HOXA2 (homeobox protein Hox-A2) is a homeodomain transcription factor of the Antp homeobox family, proboscipedia subfamily, and the paralog group 2 member of the HOXA cluster. It binds specific DNA sequences in RNA polymerase II cis-regulatory regions through its homeodomain and, depending on the target and cofactors (PBX/MEIS), represses or activates transcription in the nucleus. In the mammalian embryo it acts in cranial neural crest-derived mesenchyme of the second pharyngeal arch as a selector gene that confers second-arch (hyoid) identity, so that loss of function transforms second-arch skeletal elements into first-arch (mandibular and middle-ear) structures; it is also expressed in hindbrain rhombomeres 2-3 and the spinal cord. Human HOXA2 variants cause microtia with hearing impairment and cleft palate. The donkey protein A0A9L0JBM7 is a full-length 373-residue product, 97.6% identical to human HOXA2 with an identical homeodomain and hexapeptide.
Existing Annotations Review
GO Term
Evidence
Action
Reason
GO:0000122 negative regulation of transcription by RNA polymerase II
IEA GO_REF:0000108
ACCEPT
Summary: Negative regulation of transcription by RNA polymerase II, inferred (GO_REF:0000108) from the repressor-activity annotation. Mouse Hoxa2 binds the Six2 promoter and downregulates Six2 in second-arch mesenchyme (PMID:15634706).
Reason: The process follows directly from HOXA2's own DNA-binding repressor activity; the TF itself performs the regulation. