70.330:FF:000257
      label: CCR4-NOT core complex subunit Not4
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 2 (UniProtKB query, 2026-11-10); unreviewed entries:
      992. Swiss-Prot matches: P34909 (MOT2), Q09818 (no gene name). Experimental annotation to GO:0006401
      RNA catabolic process or an is_a/part_of descendant (QuickGO): P34909 MOT2 GO:0031087 deadenylation-independent
      decapping of nuclear-transcribed mRNA IMP PMID:15706350 (SGD); Q09818 SPAC16C9.04c GO:0000289 nuclear-transcribed
      mRNA poly(A) tail shortening IDA PMID:26804377 (PomBase).
  - number: 39
    conditions:
    - condition_type: FUNFAM
      value: 3.30.420.10:FF:000027
      curie: CATH.FunFam:3.30.420.10:FF:000027
      label: Putative CCR4-associated factor 1 7
      negated: false
    - condition_type: TAXON
      value: Spermatophyta
      curie: NCBITaxon:58024
      label: Spermatophyta
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 6 (UniProtKB query, 2026-11-10); unreviewed entries:
      1771. Swiss-Prot matches: Q9LXM2 (CAF1-9), Q9LEU4 (CAF1-10), Q9SKZ2 (CAF1-7), Q9FMS6 (CAF1-11),
      Q9S9P2 (CAF1-2), Q9SAI2 (CAF1-6). Experimental annotation to GO:0006401 RNA catabolic process or
      an is_a/part_of descendant (QuickGO): Q9FMS6 CAF1-11 GO:0000289 nuclear-transcribed mRNA poly(A)
      tail shortening IMP PMID:19065152 (TAIR); Q9LXM2 CAF1-9 GO:0000289 nuclear-transcribed mRNA poly(A)
      tail shortening IMP PMID:19065152 (TAIR).
  - number: 40
    conditions:
    - condition_type: FUNFAM
      value: 3.30.540.10:FF:000015
      curie: CATH.FunFam:3.30.540.10:FF:000015
      label: 3',5'-bisphosphate nucleotidase
      negated: false
    - condition_type: FUNFAM
      value: 3.40.190.80:FF:000003
      curie: CATH.FunFam:3.40.190.80:FF:000003
      label: PAP-specific phosphatase HAL2-like
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 6 (UniProtKB query, 2026-11-10); unreviewed entries:
      876. Swiss-Prot matches: P32179 (MET22), O94505 (tol1), Q5BCG1 (no gene name), P0CY20 (HAL21), P0CY21
      (HAL21), Q59XQ1 (HAL22). Experimental annotation to GO:0006401 RNA catabolic process or an is_a/part_of
      descendant (QuickGO): O94505 tol1 GO:0180037 rapid tRNA decay EXP PMID:35901126 (PomBase); P32179
      MET22 GO:0016078 tRNA decay IDA PMID:31619505 (SGD).
  - number: 41
    conditions:
    - condition_type: FUNFAM
      value: 3.30.70.330:FF:000508
      curie: CATH.FunFam:3.30.70.330:FF:000508
      label: Protein HRB1
      negated: false
    - condition_type: TAXON
      value: Saccharomycetes
      curie: NCBITaxon:4891
      label: Saccharomycetes
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 2 (UniProtKB query, 2026-11-10); unreviewed entries:
      29. Swiss-Prot matches: P25555 (GBP2), P38922 (HRB1). Experimental annotation to GO:0006401 RNA
      catabolic process or an is_a/part_of descendant (QuickGO): P25555 GBP2 GO:0071028 nuclear mRNA surveillance
      IMP PMID:24452287 (SGD); P38922 HRB1 GO:0071028 nuclear mRNA surveillance IMP PMID:24452287 (SGD).
