id: Q8AY15
gene_symbol: smad3a
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:7955
  label: Danio rerio
description: smad3a (SMAD family member 3a) is one of two zebrafish co-orthologs of vertebrate SMAD3, retained
  from the teleost-specific genome duplication; its paralog is smad3b. It encodes a receptor-regulated SMAD
  (R-SMAD) with an N-terminal MH1 DNA-binding domain, a linker carrying regulatory phosphosites and a C-terminal
  MH2 domain ending in the SSVS motif that TGF-beta/activin/nodal type I receptors phosphorylate. On activation
  it forms a heteromeric complex with SMAD4, enters the nucleus and binds SMAD-binding elements to regulate
  transcription of target genes. smad3a is the more conserved of the two copies (97% identical to human SMAD3).
  Its mRNA is supplied maternally and is broadly expressed, with higher levels in paraxial mesoderm and newly
  formed somites. Unlike smad3b, it is expressed with a circadian rhythm and is a direct target of Clock1a.
  With smad2 and smad3b it mediates nodal/TGF-beta signals in mesendoderm induction. Overexpressed smad3a
  activates the myf5 promoter together with Smad4, and constitutively active Smad3a promotes cardiomyocyte
  proliferation. Combined loss of smad3a and smad3b enlarges the ventral aorta but is compatible with adult
  survival.
existing_annotations:
- term:
    id: GO:0000976
    label: transcription cis-regulatory region binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: enables
  supporting_entities:
  - ARBA:ARBA00028970
  review:
    summary: ARBA electronic transfer of cis-regulatory region binding, a parent of the SMAD-binding element
      binding captured more precisely by the IBA to GO:0000978.
    action: ACCEPT
    reason: The MH1 domain and its DNA-contacting residues are conserved (smad3a-bioinformatics), and Smad3a
      occupies SMAD-binding elements of the myf5 promoter in vivo. The term is correct though less specific than
      GO:0000978.
    supported_by:
    - reference_id: PMID:21159776
      supporting_text: However, two PCR products with 218 bp containing SBE1 and SBE2 were found in embryos injected
        with either pHis-Smad3a or pHis-Smad4
- term:
    id: GO:0000978
    label: RNA polymerase II cis-regulatory region sequence-specific DNA binding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: enables
  supporting_entities:
  - FB:FBgn0011648
  - FB:FBgn0288966
  - MGI:MGI:109452
  - MGI:MGI:1328787
  - MGI:MGI:894293
  - PANTHER:PTN000344419
  - UniProtKB:P84022
  - UniProtKB:Q13485
  - UniProtKB:Q15796
  - UniProtKB:Q15797
  - UniProtKB:Q99717
  - ZFIN:ZDB-GENE-990603-7
  review:
    summary: PAINT inference from the SMAD family node that R-SMADs bind RNA polymerase II cis-regulatory DNA
      (SMAD-binding elements).
    action: ACCEPT
    reason: The node is sound and smad3a sits within it with all MH1 DNA-binding and Zn-coordinating residues
      conserved. In vivo ChIP places Smad3a on SBEs of the myf5 promoter.
    supported_by:
    - reference_id: PMID:21159776
      supporting_text: However, two PCR products with 218 bp containing SBE1 and SBE2 were found in embryos injected
        with either pHis-Smad3a or pHis-Smad4
    - reference_id: file:DANRE/smad3a/smad3a-bioinformatics/RESULTS.md
      supporting_text: Conserved in both copies and in gar
- term:
    id: GO:0000981
    label: DNA-binding transcription factor activity, RNA polymerase II-specific
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: enables
  supporting_entities:
  - FB:FBgn0011648
  - FB:FBgn0288966
  - MGI:MGI:108051
  - MGI:MGI:109452
  - MGI:MGI:1201674
  - MGI:MGI:1328787
  - MGI:MGI:894293
  - PANTHER:PTN000344419
  - UniProtKB:P84022
  - UniProtKB:Q13485
  - UniProtKB:Q15796
  - UniProtKB:Q15797
  - ZFIN:ZDB-GENE-990603-7
  review:
    summary: PAINT inference that SMAD proteins are sequence-specific RNA polymerase II transcription factors.
    action: ACCEPT
    reason: This is the core molecular function of an R-SMAD. smad3a overexpression activates the myf5 promoter
      in zebrafish embryos, and a Smad3-responsive reporter is activated by both zebrafish Smad3 paralogs.
    supported_by:
    - reference_id: PMID:21159776
      supporting_text: Using a luciferase assay to detect myf5 promoter activity when smad2 , smad3a , smad3b ,
        or smad4 mRNAs were overexpressed, we found that excessive smad2 and smad3a showed enhanced myf5 promoter
        activity but not excessive smad3b or smad4 mRNA.
