LOC101732730

UniProt ID: A0A8J0SCI2
Organism: Xenopus tropicalis
Review Status: COMPLETE
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Gene Description

LOC101732730 (UniProt A0A8J0SCI2) is a single-exon Xenopus tropicalis gene on chromosome 9 encoding a 265-residue Krueppel-type C2H2 zinc finger protein. Apart from a short polar, disordered N-terminal segment (residues 1-27), the protein consists entirely of eight tandem C2H2 zinc fingers (residues 37-260) joined by the canonical TGEKP-type linkers; it carries no KRAB, SCAN, BTB/POZ or other recognizable effector domain. It belongs to the PANTHER Krueppel C2H2 zinc finger family PTHR24381, in the small fish/amphibian subfamily SF440 ("oocyte zinc finger protein XlCOF7.1-like") whose only Swiss-Prot member is the Xenopus laevis oocyte zinc finger protein XlCOF7.2, itself known only from cDNA sequence. Like other members of this family it is expected to act in the nucleus as a sequence-specific DNA-binding transcription factor that regulates RNA polymerase II transcription; its DNA target sequence, target genes, regulatory direction (activation or repression), expression pattern and biological role have not been studied experimentally.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0005634 nucleus
IBA
GO_REF:0000033 		ACCEPT
Summary: Phylogenetic (PAINT) annotation from the Eumetazoa-level node PTN001225435 of PANTHER PTHR24381, seeded by 39 experimentally annotated mouse, rat and human Krueppel C2H2 zinc finger proteins. The target is a descendant of this node (PTHR24381:SF440 by live InterPro/PANTHER match) and retains the family's defining tandem C2H2 array, whose function (binding genomic DNA) entails a nuclear site of action. No non-nuclear branch of the family is documented.
Reason: The target is inside the clade that inherited the IBD and shows no evidence of divergence from the architecture on which the nuclear role depends. Nucleus is the correct location of activity for a DNA-binding transcription factor of this family.
Propagation Review
Root cause: NO FAILURE CORE
Sources checked:
PANTHER:PTN001225435 · PTHR24381 Eumetazoa-level PAINT node (IBD for nucleus) SUPPORTS TRANSFER
Node assessed SOUND in interpro/panther/PTHR24381/PTHR24381-review.yaml (paint snapshot 20260529): the IBD is seeded by 39 experimentally annotated eumetazoan members, nuclear localization follows from the family's conserved DNA-binding architecture, and no diverged non-nuclear branch is documented anywhere in the cached family data.
MGI:MGI:1916754 · mouse Zfp932 SUPPORTS TRANSFER
Seed inspected: identity verified via Alliance/mygene.info; carries IDA GO:0005634 (PMID:21177534, checked in QuickGO on UniProtKB:E9QAG8).
UniProtKB:Q96RE9 · human ZNF300 SUPPORTS TRANSFER
Seed inspected: identity verified against live UniProt; an experimentally characterized nuclear transcription factor (IDA GO:0001228/GO:0045944, PMID:20585888).
Supporting Evidence:
file:XENTR/A0A8J0SCI2/A0A8J0SCI2-uniprot.txt
PANTHER; PTHR24381:SF440; OOCYTE ZINC FINGER PROTEIN XLCOF7.1-LIKE; 1.
file:interpro/panther/PTHR24381/PTHR24381-review.yaml
Nuclear localization is the compartment entailed by the family's conserved function
file:XENTR/A0A8J0SCI2/A0A8J0SCI2-uniprot.txt
PROSITE; PS50157; ZINC_FINGER_C2H2_2; 8.
GO:0006357 regulation of transcription by RNA polymerase II
IBA
GO_REF:0000033 		ACCEPT
Summary: Phylogenetic (PAINT) annotation from node PTN001225435 of PTHR24381, seeded by 13 experimentally characterized mammalian Krueppel C2H2 zinc finger proteins (including human ZNF300, ZNF140, ZNF136, ZNF304, ZNF689 and mouse Zfp92, Zfp932). The seeds include both activators (ZNF300) and repressors (ZNF140, Zfp932), which is why the PAINT curator placed the direction-neutral parent term at the node. The target retains an intact eight-finger C2H2 array, so it is expected to share the family's role as a sequence-specific regulator of Pol II transcription; its direction of regulation and target genes are unknown.
Reason: Regulation of Pol II transcription is the core process for a sequence-specific DNA-binding transcription factor, and the IBA is placed at the right level of specificity: an effector-less tandem-finger protein gives no basis for choosing between positive and negative regulation.
Propagation Review
Root cause: NO FAILURE CORE
Sources checked:
PANTHER:PTN001225435 · PTHR24381 Eumetazoa-level PAINT node (IBD for GO:0006357) SUPPORTS TRANSFER
Node assessed SOUND in interpro/panther/PTHR24381/PTHR24381-review.yaml (paint snapshot 20260529). The 13 seeds include experimentally verified positive AND negative regulators, so the direction-neutral parent GO:0006357 is the correct generalization at the node; directional child terms are correctly confined to narrower nodes elsewhere in the family. Appropriate for the target, whose regulatory direction cannot be inferred from its effector-less tandem zinc-finger architecture.
UniProtKB:Q96RE9 · human ZNF300 SUPPORTS TRANSFER
Seed inspected: IDA GO:0045944 (positive regulation; PMID:20585888, checked in QuickGO), a descendant of the propagated term.
UniProtKB:P52738 · human ZNF140 SUPPORTS TRANSFER
Seed inspected: IDA GO:0000122 (negative regulation; PMID:11470777, PMID:7649249, checked in QuickGO), a descendant of the propagated term on the opposite regulatory sign from ZNF300 - which is why the direction-neutral parent sits at the node.
MGI:MGI:1916754 · mouse Zfp932 SUPPORTS TRANSFER
Seed inspected: IDA GO:0000122 (PMID:21177534, PMID:22391310, checked in QuickGO on UniProtKB:E9QAG8).
Supporting Evidence:
file:interpro/panther/PTHR24381/PTHR24381-review.yaml
