SECISBP2

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0001514 selenocysteine incorporation	IBA GO_REF:0000033	ACCEPT	Summary: Core biological process of SECISBP2. The phylogenetic (IBA) inference that SBP2 is involved in selenocysteine incorporation is strongly supported by direct experimental evidence in human (IDA, PMID:35709277) and matches the UniProt-annotated function. Supporting Evidence: file:human/SECISBP2/SECISBP2-uniprot.txt facilitates the incorporation of the rare amino acid
GO:0035368 selenocysteine insertion sequence binding	IBA GO_REF:0000033	ACCEPT	Summary: Core molecular function. The IBA call that SBP2 enables SECIS binding is confirmed experimentally in human by cryo-EM, where the RBD of SBP2 binds the SECIS kink-turn (PMID:35709277). Supporting Evidence: PMID:35709277 RBD of SBP2 adopts an L7Ae protein fold and binds to the conserved kink-turn motif of the SECIS
GO:0005739 mitochondrion	IBA GO_REF:0000033	KEEP AS NON CORE	Summary: Mitochondrial localization is not the canonical site of the core Sec-incorporation function, which occurs at cytoplasmic ribosomes. A mitochondrial isoform (mtSBP2, isoform 2) bearing an N-terminal transit peptide has been reported (PMID:19004874). Retained as non-core, isoform-specific localization. Reason: The organelle claim is true for the human gene, but only through isoform 2 (mtSBP2), whose alternative exon-2 reading frame encodes an N-terminal MTS; GFP fusion and endogenous staining co-localise with MitoTracker in a minority of cells (PMID:19004874). Examined as a synthesis row: the PAINT IBD at PTN000328589 (PTHR13284-paint.tsv, eukaryote-level node) is seeded only by Q57Y14, a Trypanosoma brucei L7Ae-domain protein whose mitochondrion annotation comes from the TrypTag genome-wide fluorescent-tagging screen (GO_REF:0000109). The human mitochondrial form arises from human alternative splicing that the authors call potentially human-specific, so the IBA reaches the right organelle without a shared inherited mechanism. Kept non-core, matching the IEA row. No sub-compartment is added: the MTS suggests import, but the authors interpret the punctate signal as the outer mitochondrial surface and could not detect mtSBP2 in mitochondrial fractions, so the lines disagree and the row stays at the root. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: PANTHER:PTN000328589 · PTN000328589 SUPPORTS TRANSFER Eukaryote-level node whose GO:0005739 IBD has a single seed, the T. brucei protein Q57Y14 (TrypTag high-throughput localisation). The outcome for human SECISBP2 is correct, but it is independently grounded by the human isoform-2 study (PMID:19004874), not by conserved mitochondrial targeting across the family. UniProtKB:Q57Y14 · Q57Y14_TRYB2 SOURCE WEAK OR INFERRED Unreviewed T. brucei entry; its mitochondrion annotation is an IDA from the genome-wide TrypTag fluorescent-tagging screen (GO_REF:0000109), a thin basis for a eukaryote-wide inference. Supporting Evidence: file:human/SECISBP2/SECISBP2-uniprot.txt [Isoform 2]: Mitochondrion PMID:19004874 This data established that the MTS encoded by the alternative reading frame in exon 2 is functional, and required for targeting the mtSBP2-GFP protein to the mitochondria. PMID:19004874 The identification of a potential mitochondrial human-specific SBP2 isoform was an intriguing and somewhat puzzling finding
GO:0003730 mRNA 3'-UTR binding	IBA GO_REF:0000033	ACCEPT	Summary: SBP2 binds the SECIS element, which resides in the 3'-UTR of selenoprotein mRNAs; this is a valid, slightly more general statement of the same SECIS-binding activity. Supported experimentally in human (IDA, PMID:16962588; PMID:17332014). Supporting Evidence: PMID:17332014 By binding to SECIS elements located in the 3'-UTR of selenoprotein mRNAs
