SNRPGP15

Summary: IBA from PANTHER node PANTHER:PTN000058285 assigning 'mRNA splicing, via spliceosome' (inherited from SNRPG and other characterised Sm-family members) to a putative product of the SNRPG processed pseudogene SNRPGP15.

Reason: SNRPGP15 is an HGNC pseudogene locus (Ensembl biotype processed_pseudogene) and A8MWD9 is PE5 with a UniProt pseudogene CAUTION. The GRCh38 locus and the UniProt-cited clone AC012318 both carry TGA at codon 75 (Arg75 in SNRPG), so the 76-residue UniProt sequence is not what the genome encodes. All 16 mass-spectrometry peptides mapped to A8MWD9 are exact SNRPG substrings, and the discriminating tryptic peptides (NIGMVEIR, GFDPFMNLVIDECVEMATSGQQK) have never been observed although SNRPG peptides are seen tens of thousands of times. No literature or experimental data exist for this locus. Sequence-level the retrocopy is 72/76 identical to SNRPG and keeps the Sm-site pocket residues (F34, N39, R63) and every SmG-RNA contact in PDB 4PJO, but changes two SmE-interface residues (M13T; V61E in the beta4/Sm2 strand), so function cannot be inferred even if a product were made. Remove; revisit only if a SNRPGP15-specific peptide is observed.

Summary: IEA 'mRNA splicing, via spliceosome' via InterPro2GO mapping from InterPro:IPR034098, a domain signature that matches any SmG-like sequence, including pseudogene translations.

Reason: SNRPGP15 is an HGNC pseudogene locus (Ensembl biotype processed_pseudogene) and A8MWD9 is PE5 with a UniProt pseudogene CAUTION. The GRCh38 locus and the UniProt-cited clone AC012318 both carry TGA at codon 75 (Arg75 in SNRPG), so the 76-residue UniProt sequence is not what the genome encodes. All 16 mass-spectrometry peptides mapped to A8MWD9 are exact SNRPG substrings, and the discriminating tryptic peptides (NIGMVEIR, GFDPFMNLVIDECVEMATSGQQK) have never been observed although SNRPG peptides are seen tens of thousands of times. No literature or experimental data exist for this locus. Automatic transfer from domain signatures adds no locus-specific evidence. Remove.

Summary: IBA from PANTHER node PANTHER:PTN000058283 assigning 'RNA binding' (inherited from SNRPG and other characterised Sm-family members) to a putative product of the SNRPG processed pseudogene SNRPGP15.

Reason: SNRPGP15 is an HGNC pseudogene locus (Ensembl biotype processed_pseudogene) and A8MWD9 is PE5 with a UniProt pseudogene CAUTION. The GRCh38 locus and the UniProt-cited clone AC012318 both carry TGA at codon 75 (Arg75 in SNRPG), so the 76-residue UniProt sequence is not what the genome encodes. All 16 mass-spectrometry peptides mapped to A8MWD9 are exact SNRPG substrings, and the discriminating tryptic peptides (NIGMVEIR, GFDPFMNLVIDECVEMATSGQQK) have never been observed although SNRPG peptides are seen tens of thousands of times. No literature or experimental data exist for this locus. Sequence-level the retrocopy is 72/76 identical to SNRPG and keeps the Sm-site pocket residues (F34, N39, R63) and every SmG-RNA contact in PDB 4PJO, but changes two SmE-interface residues (M13T; V61E in the beta4/Sm2 strand), so function cannot be inferred even if a product were made. This row is propagated from a deeper Sm/LSm node (contributes_to); the RNA-binding pocket residues are retained, but without an expressed product there is nothing to carry the activity. Marked as over-annotated rather than removed, because unlike the complex-membership and splicing rows, which depend on ring contacts this sequence alters, RNA binding is the one inherited function whose residue basis is fully intact. The PTHR10553 family review scopes RNA binding family-wide for the expressed SmG/Lsm7 members and excepts A8MWD9 on product-existence grounds only. The doubt is about whether a product exists, not about the activity; revisit if a SNRPGP15-specific peptide is observed.

Summary: IEA 'RNA binding' via InterPro2GO mapping from InterPro:IPR047575, a domain signature that matches any SmG-like sequence, including pseudogene translations.