correct level for the node. Consistent with the family's conserved architecture
file:XENTR/A0A8J0SCI2/A0A8J0SCI2-uniprot.txt
InterPro; IPR013087; Znf_C2H2_type.
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific
IBA
GO_REF:0000033 		ACCEPT
Summary: Phylogenetic (PAINT) annotation from node PTN001225435 of PTHR24381, seeded by five experimentally characterized transcription factors (mouse Zfp92; human ZNF93, ZNF140, ZNF354C, ZNF300) that span both regulatory directions. The target's eight tandem C2H2 fingers (PROSITE PS50157 x8, SMART SM00355 x8) are the DNA-binding module of this activity. Whether the target activates or represses transcription cannot be inferred: it has no KRAB, SCAN, BTB or recognizable activation domain, so the direction-agnostic parent term is the appropriate level.
Reason: This is the core molecular function expected for a Krueppel C2H2 zinc finger protein that retains an intact finger array, inherited from a soundly placed PAINT node at the correct specificity.
Propagation Review
Root cause: NO FAILURE CORE
Sources checked:
PANTHER:PTN001225435 · PTHR24381 Eumetazoa-level PAINT node (IBD for GO:0000981) SUPPORTS TRANSFER
Node assessed SOUND in interpro/panther/PTHR24381/PTHR24381-review.yaml (paint snapshot 20250904). The five seeds are experimentally characterized TFs spanning both regulatory directions (ZNF300 activator, ZNF140 repressor), so the PAINT curator's placement of the direction-agnostic parent GO:0000981 - rather than either directional child - is exactly right for descent onto effector-less members like the target.
UniProtKB:Q96RE9 · human ZNF300 SUPPORTS TRANSFER
Seed inspected: IDA GO:0001228 (PMID:20585888, checked in QuickGO), a child of the propagated term.
UniProtKB:P52738 · human ZNF140 SUPPORTS TRANSFER
Seed inspected: IDA GO:0001227 (PMID:11470777, checked in QuickGO), the opposite-direction child of the propagated term.
MGI:MGI:108094 · mouse Zfp92 SUPPORTS TRANSFER
Seed identity verified via Alliance/mygene.info (zinc finger protein 92); its individual experimental annotations were not separately inspected.
Supporting Evidence:
file:interpro/panther/PTHR24381/PTHR24381-review.yaml
such as the X. tropicalis target A0A8J0SCI2, whose direction is unknown, asserts
file:XENTR/A0A8J0SCI2/A0A8J0SCI2-uniprot.txt
SMART; SM00355; ZnF_C2H2; 8.
GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding
IBA
GO_REF:0000033 		ACCEPT
Summary: Phylogenetic (PAINT) annotation from node PTN001225435, a single-seed IBD (mouse Zfp932, with IDA for this term from two papers). Sequence-specific binding of Pol II cis-regulatory DNA is the mechanistic basis of the transcription factor activity above: each C2H2 finger coordinates zinc through two cysteines and two histidines and contacts bases in the major groove, and the target retains all eight fingers with their zinc ligands. The one documented loss of cis-regulatory-region binding in the family (the ZNF445 clade, pruned by PAINT with an IRD at PTN008615686) lies on a different branch and does not include the target. The actual DNA motif bound by the target is unknown.
Reason: A correct and appropriately specific molecular function for an intact tandem C2H2 finger protein. Sequence-specific DNA binding is part of the core function of a DNA-binding transcription factor, not a peripheral activity, so it is accepted alongside GO:0000981 (changed from the earlier KEEP_AS_NON_CORE, which treated this core binding activity as peripheral).
Propagation Review
Root cause: NO FAILURE CORE
Sources checked:
PANTHER:PTN001225435 · PTHR24381 Eumetazoa-level PAINT node (IBD for GO:0000978) SUPPORTS TRANSFER
Node assessed SOUND in interpro/panther/PTHR24381/PTHR24381-review.yaml (paint snapshot 20200709). A single-seed IBD, which is not weak support: the placement judgment is phylogenetic, and the one documented loss of cis-regulatory-region binding in this family (the ZNF445 clade) was pruned by PAINT with an IRD at its own node (PTN008615686) and does not implicate this one.
MGI:MGI:1916754 · mouse Zfp932 SUPPORTS TRANSFER
The sole IBD seed, inspected: identity verified via Alliance/mygene.info; IDA GO:0000978 from two independent papers (PMID:21177534, PMID:22391310, checked in QuickGO on UniProtKB:E9QAG8).
Supporting Evidence:
file:XENTR/A0A8J0SCI2/A0A8J0SCI2-uniprot.txt
PROSITE; PS00028; ZINC_FINGER_C2H2_1; 8.
file:interpro/panther/PTHR24381/PTHR24381-review.yaml
fingers covering residues 37-260 of its 265 residues) retains that architecture
file:XENTR/A0A8J0SCI2/A0A8J0SCI2-deep-research-falcon.md
C2H2 zinc finger proteins bind DNA through a well-characterized mechanism. Each zinc finger module is stabilized by coordination of a zinc ion (Zn²⁺) by two cysteine residues and two histidine residues, forming a compact finger-like structure
GO:0005634 nucleus
IEA
GO_REF:0000044 		ACCEPT
Summary: Electronic nucleus annotation mapped from the UniProt subcellular location line, which for this unreviewed entry is itself an ARBA rule prediction. The claim is the same one made by the IBA nucleus row and is independently supported by family membership and the intact DNA-binding finger array.
Reason: Correct location, consistent with the IBA nucleus annotation. The ARBA origin of the mapped UniProt line is not itself evidence, but the claim is supported by PANTHER family placement and domain architecture.
Supporting Evidence:
file:XENTR/A0A8J0SCI2/A0A8J0SCI2-uniprot.txt
PANTHER; PTHR24381:SF440; OOCYTE ZINC FINGER PROTEIN XLCOF7.1-LIKE; 1.
file:interpro/panther/PTHR24381/PTHR24381-review.yaml
Nuclear localization is the compartment entailed by the family's conserved function