GO:0043021 ribonucleoprotein complex binding	IBA GO_REF:0000033	MODIFY	Summary: SBP2 binds the 40S ribosomal subunit (contacting ribosomal protein eS31 and 18S rRNA) as part of the selenosome, consistent with ribonucleoprotein complex binding. Supported by cryo-EM (PMID:35709277), which shows the SID latching onto the 40S subunit to create the binding site for the EEFSEC ternary complex. Reason: The ribonucleoprotein complex that SBP2 binds is specifically the 40S ribosomal subunit (via 18S rRNA and eS31), and this docking is integral to SBP2's recoding function rather than incidental, so the more specific ribosomal small subunit binding term is proposed. Propagation Review Root cause: NO FAILURE CORE Proposed replacements: ribosomal small subunit binding Supporting Evidence: PMID:35709277 the N-terminal part of the SID latches onto the 40S through contacts with the rRNA and eS31
GO:1990904 ribonucleoprotein complex	IBA GO_REF:0000033	KEEP AS NON CORE	Summary: SBP2 is a component of the selenosome, a ribonucleoprotein assembly comprising the SECIS RNA, SBP2, EEFSEC, Sec-tRNA(Sec) and the ribosome. Valid but non-core component annotation. Supporting Evidence: PMID:35709277 40S ribosomal subunit enables Sec-specific elongation
GO:0001514 selenocysteine incorporation	IEA GO_REF:0000117	ACCEPT	Summary: ARBA electronic annotation restating the core biological process, which is independently supported by direct experimental evidence (PMID:35709277). Redundant with the IDA/IBA calls but not incorrect. Supporting Evidence: file:human/SECISBP2/SECISBP2-uniprot.txt facilitates the incorporation of the rare amino acid
GO:0005634 nucleus	IEA GO_REF:0000044	KEEP AS NON CORE	Summary: UniProt records nuclear localization for isoform 1 (which also carries an NLS motif). SBP2 performs its core recoding function at cytoplasmic ribosomes, so nuclear localization is retained as non-core. Supporting Evidence: file:human/SECISBP2/SECISBP2-uniprot.txt [Isoform 1]: Nucleus
GO:0005739 mitochondrion	IEA GO_REF:0000044	KEEP AS NON CORE	Summary: Mitochondrial localization derives from the UniProt subcellular-location mapping and reflects the mtSBP2 (isoform 2) transit-peptide-bearing form reported in PMID:19004874. Non-core, isoform-specific. Reason: Examined as a synthesis row: GO_REF:0000044 maps UniProt SL-0173 (Mitochondrion), which UniProt records for isoform 2 with ECO:0000269 from PMID:19004874, so the feature the mapping assumes is really present (for isoform 2 only; isoform 1 is recorded as nuclear by curator inference). The organelle claim is correct and non-core, as the canonical Sec-incorporation function occurs on cytoplasmic ribosomes. Stays at the root: the paper's MTS points to import, but its imaging suggested an outer-surface pool and mitochondrial fractionation did not detect mtSBP2, so no sub-compartment is supported. Supporting Evidence: file:human/SECISBP2/SECISBP2-uniprot.txt [Isoform 2]: Mitochondrion
GO:0035368 selenocysteine insertion sequence binding	IEA GO_REF:0000120	ACCEPT	Summary: Automated (InterPro/ARBA) annotation of the core SECIS-binding molecular function, independently confirmed by direct experimental evidence (PMID:35709277). Supporting Evidence: PMID:35709277 RBD of SBP2 adopts an L7Ae protein fold and binds to the conserved kink-turn motif of the SECIS
GO:0005515 protein binding	IPI PMID:25416956 A proteome-scale map of the human interactome network.	REMOVE	Summary: Bare "protein binding" from a systematic binary interactome screen (interaction with GOLGA2). Uninformative about SECISBP2 function and no biological role is established for this pairwise interaction. Reason: High-throughput two-hybrid interaction (with GOLGA2); the generic protein binding term conveys no functional information and no role for this interaction in SECISBP2 biology has been shown. Removal does not mean the interaction is false.
GO:0005515 protein binding	IPI PMID:32296183 A reference map of the human binary protein interactome.	REMOVE	Summary: Bare "protein binding" from the HuRI human binary reference interactome (interaction with FAM168A). Uninformative and functionally uncharacterized. Reason: High-throughput reference-interactome (Y2H) interaction (with FAM168A); the generic protein binding term conveys no functional information. Removal does not mean the interaction is false.