Reason: SNRPGP15 is an HGNC pseudogene locus (Ensembl biotype processed_pseudogene) and A8MWD9 is PE5 with a UniProt pseudogene CAUTION. The GRCh38 locus and the UniProt-cited clone AC012318 both carry TGA at codon 75 (Arg75 in SNRPG), so the 76-residue UniProt sequence is not what the genome encodes. All 16 mass-spectrometry peptides mapped to A8MWD9 are exact SNRPG substrings, and the discriminating tryptic peptides (NIGMVEIR, GFDPFMNLVIDECVEMATSGQQK) have never been observed although SNRPG peptides are seen tens of thousands of times. No literature or experimental data exist for this locus. Automatic transfer from domain signatures adds no locus-specific evidence. Marked as over-annotated rather than removed, for consistency with the IBA RNA-binding row; the Sm-site RNA-contact residues are retained, and the PTHR10553 family review scopes RNA binding family-wide for the expressed SmG/Lsm7 members while excepting A8MWD9 on product-existence grounds only, so the activity is not contradicted and only the existence of a product is in doubt.

Summary: IEA 'nucleus' via UniProt subcellular-location mapping (UniProtKB-SubCell:SL-0191); the UniProt SUBCELLULAR LOCATION line is itself by-similarity (ECO:0000250) with no data for this entry.

Reason: SNRPGP15 is an HGNC pseudogene locus (Ensembl biotype processed_pseudogene) and A8MWD9 is PE5 with a UniProt pseudogene CAUTION. The GRCh38 locus and the UniProt-cited clone AC012318 both carry TGA at codon 75 (Arg75 in SNRPG), so the 76-residue UniProt sequence is not what the genome encodes. All 16 mass-spectrometry peptides mapped to A8MWD9 are exact SNRPG substrings, and the discriminating tryptic peptides (NIGMVEIR, GFDPFMNLVIDECVEMATSGQQK) have never been observed although SNRPG peptides are seen tens of thousands of times. No literature or experimental data exist for this locus. Automatic transfer from domain signatures adds no locus-specific evidence. Remove.

Summary: IEA 'spliceosomal complex' via InterPro2GO mapping from InterPro:IPR034098, a domain signature that matches any SmG-like sequence, including pseudogene translations.

Reason: SNRPGP15 is an HGNC pseudogene locus (Ensembl biotype processed_pseudogene) and A8MWD9 is PE5 with a UniProt pseudogene CAUTION. The GRCh38 locus and the UniProt-cited clone AC012318 both carry TGA at codon 75 (Arg75 in SNRPG), so the 76-residue UniProt sequence is not what the genome encodes. All 16 mass-spectrometry peptides mapped to A8MWD9 are exact SNRPG substrings, and the discriminating tryptic peptides (NIGMVEIR, GFDPFMNLVIDECVEMATSGQQK) have never been observed although SNRPG peptides are seen tens of thousands of times. No literature or experimental data exist for this locus. Automatic transfer from domain signatures adds no locus-specific evidence. Remove.

Summary: IBA from PANTHER node PANTHER:PTN000058285 assigning 'U5 snRNP' (inherited from SNRPG and other characterised Sm-family members) to a putative product of the SNRPG processed pseudogene SNRPGP15.

Reason: SNRPGP15 is an HGNC pseudogene locus (Ensembl biotype processed_pseudogene) and A8MWD9 is PE5 with a UniProt pseudogene CAUTION. The GRCh38 locus and the UniProt-cited clone AC012318 both carry TGA at codon 75 (Arg75 in SNRPG), so the 76-residue UniProt sequence is not what the genome encodes. All 16 mass-spectrometry peptides mapped to A8MWD9 are exact SNRPG substrings, and the discriminating tryptic peptides (NIGMVEIR, GFDPFMNLVIDECVEMATSGQQK) have never been observed although SNRPG peptides are seen tens of thousands of times. No literature or experimental data exist for this locus. Sequence-level the retrocopy is 72/76 identical to SNRPG and keeps the Sm-site pocket residues (F34, N39, R63) and every SmG-RNA contact in PDB 4PJO, but changes two SmE-interface residues (M13T; V61E in the beta4/Sm2 strand), so function cannot be inferred even if a product were made. Remove; revisit only if a SNRPGP15-specific peptide is observed.

Summary: IBA from PANTHER node PANTHER:PTN000058285 assigning 'U1 snRNP' (inherited from SNRPG and other characterised Sm-family members) to a putative product of the SNRPG processed pseudogene SNRPGP15.