Core Functions

Predicted sequence-specific DNA-binding transcription factor that regulates RNA polymerase II transcription from the nucleus, through an array of eight tandem C2H2 zinc fingers inherited from the PTHR24381 Krueppel zinc finger family. Its DNA target motif, target genes, and whether it activates or represses transcription are unknown; it has no recognizable effector domain.

Molecular Function:
DNA-binding transcription factor activity, RNA polymerase II-specific
Directly Involved In:
regulation of transcription by RNA polymerase II
Cellular Locations:
nucleus
Supporting Evidence:
  • file:XENTR/A0A8J0SCI2/A0A8J0SCI2-uniprot.txt
    PANTHER; PTHR24381:SF440; OOCYTE ZINC FINGER PROTEIN XLCOF7.1-LIKE; 1.
  • file:XENTR/A0A8J0SCI2/A0A8J0SCI2-uniprot.txt
    PROSITE; PS50157; ZINC_FINGER_C2H2_2; 8.
  • file:interpro/panther/PTHR24381/PTHR24381-review.yaml
    such as the X. tropicalis target A0A8J0SCI2, whose direction is unknown, asserts

References

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Suggested Questions for Experts

Q: What DNA sequence does the eight-finger array of LOC101732730 recognize, and does the protein activate or repress transcription in the absence of a KRAB, SCAN or BTB effector domain?