GO:0005515 protein binding	IPI PMID:32814053 Interactome Mapping Provides a Network of Neurodegenerative ...	REMOVE	Summary: Bare "protein binding" from a neurodegeneration-focused interactome map (interaction with HTT/huntingtin). Uninformative for SECISBP2's molecular function; no established biological role. Reason: High-throughput interactome-mapping interaction (with HTT); the generic protein binding term conveys no functional information. Removal does not mean the interaction is false.
GO:0005654 nucleoplasm	IDA GO_REF:0000052	KEEP AS NON CORE	Summary: HPA immunofluorescence localizes SBP2 to the nucleoplasm, consistent with the UniProt nuclear localization of isoform 1. Non-core relative to the cytoplasmic ribosome-associated recoding function. Supporting Evidence: file:human/SECISBP2/SECISBP2-uniprot.txt [Isoform 1]: Nucleus
GO:0001514 selenocysteine incorporation	IDA PMID:35709277 Structure of the mammalian ribosome as it decodes the seleno...	ACCEPT	Summary: Direct experimental evidence (cryo-EM plus functional readthrough assays) that SBP2 is required for selenocysteine incorporation at the UGA codon. This is the core biological process of the gene. Supporting Evidence: PMID:35709277 40S ribosomal subunit enables Sec-specific elongation
GO:0035368 selenocysteine insertion sequence binding	IDA PMID:35709277 Structure of the mammalian ribosome as it decodes the seleno...	ACCEPT	Summary: Direct structural evidence that the SBP2 RBD binds the SECIS kink-turn motif. This is the core molecular function of the gene. Supporting Evidence: PMID:35709277 RBD of SBP2 adopts an L7Ae protein fold and binds to the conserved kink-turn motif of the SECIS
GO:0003730 mRNA 3'-UTR binding	IDA PMID:16962588 Identification and characterization of selenoprotein K: an a...	ACCEPT	Summary: SBP2 was shown to bind the SelK SECIS element, which lies in the 3'-UTR of the SelK mRNA. This is the same SECIS-binding activity captured at a more general MF term. Retained as supporting the core RNA-binding role. Supporting Evidence: PMID:16962588 to the SelK SECIS element through the conserved non-Watson-Crick base pair
GO:0003677 DNA binding	EXP PMID:19467292 SECIS-binding protein 2, a key player in selenoprotein synth...	MARK AS OVER ANNOTATED	Summary: This EXP annotation is sourced from DisProt (DP00420) via a paper that characterizes SBP2 as an intrinsically disordered protein whose RNA-binding domain is folded and functional. The paper establishes RNA binding and disorder, not DNA binding; SBP2 has no characterized DNA-binding function. Flagged as over-annotation (retained per policy since it is experimental/EXP, not removed). Reason: The cited DisProt paper concerns intrinsic disorder and RNA binding; no DNA-binding activity is demonstrated for SBP2. SECIS/SECIS-element binding (an RNA) is the established nucleic-acid-binding activity. Supporting Evidence: PMID:19467292 whereas the RNA binding domain appears to be folded and functional
GO:0003730 mRNA 3'-UTR binding	IDA PMID:17332014 An improved definition of the RNA-binding specificity of SEC...	ACCEPT	Summary: SELEX and footprinting define SBP2's RNA-binding specificity for SECIS/K-turn motifs located in the 3'-UTR of selenoprotein mRNAs. Directly supports the core SECIS/3'-UTR-binding activity. Supporting Evidence: PMID:17332014 By binding to SECIS elements located in the 3'-UTR of selenoprotein mRNAs
GO:0003723 RNA binding	HDA PMID:22658674 Insights into RNA biology from an atlas of mammalian mRNA-bi...	KEEP AS NON CORE	Summary: High-throughput mRNA interactome capture (UV crosslinking in HeLa) identified SBP2 as an RNA-binding protein. Correct but a general parent of the specific SECIS (mRNA 3'-UTR) binding activity; retained as non-core supporting evidence. Supporting Evidence: PMID:22658674 We identify 860 proteins that qualify as RBPs by biochemical

Gene Description

Existing Annotations Review

Core Functions

Sequence- and structure-specific recognition of the SECIS element (a kink-turn stem-loop) in the 3'-UTR of selenoprotein mRNAs via the L7Ae/L30-family RNA-binding domain.

References

📚 Additional Documentation

Notes

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