Reason: SNRPGP15 is an HGNC pseudogene locus (Ensembl biotype processed_pseudogene) and A8MWD9 is PE5 with a UniProt pseudogene CAUTION. The GRCh38 locus and the UniProt-cited clone AC012318 both carry TGA at codon 75 (Arg75 in SNRPG), so the 76-residue UniProt sequence is not what the genome encodes. All 16 mass-spectrometry peptides mapped to A8MWD9 are exact SNRPG substrings, and the discriminating tryptic peptides (NIGMVEIR, GFDPFMNLVIDECVEMATSGQQK) have never been observed although SNRPG peptides are seen tens of thousands of times. No literature or experimental data exist for this locus. Sequence-level the retrocopy is 72/76 identical to SNRPG and keeps the Sm-site pocket residues (F34, N39, R63) and every SmG-RNA contact in PDB 4PJO, but changes two SmE-interface residues (M13T; V61E in the beta4/Sm2 strand), so function cannot be inferred even if a product were made. Remove; revisit only if a SNRPGP15-specific peptide is observed.

Summary: IBA from PANTHER node PANTHER:PTN000058285 assigning 'U2 snRNP' (inherited from SNRPG and other characterised Sm-family members) to a putative product of the SNRPG processed pseudogene SNRPGP15.

Reason: SNRPGP15 is an HGNC pseudogene locus (Ensembl biotype processed_pseudogene) and A8MWD9 is PE5 with a UniProt pseudogene CAUTION. The GRCh38 locus and the UniProt-cited clone AC012318 both carry TGA at codon 75 (Arg75 in SNRPG), so the 76-residue UniProt sequence is not what the genome encodes. All 16 mass-spectrometry peptides mapped to A8MWD9 are exact SNRPG substrings, and the discriminating tryptic peptides (NIGMVEIR, GFDPFMNLVIDECVEMATSGQQK) have never been observed although SNRPG peptides are seen tens of thousands of times. No literature or experimental data exist for this locus. Sequence-level the retrocopy is 72/76 identical to SNRPG and keeps the Sm-site pocket residues (F34, N39, R63) and every SmG-RNA contact in PDB 4PJO, but changes two SmE-interface residues (M13T; V61E in the beta4/Sm2 strand), so function cannot be inferred even if a product were made. Remove; revisit only if a SNRPGP15-specific peptide is observed.

Summary: IBA from PANTHER node PANTHER:PTN000058285 assigning 'U4 snRNP' (inherited from SNRPG and other characterised Sm-family members) to a putative product of the SNRPG processed pseudogene SNRPGP15.

Reason: SNRPGP15 is an HGNC pseudogene locus (Ensembl biotype processed_pseudogene) and A8MWD9 is PE5 with a UniProt pseudogene CAUTION. The GRCh38 locus and the UniProt-cited clone AC012318 both carry TGA at codon 75 (Arg75 in SNRPG), so the 76-residue UniProt sequence is not what the genome encodes. All 16 mass-spectrometry peptides mapped to A8MWD9 are exact SNRPG substrings, and the discriminating tryptic peptides (NIGMVEIR, GFDPFMNLVIDECVEMATSGQQK) have never been observed although SNRPG peptides are seen tens of thousands of times. No literature or experimental data exist for this locus. Sequence-level the retrocopy is 72/76 identical to SNRPG and keeps the Sm-site pocket residues (F34, N39, R63) and every SmG-RNA contact in PDB 4PJO, but changes two SmE-interface residues (M13T; V61E in the beta4/Sm2 strand), so function cannot be inferred even if a product were made. Remove; revisit only if a SNRPGP15-specific peptide is observed.

Summary: IBA from PANTHER node PANTHER:PTN000058284 assigning 'U12-type spliceosomal complex' (inherited from SNRPG and other characterised Sm-family members) to a putative product of the SNRPG processed pseudogene SNRPGP15.

Reason: SNRPGP15 is an HGNC pseudogene locus (Ensembl biotype processed_pseudogene) and A8MWD9 is PE5 with a UniProt pseudogene CAUTION. The GRCh38 locus and the UniProt-cited clone AC012318 both carry TGA at codon 75 (Arg75 in SNRPG), so the 76-residue UniProt sequence is not what the genome encodes. All 16 mass-spectrometry peptides mapped to A8MWD9 are exact SNRPG substrings, and the discriminating tryptic peptides (NIGMVEIR, GFDPFMNLVIDECVEMATSGQQK) have never been observed although SNRPG peptides are seen tens of thousands of times. No literature or experimental data exist for this locus. Sequence-level the retrocopy is 72/76 identical to SNRPG and keeps the Sm-site pocket residues (F34, N39, R63) and every SmG-RNA contact in PDB 4PJO, but changes two SmE-interface residues (M13T; V61E in the beta4/Sm2 strand), so function cannot be inferred even if a product were made. Remove; revisit only if a SNRPGP15-specific peptide is observed.

Summary: IEA 'small nuclear ribonucleoprotein complex' via ARBA machine-learning rule ARBA:ARBA00033820, triggered by the Sm/SmG signatures.

Reason: SNRPGP15 is an HGNC pseudogene locus (Ensembl biotype processed_pseudogene) and A8MWD9 is PE5 with a UniProt pseudogene CAUTION. The GRCh38 locus and the UniProt-cited clone AC012318 both carry TGA at codon 75 (Arg75 in SNRPG), so the 76-residue UniProt sequence is not what the genome encodes. All 16 mass-spectrometry peptides mapped to A8MWD9 are exact SNRPG substrings, and the discriminating tryptic peptides (NIGMVEIR, GFDPFMNLVIDECVEMATSGQQK) have never been observed although SNRPG peptides are seen tens of thousands of times. No literature or experimental data exist for this locus. Automatic transfer from domain signatures adds no locus-specific evidence. Remove.

Summary: IBA from PANTHER node PANTHER:PTN000058285 assigning 'SMN-Sm protein complex' (inherited from SNRPG and other characterised Sm-family members) to a putative product of the SNRPG processed pseudogene SNRPGP15.

Reason: SNRPGP15 is an HGNC pseudogene locus (Ensembl biotype processed_pseudogene) and A8MWD9 is PE5 with a UniProt pseudogene CAUTION. The GRCh38 locus and the UniProt-cited clone AC012318 both carry TGA at codon 75 (Arg75 in SNRPG), so the 76-residue UniProt sequence is not what the genome encodes. All 16 mass-spectrometry peptides mapped to A8MWD9 are exact SNRPG substrings, and the discriminating tryptic peptides (NIGMVEIR, GFDPFMNLVIDECVEMATSGQQK) have never been observed although SNRPG peptides are seen tens of thousands of times. No literature or experimental data exist for this locus. Sequence-level the retrocopy is 72/76 identical to SNRPG and keeps the Sm-site pocket residues (F34, N39, R63) and every SmG-RNA contact in PDB 4PJO, but changes two SmE-interface residues (M13T; V61E in the beta4/Sm2 strand), so function cannot be inferred even if a product were made. Remove; revisit only if a SNRPGP15-specific peptide is observed.

Summary: IBA from PANTHER node PANTHER:PTN000058285 assigning 'P granule' (inherited from SNRPG and other characterised Sm-family members) to a putative product of the SNRPG processed pseudogene SNRPGP15.

Reason: SNRPGP15 is an HGNC pseudogene locus (Ensembl biotype processed_pseudogene) and A8MWD9 is PE5 with a UniProt pseudogene CAUTION. The GRCh38 locus and the UniProt-cited clone AC012318 both carry TGA at codon 75 (Arg75 in SNRPG), so the 76-residue UniProt sequence is not what the genome encodes. All 16 mass-spectrometry peptides mapped to A8MWD9 are exact SNRPG substrings, and the discriminating tryptic peptides (NIGMVEIR, GFDPFMNLVIDECVEMATSGQQK) have never been observed although SNRPG peptides are seen tens of thousands of times. No literature or experimental data exist for this locus. Sequence-level the retrocopy is 72/76 identical to SNRPG and keeps the Sm-site pocket residues (F34, N39, R63) and every SmG-RNA contact in PDB 4PJO, but changes two SmE-interface residues (M13T; V61E in the beta4/Sm2 strand), so function cannot be inferred even if a product were made. The P granule term is in any case not experimentally supported for human SNRPG; it comes from a nematode donor and is the weakest of the inherited claims. Remove; revisit only if a SNRPGP15-specific peptide is observed.

Summary: IBA from PANTHER node PANTHER:PTN000058284 assigning 'U2-type prespliceosome' (inherited from SNRPG and other characterised Sm-family members) to a putative product of the SNRPG processed pseudogene SNRPGP15.

Reason: SNRPGP15 is an HGNC pseudogene locus (Ensembl biotype processed_pseudogene) and A8MWD9 is PE5 with a UniProt pseudogene CAUTION. The GRCh38 locus and the UniProt-cited clone AC012318 both carry TGA at codon 75 (Arg75 in SNRPG), so the 76-residue UniProt sequence is not what the genome encodes. All 16 mass-spectrometry peptides mapped to A8MWD9 are exact SNRPG substrings, and the discriminating tryptic peptides (NIGMVEIR, GFDPFMNLVIDECVEMATSGQQK) have never been observed although SNRPG peptides are seen tens of thousands of times. No literature or experimental data exist for this locus. Sequence-level the retrocopy is 72/76 identical to SNRPG and keeps the Sm-site pocket residues (F34, N39, R63) and every SmG-RNA contact in PDB 4PJO, but changes two SmE-interface residues (M13T; V61E in the beta4/Sm2 strand), so function cannot be inferred even if a product were made. Remove; revisit only if a SNRPGP15-specific peptide is observed.

Summary: IBA from PANTHER node PANTHER:PTN000058285 assigning 'precatalytic spliceosome' (inherited from SNRPG and other characterised Sm-family members) to a putative product of the SNRPG processed pseudogene SNRPGP15.

Reason: SNRPGP15 is an HGNC pseudogene locus (Ensembl biotype processed_pseudogene) and A8MWD9 is PE5 with a UniProt pseudogene CAUTION. The GRCh38 locus and the UniProt-cited clone AC012318 both carry TGA at codon 75 (Arg75 in SNRPG), so the 76-residue UniProt sequence is not what the genome encodes. All 16 mass-spectrometry peptides mapped to A8MWD9 are exact SNRPG substrings, and the discriminating tryptic peptides (NIGMVEIR, GFDPFMNLVIDECVEMATSGQQK) have never been observed although SNRPG peptides are seen tens of thousands of times. No literature or experimental data exist for this locus. Sequence-level the retrocopy is 72/76 identical to SNRPG and keeps the Sm-site pocket residues (F34, N39, R63) and every SmG-RNA contact in PDB 4PJO, but changes two SmE-interface residues (M13T; V61E in the beta4/Sm2 strand), so function cannot be inferred even if a product were made. Remove; revisit only if a SNRPGP15-specific peptide is observed.

Summary: IBA from PANTHER node PANTHER:PTN000058284 assigning 'catalytic step 2 spliceosome' (inherited from SNRPG and other characterised Sm-family members) to a putative product of the SNRPG processed pseudogene SNRPGP15.

Reason: SNRPGP15 is an HGNC pseudogene locus (Ensembl biotype processed_pseudogene) and A8MWD9 is PE5 with a UniProt pseudogene CAUTION. The GRCh38 locus and the UniProt-cited clone AC012318 both carry TGA at codon 75 (Arg75 in SNRPG), so the 76-residue UniProt sequence is not what the genome encodes. All 16 mass-spectrometry peptides mapped to A8MWD9 are exact SNRPG substrings, and the discriminating tryptic peptides (NIGMVEIR, GFDPFMNLVIDECVEMATSGQQK) have never been observed although SNRPG peptides are seen tens of thousands of times. No literature or experimental data exist for this locus. Sequence-level the retrocopy is 72/76 identical to SNRPG and keeps the Sm-site pocket residues (F34, N39, R63) and every SmG-RNA contact in PDB 4PJO, but changes two SmE-interface residues (M13T; V61E in the beta4/Sm2 strand), so function cannot be inferred even if a product were made. Remove; revisit only if a SNRPGP15-specific peptide is observed.

Summary: IBA from PANTHER node PANTHER:PTN000058285 assigning 'spliceosomal tri-snRNP complex' (inherited from SNRPG and other characterised Sm-family members) to a putative product of the SNRPG processed pseudogene SNRPGP15.

Reason: SNRPGP15 is an HGNC pseudogene locus (Ensembl biotype processed_pseudogene) and A8MWD9 is PE5 with a UniProt pseudogene CAUTION. The GRCh38 locus and the UniProt-cited clone AC012318 both carry TGA at codon 75 (Arg75 in SNRPG), so the 76-residue UniProt sequence is not what the genome encodes. All 16 mass-spectrometry peptides mapped to A8MWD9 are exact SNRPG substrings, and the discriminating tryptic peptides (NIGMVEIR, GFDPFMNLVIDECVEMATSGQQK) have never been observed although SNRPG peptides are seen tens of thousands of times. No literature or experimental data exist for this locus. Sequence-level the retrocopy is 72/76 identical to SNRPG and keeps the Sm-site pocket residues (F34, N39, R63) and every SmG-RNA contact in PDB 4PJO, but changes two SmE-interface residues (M13T; V61E in the beta4/Sm2 strand), so function cannot be inferred even if a product were made. Remove; revisit only if a SNRPGP15-specific peptide is observed.