Q: Is LOC101732730, a single-exon gene, an expressed functional gene or a retrotransposed copy of a multi-exon SF440 paralog, and is it expressed in oocytes or early embryos as the X. laevis XlCOF proteins are?

Suggested Experiments

Experiment: Determine the DNA-binding specificity of the zinc finger array (e.g. ChIP-exo or ChIP-seq of tagged protein in Xenopus embryos or cells, or in vitro SELEX), and test regulatory direction with a GAL4-DBD fusion reporter assay.

Experiment: Measure expression across oogenesis and early development (RNA-seq time-course re-analysis or in situ hybridization) to establish where and when the gene acts.

External Prediction Reviews

These computational predictions are reviewed separately from the GOA annotation set used for this review. The assessments below are from this project and do not constitute official GO annotations or endorsement by GO/UniProt. They are not included in the existing annotation review above.

ProtNLM2 External predictions

View prediction review YAML · A0A8J0SCI2-protnlm-predictions-review.yaml · Review status: COMPLETE

The C2H2 zinc-finger architecture supports the existing curated transcription-factor and nuclear annotations. Whether this factor specifically activates transcription is unresolved.

Source documents: genes/XENTR/A0A8J0SCI2/A0A8J0SCI2-uniprot.txt · genes/XENTR/A0A8J0SCI2/A0A8J0SCI2-goa.tsv · genes/XENTR/A0A8J0SCI2/A0A8J0SCI2-hypotheses/prediction-tf-activator/openscientist.md

Review score: 2 = concordant with evidence; 1 = uncertain; 0 = discordant with evidence. This is an assessment score, not a model probability.

GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding GO_MF
CNN — Correct but not novel Review score: 2/2
Prediction method: ProtNLM2 · Version: UniProt 2024_06 pilot
Review rationale: The target contains eight tandem C2H2 zinc-finger domains, consistent with sequence-specific DNA recognition. The cached GOA record has an exact curated IBA for RNA polymerase II cis-regulatory region sequence-specific DNA binding, alongside the corresponding transcription-factor activity. This is a curator-assessed phylogenetic inference consistent with the target architecture, not an ARBA assertion. The available evidence supports the function without identifying a particular DNA motif or target gene.
Supporting Evidence:
GO:0006357 regulation of transcription by RNA polymerase II GO_BP
CNN — Correct but not novel Review score: 2/2
Prediction method: ProtNLM2 · Version: UniProt 2024_06 pilot
Review rationale: The target has the tandem C2H2 zinc-finger architecture of a sequence-specific DNA-binding factor. The exact regulation of transcription by RNA polymerase II annotation is present as a curated IBA in the cached GOA record, together with compatible DNA-binding transcription-factor activity. These phylogenetic annotations and the target architecture support the broad regulatory process. They do not specify whether the factor activates or represses its targets.
Supporting Evidence:
GO:0005634 nucleus GO_CC
CNN — Correct but not novel Review score: 2/2
Prediction method: ProtNLM2 · Version: UniProt 2024_06 pilot
Review rationale: The target zinc-finger architecture is compatible with its curated DNA-binding transcription-factor assignment. Nucleus is already present as a curated IBA in the cached GOA record, supporting this localization through a phylogenetic judgment consistent with the molecular function. No target localization experiment is asserted. The exact overlap makes this a supported, non-novel annotation.
Supporting Evidence:
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific GO_MF
UNC — Uncertain Review score: 1/2
Prediction method: ProtNLM2 · Version: UniProt 2024_06 pilot
Review rationale: The zinc-finger array and existing curated IBA support a DNA-binding RNA polymerase II transcription factor. They do not determine whether its effect on transcription is activating, repressing, or context-dependent. Absence of a recognizable activation domain is not decisive because activation can depend on partners or short interaction regions. The activator-specific term is absent from the cached annotations, and evidence for regulatory direction is needed. The OpenScientist analysis judged the term NPI because the effector-less zinc-finger array cannot specify regulatory direction; that same argument leaves activation undetermined rather than excluded, so the call is UNC.
Supporting Evidence:

Deep Research

Falcon

(A0A8J0SCI2-deep-research-falcon.md)

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OpenScientist

(A0A8J0SCI2-hypotheses/prediction-tf-activator/openscientist.md)

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📚 Additional Documentation

Notes

(A0A8J0SCI2-notes.md)

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📄 View Raw YAML

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