  - number: 42
    conditions:
    - condition_type: FUNFAM
      value: 3.40.50.300:FF:000141
      curie: CATH.FunFam:3.40.50.300:FF:000141
      label: ATP-dependent RNA helicase DOB1
      negated: false
    - condition_type: TAXON
      value: Taphrinomycotina
      curie: NCBITaxon:451866
      label: Taphrinomycotina
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 2 (UniProtKB query, 2026-11-10); unreviewed entries:
      16. Swiss-Prot matches: O13799 (no gene name), O14232 (mtr4). Experimental annotation to GO:0006401
      RNA catabolic process or an is_a/part_of descendant (QuickGO): O13799 SPAC17H9.02 GO:0033621 nuclear
      mRNA surveillance of meiosis-specific transcripts IMP PMID:24713849 (PomBase); O14232 mtr4 GO:0006401
      RNA catabolic process IDA PMID:29906447 (PomBase).
  - number: 43
    conditions:
    - condition_type: FUNFAM
      value: 4.10.1000.10:FF:000018
      curie: CATH.FunFam:4.10.1000.10:FF:000018
      label: Zinc finger protein
      negated: false
    - condition_type: TAXON
      value: Saccharomycetales
      curie: NCBITaxon:4892
      label: Saccharomycetales
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 2 (UniProtKB query, 2026-11-10); unreviewed entries:
      59. Swiss-Prot matches: P47977 (TIS11), P47976 (CTH1). Experimental annotation to GO:0006401 RNA
      catabolic process or an is_a/part_of descendant (QuickGO): P47976 CTH1 GO:0000956 nuclear-transcribed
      mRNA catabolic process IGI PMID:15652485 (SGD); P47977 TIS11 GO:0000956 nuclear-transcribed mRNA
      catabolic process IMP PMID:15652485 (SGD).
  - number: 44
    conditions:
    - condition_type: FUNFAM
      value: 1.10.3380.30:FF:000004
      curie: CATH.FunFam:1.10.3380.30:FF:000004
      label: Superkiller viralicidic activity 2-like 2
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 3 (UniProtKB query, 2026-11-10); unreviewed entries:
      1219. Swiss-Prot matches: P42285 (MTREX), Q9CZU3 (Mtrex), P35207 (SKI2). Experimental annotation
      to GO:0006401 RNA catabolic process or an is_a/part_of descendant (QuickGO): P35207 SKI2 GO:0000956
      nuclear-transcribed mRNA catabolic process IDA PMID:23953113 (ComplexPortal); P42285 MTREX GO:0006401
      RNA catabolic process IDA PMID:29906447 (UniProt).
  - number: 45
    conditions:
    - condition_type: FUNFAM
      value: 3.30.1010.10:FF:000026
      curie: CATH.FunFam:3.30.1010.10:FF:000026
      label: Serine/threonine-protein kinase smg-1
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 3 (UniProtKB query, 2026-11-10); unreviewed entries:
      37. Swiss-Prot matches: O01510 (smg-1), Q70PP2 (nonC), Q61CW2 (smg-1). Experimental annotation to
      GO:0006401 RNA catabolic process or an is_a/part_of descendant (QuickGO): O01510 smg-1 GO:0000184
      nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IMP PMID:15314158 (WB); Q70PP2
      nonC GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IDA PMID:20826458
      (FlyBase).
  - number: 46
    conditions:
    - condition_type: FUNFAM
      value: 3.30.230.70:FF:000004
      curie: CATH.FunFam:3.30.230.70:FF:000004
      label: Exosome complex component Rrp41
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 29 (UniProtKB query, 2026-11-10); unreviewed
      entries: 2312. Swiss-Prot matches: P46948 (SKI6), O42872 (ski6), Q9SP08 (RRP41), Q9UXC2 (rrp41),
      Q17533 (exos-4.1), O29757 (rrp41), Q8PTT8 (rrp41), Q8TYC1 (rrp41), and 21 more. Experimental annotation
      to GO:0006401 RNA catabolic process or an is_a/part_of descendant (QuickGO): O42872 ski6 GO:0071027
      nuclear RNA surveillance IMP PMID:25240800 (PomBase); P46948 SKI6 GO:0000956 nuclear-transcribed
      mRNA catabolic process IMP PMID:9482746 (SGD).