    - reference_id: PMID:25286120
      supporting_text: Reporter fluorescence is activated in phospho-Smad3 positive cells and is responsive to
        both Smad3 isoforms, Smad3a and 3b.
- term:
    id: GO:0000981
    label: DNA-binding transcription factor activity, RNA polymerase II-specific
  evidence_type: TAS
  original_reference_id: PMID:28887217
  qualifier: contributes_to
  review:
    summary: ZFIN TAS from the Eaf1/2 paper, which describes Smad-containing TGF-beta transcriptional complexes
      repressed by Eaf1/2.
    action: ACCEPT
    reason: The activity is correct for smad3a; the contributes_to qualifier reflects that R-SMADs act in heteromeric
      complexes with SMAD4 and cofactors. The cached paper is abstract-only, so the curator's reading is deferred
      to; the function itself is well supported by other data.
    supported_by:
    - reference_id: PMID:28887217
      supporting_text: Furthermore, Eaf1/2 might co-localize and interact with TGF-β transcriptional factors in
        the transcriptional complex as repressors to target and suppress TGF-β signaling activity.
- term:
    id: GO:0001714
    label: endodermal cell fate specification
  evidence_type: IMP
  original_reference_id: PMID:28887217
  qualifier: involved_in
  review:
    summary: ZFIN IMP from the Eaf1/2 study of mesoderm and endoderm formation.
    action: KEEP_AS_NON_CORE
    reason: Nodal-Smad2/3 signalling specifies endoderm in zebrafish, and dominant-negative Smad3a blocks mesendoderm
      induction (PMID:18025082). The cached paper is abstract-only, and the loss-of-function reagent recorded
      for the sibling rows is an eaf1 morpholino, so which smad3a manipulation underlies this row cannot be checked.
      Deferring to the curator, but this is a developmental output of the signalling core, shared with smad2
      and smad3b, and so non-core.
    supported_by:
    - reference_id: PMID:18025082
      supporting_text: Thus, our data reveal that Nodal signaling and mesendoderm induction depend on Smad2/3
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:16890162
  qualifier: enables
  supporting_entities:
  - ZFIN:ZDB-GENE-031030-4
  review:
    summary: Interaction with Tob1a, which the paper reports inhibits Smad3 transcriptional activity.
    action: REMOVE
    reason: Generic protein binding carries no functional information. The Tob1a interaction is not disputed,
      but the cached abstract does not describe an activity of Smad3a beyond being bound and inhibited, so there
      is no evidence-backed, more informative replacement term.
    supported_by:
    - reference_id: PMID:16890162
      supporting_text: Although Tob1a can also inhibit the transcriptional activity of the Nodal effector Smad3,
        its role in limiting dorsal development is executed primarily by antagonizing the beta-catenin signal.
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  supporting_entities:
  - UniProtKB-SubCell:SL-0191
  review:
    summary: Nuclear location mapped from the UniProt subcellular-location rule for SMADs.
    action: ACCEPT
    reason: Activated R-SMADs enter the nucleus with SMAD4 to bind DNA; Smad3a occupies myf5 promoter elements
      in vivo.
    supported_by:
    - reference_id: PMID:21159776
      supporting_text: However, two PCR products with 218 bp containing SBE1 and SBE2 were found in embryos injected
        with either pHis-Smad3a or pHis-Smad4
- term:
    id: GO:0005667
    label: transcription regulator complex
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: part_of
  supporting_entities:
  - InterPro:IPR013019
  review:
    summary: InterPro2GO mapping from the MH1 domain.
    action: ACCEPT
    reason: R-SMADs act in heteromeric transcription regulator complexes with SMAD4 and DNA-binding cofactors.
      The more specific heteromeric SMAD protein complex (IBA) is the better description.