  - number: 47
    conditions:
    - condition_type: FUNFAM
      value: 3.30.70.330:FF:000538
      curie: CATH.FunFam:3.30.70.330:FF:000538
      label: Nuclear cap-binding protein subunit 2
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 3 (UniProtKB query, 2026-11-10); unreviewed entries:
      295. Swiss-Prot matches: Q08920 (CBC2), Q9P383 (cbc2), Q754W7 (CBC2). Experimental annotation to
      GO:0006401 RNA catabolic process or an is_a/part_of descendant (QuickGO): Q08920 CBC2 GO:0000956
      nuclear-transcribed mRNA catabolic process IMP PMID:10733586 (ComplexPortal).
  - number: 48
    conditions:
    - condition_type: FUNFAM
      value: 3.40.50.1010:FF:000021
      curie: CATH.FunFam:3.40.50.1010:FF:000021
      label: DIS3-like exonuclease 1 isoform X1
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 9 (UniProtKB query, 2026-11-10); unreviewed entries:
      1163. Swiss-Prot matches: Q8TF46 (DIS3L), P37202 (dis3), Q5U2P0 (Dis3l), Q8C0S1 (Dis3l), A2RV18
      (dis3l), A0JN80 (DIS3L), Q6GN11 (dis3l), Q5R5N8 (DIS3L), and 1 more. Experimental annotation to
      GO:0006401 RNA catabolic process or an is_a/part_of descendant (QuickGO): P37202 dis3 GO:0006401
      RNA catabolic process IDA PMID:29906447 (PomBase); Q8TF46 DIS3L GO:0006401 RNA catabolic process
      IDA PMID:20531386 (ComplexPortal).
  - number: 49
    conditions:
    - condition_type: FUNFAM
      value: 3.40.50.10890:FF:000003
      curie: CATH.FunFam:3.40.50.10890:FF:000003
      label: Integrator complex subunit 9
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 7 (UniProtKB query, 2026-11-10); unreviewed entries:
      1129. Swiss-Prot matches: Q9NV88 (INTS9), Q95TS5 (IntS9), Q8K114 (Ints9), Q2KJA6 (INTS9), Q4R5Z4
      (INTS9), Q6DFF4 (ints9), Q5ZKK2 (INTS9). Experimental annotation to GO:0006401 RNA catabolic process
      or an is_a/part_of descendant (QuickGO): Q95TS5 IntS9 GO:0160240 RNA polymerase II transcription
      initiation surveillance IDA PMID:31530651 (UniProt); Q9NV88 INTS9 GO:0160240 RNA polymerase II transcription
      initiation surveillance IDA PMID:33243860 (UniProt).
  - number: 50
    conditions:
    - condition_type: FUNFAM
      value: 3.90.730.10:FF:000001
      curie: CATH.FunFam:3.90.730.10:FF:000001
      label: Ribonuclease T2
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 5 (UniProtKB query, 2026-11-10); unreviewed entries:
      921. Swiss-Prot matches: O00584 (RNASET2), B8XY56 (rnaset2), C0HKG5 (Rnaset2a), C0HKG6 (Rnaset2b),
      Q7M329 (RNASET2). Experimental annotation to GO:0006401 RNA catabolic process or an is_a/part_of
      descendant (QuickGO): B8XY56 rnaset2 GO:0016075 rRNA catabolic process IMP PMID:21199949 (ZFIN);
      O00584 RNASET2 GO:0006401 RNA catabolic process IDA PMID:22735700 (UniProt).
  - number: 51
    conditions:
    - condition_type: FUNFAM
      value: 3.90.79.10:FF:000055
      curie: CATH.FunFam:3.90.79.10:FF:000055
      label: U8 snoRNA-decapping enzyme
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 4 (UniProtKB query, 2026-11-10); unreviewed entries:
      185. Swiss-Prot matches: Q96DE0 (NUDT16), Q6P3D0 (Nudt16), A1A4Q9 (NUDT16), Q2V8X7 (NUDT16). Experimental
      annotation to GO:0006401 RNA catabolic process or an is_a/part_of descendant (QuickGO): Q6P3D0 Nudt16
      GO:0006402 mRNA catabolic process IMP PMID:21070968 (UniProt); Q96DE0 NUDT16 GO:0006402 mRNA catabolic
      process IDA PMID:21070968 (UniProt).
  - number: 52
    conditions:
    - condition_type: FUNFAM
      value: 4.10.1000.10:FF:000013
      curie: CATH.FunFam:4.10.1000.10:FF:000013
      label: zinc finger CCCH domain-containing protein 4 isoform X1
      negated: false
    notes: >-
      Swiss-Prot entries matching the whole conjunction: 2 (UniProtKB query, 2026-11-10); unreviewed entries:
      466. Swiss-Prot matches: Q9UPT8 (ZC3H4), Q6ZPZ3 (Zc3h4). Experimental annotation to GO:0006401 RNA
      catabolic process or an is_a/part_of descendant (QuickGO): Q6ZPZ3 Zc3h4 GO:0071027 nuclear RNA surveillance
      IDA PMID:33767452 (UniProt); Q9UPT8 ZC3H4 GO:0071027 nuclear RNA surveillance IDA PMID:33913806
      (UniProt).
  go_annotations:
  - go_id: GO:0006401
    go_label: RNA catabolic process
    aspect: BP
  entries: []
  reviewed_protein_count: 0
  unreviewed_protein_count: 0
  created_date: '2021-10-20'
  modified_date: '2026-07-18'
  source_condition_set_count: 52
  retrieved_date: '2026-11-09'
review_summary: >-
  All 52 live condition sets were examined by retrieving the Swiss-Prot entries that match the whole conjunction
  and looking up their curated annotations to GO:0006401 and its is_a/part_of descendants. In 51 sets
  at least one Swiss-Prot match has an experimental annotation (IDA, IMP, IGI, IPI or EXP). The exception
  is set 28 (three pelota FunFams), whose two Swiss-Prot matches, Arabidopsis PEL1 (Q9ZT87) and PEL2 (Q9M2H7),
  carry GO:0070481 nuclear-transcribed mRNA catabolic process, non-stop decay by IEP only. The matched
  families include exosome subunits, decapping enzymes, deadenylases, the SKI2 and MTR4 helicases, TRAMP
  and terminal uridylyl transferases, and ZFP36-type zinc finger proteins. The check uses Swiss-Prot,
  the source ARBA rules are mined from, so it shows that no set lacks curated support; it does not measure
  precision on unreviewed entries.
action: ACCEPT
action_rationale: >-
  Every condition set has Swiss-Prot matches curated to RNA catabolic process or a descendant, 51 of 52
  with experimental evidence. The helicases, nucleotidyltransferases and RNA-binding proteins in the rule
  take part in RNA decay pathways, which is what a biological process term records; it does not require
  the protein to be a nuclease.
annotation_assessments:
- annotation_kind: GO_TERM
  value: GO:0006401
  label: RNA catabolic process
  assessment: CORRECT
  correct_examples:
  - P35207
  - P42285
  - P53632
  - O13833
  - P22893
  - P0DMV8
  notes: >-
    P35207 SKI2 GO:0006402 mRNA catabolic process IDA PMID:23953113 (ComplexPortal) and GO:0000956 IMP
    PMID:10611222 (SGD); P42285 MTREX GO:0006401 IDA PMID:29906447 (UniProt); P53632 PAP2 GO:0071035 nuclear
    polyadenylation-dependent rRNA catabolic process IMP PMID:15935758 (SGD); O13833 cid1 GO:0036450 polyuridylation-dependent
    decapping of nuclear-transcribed mRNA IMP PMID:19430462 (PomBase); P22893 Zfp36 GO:0000288 nuclear-transcribed
    mRNA catabolic process, deadenylation-dependent decay IDA PMID:15814898 (MGI); P0DMV8 HSPA1A GO:0006402
    IDA PMID:10205060 (UniProt). Per-set receipts are in the condition set notes. Set 28 has IEP support
    only.