- term:
    id: GO:0005667
    label: transcription regulator complex
  evidence_type: TAS
  original_reference_id: PMID:28887217
  qualifier: part_of
  review:
    summary: ZFIN TAS from the Eaf1/2 paper, which proposes that Eaf1/2 act inside TGF-beta transcriptional complexes.
    action: ACCEPT
    reason: Consistent with the conserved R-SMAD mechanism. The paper is abstract-only here; the location is
      correct for smad3a regardless.
    supported_by:
    - reference_id: PMID:28887217
      supporting_text: Furthermore, Eaf1/2 might co-localize and interact with TGF-β transcriptional factors in
        the transcriptional complex as repressors to target and suppress TGF-β signaling activity.
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  supporting_entities:
  - UniProtKB-SubCell:SL-0086
  review:
    summary: Cytoplasmic location mapped from the UniProt subcellular-location rule.
    action: ACCEPT
    reason: Unstimulated R-SMADs are cytoplasmic and shuttle to the nucleus after receptor phosphorylation;
      the zebrafish study of myf5 regulation also describes cytoplasmic Smad2-Smad3a without Smad4.
    supported_by:
    - reference_id: PMID:21159776
      supporting_text: Although there is some active Smad2·Smad3a in cytoplasm, Smad2·Smad3a is unable to enter
        the nucleus to activate the myf5 promoter without the assistance of Smad4 protein.
- term:
    id: GO:0006355
    label: regulation of DNA-templated transcription
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: involved_in
  supporting_entities:
  - InterPro:IPR001132
  - InterPro:IPR003619
  - InterPro:IPR013019
  - InterPro:IPR013790
  review:
    summary: InterPro2GO mapping from the SMAD/MH1/MH2 domains.
    action: ACCEPT
    reason: Correct but general; the IBA to positive regulation of transcription by RNA polymerase II is more
      specific.
- term:
    id: GO:0006355
    label: regulation of DNA-templated transcription
  evidence_type: IPI
  original_reference_id: PMID:21159776
  qualifier: acts_upstream_of_or_within
  supporting_entities:
  - ZFIN:ZDB-GENE-000616-6
  review:
    summary: From the Dkk3r/myf5 study, where Smad3a with Smad4 activates the myf5 promoter.
    action: ACCEPT
    reason: Correct. The data show activation of an RNA polymerase II promoter (myf5) by Smad3a with Smad4,
      which the IBA row to GO:0045944 (positive regulation of transcription by RNA polymerase II) captures
      more specifically; kept at this level for consistency with the InterPro row to the same term.
    supported_by:
    - reference_id: PMID:21159776
      supporting_text: Although the ability of Smad2 and Smad3a to activate the myf5 promoter requires Smad4 to
        form a complex and enter the nucleus, Smad3b only plays a minor role in myf5 promoter activation.
- term:
    id: GO:0007179
    label: transforming growth factor beta receptor signaling pathway
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  supporting_entities:
  - MGI:MGI:108051
  - MGI:MGI:1201674
  - PANTHER:PTN002672225
  - RGD:3031
  - RGD:3032
  - UniProtKB:P84022
  - UniProtKB:Q15796
  - ZFIN:ZDB-GENE-000509-3
  - ZFIN:ZDB-GENE-990603-7
  review:
    summary: PAINT inference at the SMAD2/3 node. smad3a itself (ZFIN:ZDB-GENE-000509-3) is among the descendant
      evidence, reflecting its own experimental annotation.
    action: ACCEPT
    reason: Core process of an R-SMAD. The receptor-phosphorylated SSVS motif is conserved, and a Smad3-responsive
      reporter that responds to both paralogs is repressed by ALK4/ALK5 inhibitors.
    supported_by:
    - reference_id: PMID:25286120
      supporting_text: Moreover, Alk4 and Alk5 inhibitors strongly repress the reporter activity.
- term:
    id: GO:0007179
    label: transforming growth factor beta receptor signaling pathway
  evidence_type: IMP
  original_reference_id: PMID:28887217
  qualifier: involved_in
  review:
    summary: ZFIN IMP from the Eaf1/2 study using TGF-beta reporters.
    action: ACCEPT
    reason: The paper is abstract-only here, so the smad3a manipulation cannot be seen. The process is the
      core of smad3a function and is independently supported (reporter, dominant-negative and constitutively
      active Smad3a data). Deferring to the curator.
    supported_by:
    - reference_id: PMID:25286120
      supporting_text: Reporter fluorescence is activated in phospho-Smad3 positive cells and is responsive to
        both Smad3 isoforms, Smad3a and 3b.
- term:
    id: GO:0007179
    label: transforming growth factor beta receptor signaling pathway
  evidence_type: IMP
  original_reference_id: PMID:28887217
  qualifier: involved_in
  supporting_entities:
  - ZFIN:ZDB-MRPHLNO-090820-4
  review:
    summary: Same finding as the previous row; the WITH field records the eaf1 morpholino (ZDB-MRPHLNO-090820-4,
      MO1-eaf1 on ZFIN).
    action: ACCEPT
    reason: The process is correct for smad3a; the genotype details are in the full text, which is not cached.
      Deferring to the curator.
- term:
    id: GO:0007498
    label: mesoderm development
  evidence_type: IGI
  original_reference_id: PMID:28687631
  qualifier: acts_upstream_of_or_within
  supporting_entities:
  - ZFIN:ZDB-GENE-990630-14
  review:
    summary: smad3a mRNA restores mesoderm marker expression reduced by clock1a knockdown.
    action: KEEP_AS_NON_CORE
    reason: The genetic interaction is shown (rescue of clock1a morphants by smad3a mRNA), and Smad2/3 activity
      is required for mesendoderm induction. It is a developmental outcome of the signalling function, shared
      with smad2 and smad3b.
    supported_by:
    - reference_id: PMID:28687631
      supporting_text: These effects were largely compromised by co-injection of smad3a- mRNA.
    - reference_id: PMID:18025082
      supporting_text: Thus, our data reveal that Nodal signaling and mesendoderm induction depend on Smad2/3
- term:
    id: GO:0007501
    label: mesodermal cell fate specification
  evidence_type: IMP
  original_reference_id: PMID:28887217
  qualifier: involved_in
  review:
    summary: ZFIN IMP from the Eaf1/2 study.
    action: KEEP_AS_NON_CORE
    reason: Supported in principle by the Smad2/3 requirement for mesendoderm induction (PMID:18025082). The
      cached paper is abstract-only; deferring to the curator. Non-core developmental outcome.
    supported_by:
    - reference_id: PMID:18025082
      supporting_text: Smad2/3-deficient cells transplanted into the blastodermal margin of wild-type hosts preferentially
        differentiated into ectodermal tissues rather than mesendodermal tissues, supporting the idea that response
        of cells to mesendoderm inducers requires Smad2/3 activities.
- term:
    id: GO:0007501
    label: mesodermal cell fate specification
  evidence_type: IMP
  original_reference_id: PMID:28887217
  qualifier: involved_in
  supporting_entities:
  - ZFIN:ZDB-MRPHLNO-090820-4
  review:
    summary: Same finding as the previous row, recorded with the eaf1 morpholino in WITH.
    action: KEEP_AS_NON_CORE
    reason: As for the previous row.
- term:
    id: GO:0009653
    label: anatomical structure morphogenesis
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  supporting_entities:
  - FB:FBgn0011648
  - FB:FBgn0025800
  - FB:FBgn0288966
  - MGI:MGI:108051
  - MGI:MGI:109452
  - MGI:MGI:1100518
  - MGI:MGI:1201674
  - MGI:MGI:1336883
  - MGI:MGI:894293
  - PANTHER:PTN000344419
  - RGD:620158
  - RGD:71004
  - UniProtKB:A0A8J0R1N9
  - UniProtKB:A0A8J0T288
  - UniProtKB:A0A8J1IQ47
  - UniProtKB:O43541
  - UniProtKB:Q6IRR4
  - WB:WBGene00004856
  - WB:WBGene00004857
  - WB:WBGene00004858
  - Xenbase:XB-GENE-1018193
  - Xenbase:XB-GENE-482930
  - Xenbase:XB-GENE-484686
  - Xenbase:XB-GENE-485691
  - Xenbase:XB-GENE-486004
  - ZFIN:ZDB-GENE-000509-3
  - ZFIN:ZDB-GENE-990603-7
  - ZFIN:ZDB-GENE-990603-8
  - ZFIN:ZDB-GENE-990603-9
  review:
    summary: Very broad family-level PAINT process.
    action: KEEP_AS_NON_CORE
    reason: SMAD signalling shapes many structures, so the term is not wrong, but it is uninformative and describes
      downstream outcomes rather than what smad3a does.
- term:
    id: GO:0009880
    label: embryonic pattern specification
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: involved_in
  supporting_entities:
  - ARBA:ARBA00084933
  review:
    summary: ARBA transfer of embryonic patterning.
    action: KEEP_AS_NON_CORE
    reason: Smad2/3 activity is needed for mesendoderm induction and neuroectoderm patterning in zebrafish (shown
      with dominant-negative constructs that block Smad2/3 generally). Plausible but non-core.
    supported_by:
    - reference_id: PMID:19580801
      supporting_text: Collectively, these data indicate that Smad2/3 activities are required for neural induction
        and neuroectodermal posteriorization in zebrafish.
- term:
    id: GO:0009953
    label: dorsal/ventral pattern formation
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: involved_in
  supporting_entities:
  - ARBA:ARBA00027261
  review:
    summary: ARBA transfer of dorsal/ventral patterning, a SMAD family-wide rule dominated by BMP-pathway SMADs.
    action: MARK_AS_OVER_ANNOTATED
    reason: Dorsal/ventral patterning in the zebrafish embryo is driven mainly by BMP-SMAD1/5 signalling. No
      smad3a loss-of-function evidence shows a dorsal/ventral patterning defect. The organizer-gene induction
      reported for smad3b comes from overexpression. The ARBA rule is too broad for this R-SMAD.
- term:
    id: GO:0030154
    label: cell differentiation
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  supporting_entities:
  - FB:FBgn0011648
  - FB:FBgn0025800
  - FB:FBgn0288966
  - MGI:MGI:108051
  - MGI:MGI:109452
  - MGI:MGI:1201674
  - MGI:MGI:1328787
  - MGI:MGI:1859993
  - MGI:MGI:894293
  - PANTHER:PTN000344419
  - RGD:3032
  - RGD:3033
  - UniProtKB:O15198
  - UniProtKB:O43541
  - UniProtKB:Q13485
  - UniProtKB:Q15797
  - UniProtKB:Q99717
  - ZFIN:ZDB-GENE-000509-3
  - ZFIN:ZDB-GENE-031014-1
  - ZFIN:ZDB-GENE-990603-7
  - ZFIN:ZDB-GENE-990603-8
  - ZFIN:ZDB-GENE-991119-8
  review:
    summary: Broad family-level PAINT process.
    action: KEEP_AS_NON_CORE
    reason: Correct in general (e.g. smad3a knockdown alters neural differentiation) but uninformative.
    supported_by:
    - reference_id: PMID:25286120
      supporting_text: Similarly, smad3a and 3b knock-down alter neural differentiation showing that both paralogues
        play a positive role in neural differentiation.
- term:
    id: GO:0030509
    label: BMP signaling pathway
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: involved_in
  supporting_entities:
  - ARBA:ARBA00086900
  review:
    summary: ARBA transfer of BMP signalling, a SMAD family-wide rule.
    action: MARK_AS_OVER_ANNOTATED
    reason: SMAD3 is the receptor-regulated SMAD of the TGF-beta/activin/nodal branch; its C-terminal SSVS motif
      is phosphorylated by TGF-beta type I receptors, and in zebrafish the Smad3 reporter is blocked by ALK4/ALK5
      inhibitors. BMP signals regulate smad7 alongside Smad3 but that does not place Smad3a in the BMP pathway.
      No zebrafish evidence shows BMP receptors signalling through smad3a.
    supported_by:
    - reference_id: PMID:25286120
      supporting_text: Moreover, Alk4 and Alk5 inhibitors strongly repress the reporter activity.
- term:
    id: GO:0032924
    label: activin receptor signaling pathway
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  supporting_entities:
  - FB:FBgn0025800
  - PANTHER:PTN001008908
  - UniProtKB:P84022
  - UniProtKB:Q15796
  review:
    summary: PAINT inference at the SMAD2/3 node for activin signalling.
    action: ACCEPT
    reason: SMAD2/3 are the R-SMADs of the activin/nodal branch; smad3a is inside the node with conserved
      receptor-phosphorylation motif.
- term:
    id: GO:0038092
    label: nodal signaling pathway
  evidence_type: TAS
  original_reference_id: PMID:28687631
  qualifier: involved_in
  review:
    summary: ZFIN TAS from the Clock1a paper, which frames smad3a as the nodal effector in early mesoderm induction.
    action: ACCEPT
    reason: Supported by the Clock1a study and by dominant-negative Smad3a blocking nodal-induced mesendoderm.
    supported_by:
    - reference_id: PMID:28687631
      supporting_text: Here we show that Clock1a coordinated mesoderm development and primitive hematopoiesis in
        zebrafish embryos by directly up-regulating Nodal-Smad3 signaling.
    - reference_id: PMID:18025082
      supporting_text: Overexpression of these mutants abolished mesendoderm induction by ectopic Nodal signaling
        in zebrafish embryos.
- term:
    id: GO:0043565
    label: sequence-specific DNA binding
  evidence_type: IPI
  original_reference_id: PMID:21159776
  qualifier: enables
  supporting_entities:
  - ZFIN:ZDB-GENE-000616-6
  review:
    summary: In vivo ChIP places His-tagged Smad3a on two SMAD-binding elements of the myf5 upstream region.
    action: ACCEPT
    reason: Direct in vivo evidence of sequence-specific DNA binding by smad3a; the IBA to GO:0000978 captures
      the same function more specifically.
    supported_by:
    - reference_id: PMID:21159776
      supporting_text: However, two PCR products with 218 bp containing SBE1 and SBE2 were found in embryos injected
        with either pHis-Smad3a or pHis-Smad4
- term:
    id: GO:0045944
    label: positive regulation of transcription by RNA polymerase II
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  supporting_entities:
  - FB:FBgn0025800
  - MGI:MGI:108051
  - MGI:MGI:1201674
  - PANTHER:PTN001008908
  - RGD:3031
  - RGD:3032
  - UniProtKB:P84022
  - UniProtKB:Q15796
  - WB:WBGene00000904
  review:
    summary: PAINT inference at the SMAD2/3 node.
    action: ACCEPT
    reason: smad3a activates the myf5 promoter in embryos.
    supported_by:
    - reference_id: PMID:21159776
      supporting_text: Using a luciferase assay to detect myf5 promoter activity when smad2 , smad3a , smad3b ,
        or smad4 mRNAs were overexpressed, we found that excessive smad2 and smad3a showed enhanced myf5 promoter
        activity but not excessive smad3b or smad4 mRNA.
- term:
    id: GO:0060215
    label: primitive hemopoiesis
  evidence_type: IGI
  original_reference_id: PMID:28687631
  qualifier: acts_upstream_of_or_within
  supporting_entities:
  - ZFIN:ZDB-GENE-990630-14
  review:
    summary: smad3a mRNA restores scl expression reduced by clock1a knockdown.
    action: KEEP_AS_NON_CORE
    reason: The genetic interaction is shown, and the acts_upstream_of_or_within qualifier correctly limits
      the claim. Primitive hemopoiesis follows from nodal-dependent mesoderm induction, so this is an indirect,
      non-core outcome.
    supported_by:
    - reference_id: PMID:28687631
      supporting_text: These effects were largely compromised by co-injection of smad3a- mRNA.
- term:
    id: GO:0060395
    label: SMAD protein signal transduction
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  supporting_entities:
  - FB:FBgn0011648
  - FB:FBgn0025800
  - FB:FBgn0288966
  - MGI:MGI:108051
  - MGI:MGI:109452
  - MGI:MGI:1100518
  - MGI:MGI:1201674
  - MGI:MGI:1328787
  - MGI:MGI:1859993
  - MGI:MGI:894293
  - PANTHER:PTN000344419
  - RGD:3031
  - RGD:3032
  - UniProtKB:O15105
  - UniProtKB:P84022
  - UniProtKB:Q13485
  - UniProtKB:Q15796
  - UniProtKB:Q15797
  - UniProtKB:Q9W734
  review:
    summary: PAINT inference at the SMAD family node.
    action: ACCEPT
    reason: Core process for an R-SMAD.
- term:
    id: GO:0070411
    label: I-SMAD binding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: enables
  supporting_entities:
  - PANTHER:PTN000344419
  - UniProtKB:O15105
  - UniProtKB:O43541
  - UniProtKB:Q13485
  - UniProtKB:Q15796
  - UniProtKB:Q15797
  review:
    summary: PAINT inference that SMADs bind inhibitory SMADs (SMAD6/7).
    action: ACCEPT
    reason: Binding of SMAD7 to R-SMADs is a conserved feedback mechanism, and zebrafish smad7 is itself a Smad3
      target. No residue loss in the MH2 domain of smad3a (99.5% identical to human over MH2).
    supported_by:
    - reference_id: PMID:12112463
      supporting_text: Furthermore, we show that Smad3 and BMP signals activate smad7.
- term:
    id: GO:0071144
    label: heteromeric SMAD protein complex
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: part_of
  supporting_entities:
  - FB:FBgn0011648
  - FB:FBgn0025800
  - FB:FBgn0288966
  - PANTHER:PTN000344419
  - UniProtKB:P84022
  - UniProtKB:Q13485
  - UniProtKB:Q15796
  - UniProtKB:Q15797
  review:
    summary: PAINT inference that R-SMADs form heteromeric complexes with SMAD4.
    action: ACCEPT
    reason: In zebrafish, Smad3a needs Smad4 to form a complex and enter the nucleus to activate myf5.
    supported_by:
    - reference_id: PMID:21159776
      supporting_text: In addition, Smad2·Smad3a required the recruitment of Smad4 to enter the nucleus.
core_functions:
- description: Receptor-regulated SMAD of the TGF-beta/activin/nodal branch. After C-terminal phosphorylation it
    forms a heteromeric complex with SMAD4, enters the nucleus, binds SMAD-binding elements and activates RNA
    polymerase II target genes (e.g. myf5). Molecular function shared with smad3b.
  molecular_function:
    id: GO:0000981
    label: DNA-binding transcription factor activity, RNA polymerase II-specific
  directly_involved_in:
  - id: GO:0007179
    label: transforming growth factor beta receptor signaling pathway
  - id: GO:0038092
    label: nodal signaling pathway
  - id: GO:0032924
    label: activin receptor signaling pathway
  locations:
  - id: GO:0005634
    label: nucleus
  - id: GO:0005737
    label: cytoplasm
  in_complex:
    id: GO:0071144
    label: heteromeric SMAD protein complex
  supported_by:
  - reference_id: PMID:21159776
    supporting_text: Although the ability of Smad2 and Smad3a to activate the myf5 promoter requires Smad4 to form
      a complex and enter the nucleus, Smad3b only plays a minor role in myf5 promoter activation.
  - reference_id: PMID:25286120
    supporting_text: Reporter fluorescence is activated in phospho-Smad3 positive cells and is responsive to both
      Smad3 isoforms, Smad3a and 3b.
  - reference_id: PMID:18025082
    supporting_text: Thus, our data reveal that Nodal signaling and mesendoderm induction depend on Smad2/3
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO terms
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied
    by conservative changes to GO terms applied by UniProt
  findings: []
- id: GO_REF:0000117
  title: Electronic Gene Ontology annotations created by ARBA machine learning models
  findings: []
- id: PMID:16890162
  title: Tob1 controls dorsal development of zebrafish embryos by antagonizing maternal beta-catenin transcriptional
    activity.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: Abstract only. Tob1a inhibits Smad3 transcriptional activity; source of the generic protein-binding
      IPI rows on both smad3 paralogs.
- id: PMID:21159776
  title: dickkopf-3-related gene regulates the expression of zebrafish myf5 gene through phosphorylated p38a-dependent
    Smad4 activity.
  findings:
  - statement: Smad3a with Smad4 activates the myf5 promoter and occupies its SMAD-binding elements in vivo; smad3b
      overexpression does not activate the promoter.
    supporting_text: Using a luciferase assay to detect myf5 promoter activity when smad2 , smad3a , smad3b , or
      smad4 mRNAs were overexpressed, we found that excessive smad2 and smad3a showed enhanced myf5 promoter activity
      but not excessive smad3b or smad4 mRNA.
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: Full text cached. One of the few side-by-side paralog comparisons.
- id: PMID:28687631
  title: Clock1a affects mesoderm development and primitive hematopoiesis by regulating Nodal-Smad3 signaling in
    the zebrafish embryo.
  findings:
  - statement: Clock1a directly activates the smad3a promoter through an E-box; smad3a mRNA rescues clock1a morphant
      mesoderm and scl markers.
    supporting_text: Mechanistically, Clock1a activates the smad3a promoter via its E-box1 element (CAGATG).
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: Full text cached. smad3a-specific regulatory input (circadian clock).
- id: PMID:28887217
  title: Transcriptional factors Eaf1/2 inhibit endoderm and mesoderm formation via suppressing TGF-β signaling.
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: UNVERIFIED
    review_notes: Abstract only; the smad3a manipulation behind the ZFIN IMP rows cannot be seen. The WITH field
      of two rows is the eaf1 morpholino (MO1-eaf1).
- id: PMID:10767528
  title: Cloning and characterization of zebrafish smad2, smad3 and smad4.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: Abstract only; describes "smad3" before smad3b was known. That this is smad3a is my inference.
- id: PMID:12112463
  title: Zebrafish Smad7 is regulated by Smad3 and BMP signals.
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: Abstract only; first description of smad3b; Smad3 activates smad7.
- id: PMID:18025082
  title: smad2 and smad3 are required for mesendoderm induction by transforming growth factor-beta/nodal signals
    in zebrafish.
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: Abstract only; dominant-negative Smad2, Smad3a and Smad3b block nodal-induced mesendoderm.
- id: PMID:19580801
  title: Smad2/3 activities are required for induction and patterning of the neuroectoderm in zebrafish.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: Abstract only; uses dnsmad3b as a general Smad2/3 blocker.
- id: PMID:25286120
  title: A Smad3 transgenic reporter reveals TGF-beta control of zebrafish spinal cord development.
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: Abstract only; reporter responds to both paralogs; both knockdowns alter neural differentiation.
- id: PMID:27703851
  title: 'Evolution history of duplicated smad3 genes in teleost: insights from Japanese flounder, Paralichthys olivaceus.'
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: Full text; synteny and phylogeny place the smad3a/b duplication at the TGD.
- id: PMID:29196619
  title: Opposite effects of Activin type 2 receptor ligands on cardiomyocyte proliferation during development and
    repair.
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: Full text; constitutively active Smad3a and Smad3b both increase cardiomyocyte proliferation.
- id: PMID:29940038
  title: Interactions between the circadian clock and TGF-β signaling pathway in zebrafish.
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: Full text; smad3a but not smad3b is expressed rhythmically.
- id: PMID:33816481
  title: Inhibition of TGF-β/Smad3 Signaling Disrupts Cardiomyocyte Cell Cycle Progression and Epithelial-Mesenchymal
    Transition-Like Response During Ventricle Regeneration.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: smad3a upregulated after ventricle ablation; SIS3 inhibitor is not paralog-specific.
- id: PMID:36926042
  title: Novel SMAD3 variant identified in a patient with familial aortopathy modeled using a zebrafish embryo assay.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: Uses smad3a mRNA with human variants; confirms conservation.
- id: PMID:40066353
  title: 'Modeling thoracic aortic genetic variants in the zebrafish: useful for predicting clinical pathogenicity?'
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: Review; states that both smad3 ohnologs had to be targeted because of redundancy (single-mutant
      data not shown).
- id: PMID:42584512
  title: Smad3 deficiency attenuates disease severity in a zebrafish model for Smad6-related aortic disease.
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: Abstract only; smad3a/b double knockout enlarges ventral aorta and survives to adulthood.
- id: file:DANRE/smad3a/smad3a-bioinformatics/RESULTS.md
  title: smad3a/smad3b/human SMAD3/gar SMAD3 protein comparison and Bgee/ZFIN expression comparison
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: Manual audit verified the sidecar supports both copies as SMAD3 orthologs retaining the MH1/MH2
      domains and receptor-phosphorylated tail, with smad3b linker divergence that remains biochemically untested.
  findings:
  - statement: Both paralogs keep all annotated functional residues of human SMAD3 except S418 (N in smad3b);
      smad3a is the more conserved copy.
    supporting_text: Conserved in both copies and in gar
suggested_questions:
- question: Do smad3a single mutants have any phenotype, and is smad3b upregulated in smad3a PTC mutants (transcriptional
    adaptation)?
- question: Does the circadian, Clock1a-driven expression of smad3a (absent from smad3b) have a physiological consequence
    that smad3b cannot supply?
- question: Is the difference in myf5 promoter activation between Smad3a and Smad3b a real protein difference, e.g.
    linked to the diverged smad3b linker?
suggested_experiments:
- hypothesis: smad3a and smad3b are redundant for the ventral aorta phenotype.
  description: Compare ventral aorta diameter in smad3a-/-, smad3b-/-, smad3a-/-;smad3b+/- and double mutants, including
    an RNA-less smad3a allele to exclude transcriptional adaptation.
  experiment_type: genetic interaction analysis
- hypothesis: Smad3a and Smad3b have equivalent transcriptional activity.
  description: Side-by-side SBE-reporter and target-gene assays of equal doses of Smad3a, Smad3b and a Smad3b linker-swap
    (smad3a linker) in MZ smad3a;smad3b embryos.
  experiment_type: cross-rescue