confidence: 0.7
corrections:
- date: '2026-11-10'
  withdrawn_claim: >-
    The rule wrongly gives a catabolic annotation to RNA helicases such as SKI2, which unwind RNA rather
    than degrade it.
  correction: >-
    SKI2 and MTR4 helicases are experimentally annotated to RNA catabolic terms; taking part in a decay
    pathway is what the process term records.
  error_type: REFUTED_BY_CURATED_ANNOTATION
  evidence:
  - UniProtKB:P35207 SKI2 GO:0006402 IDA PMID:23953113 (ComplexPortal)
  - UniProtKB:P35207 SKI2 GO:0000956 IMP PMID:10611222 (SGD)
  - UniProtKB:P42285 MTREX GO:0006401 IDA PMID:29906447 (UniProt)
- date: '2026-11-10'
  withdrawn_claim: >-
    Terminal transferases (PAPD5/PAPD7, Cid1) are synthetic enzymes and so cannot be annotated to RNA
    catabolism.
  correction: >-
    Tailing by these enzymes marks RNA for decay, and they carry experimental annotations to descendants
    of GO:0006401.
  error_type: ONTOLOGY_MISREAD
  evidence:
  - UniProtKB:P53632 PAP2 GO:0071035 IMP PMID:15935758 (SGD)
  - UniProtKB:O13833 cid1 GO:0036450 IMP PMID:19430462 (PomBase)
  - >-
    Live sets 5, 16, 17 and 20 each have Swiss-Prot matches with experimental annotations (see set notes)
- date: '2026-11-10'
  withdrawn_claim: Zinc finger and heat shock proteins in the rule lack catabolic function.
  correction: >-
    The CCCH zinc finger sets match ZFP36-family proteins and the heat shock set matches HSPA1A/HSPA1B,
    all experimentally annotated to mRNA catabolic terms.
  error_type: REFUTED_BY_CURATED_ANNOTATION
  evidence:
  - UniProtKB:P22893 Zfp36 GO:0000288 IDA PMID:15814898 (MGI)
  - UniProtKB:P0DMV8 HSPA1A GO:0006402 IDA PMID:10205060 (UniProt)
  - 'Live sets 7, 23 and 43: see set notes'
- date: '2026-11-10'
  withdrawn_claim: >-
    The process term should be replaced by molecular function terms such as exonuclease activity or RNA
    helicase activity.
  correction: >-
    A molecular function term is not a more specific form of a biological process term; the two aspects
    are annotated independently.
  error_type: ONTOLOGY_MISREAD
  evidence:
  - >-
    GO:0006401 aspect biological_process (QuickGO); GO:0004527 and GO:0003724 are molecular_function terms
- date: '2026-11-10'
  withdrawn_claim: GO:0008260 is the decapping term for the DcpS family.
  correction: GO:0008260 is succinyl-CoA:3-oxo-acid CoA-transferase activity.
  error_type: WRONG_IDENTIFIER_MEANING
  evidence:
  - 'QuickGO GO:0008260 label: succinyl-CoA:3-oxo-acid CoA-transferase activity'
- date: '2026-11-10'
  withdrawn_claim: >-
    The rule should be deprecated because it has 51 condition sets and inconsistent taxon restrictions.
  correction: >-
    Neither the number of sets nor the presence of narrow taxon conditions shows that an annotation is
    wrong; all 52 live sets were checked individually.
  error_type: SIZE_AS_EVIDENCE
  evidence:
  - >-
    51 of 52 live sets have a Swiss-Prot match with an experimental annotation to GO:0006401 or a descendant;
    set 28 has IEP only (Q9ZT87, Q9M2H7 GO:0070481 IEP PMID:30107878, TAIR)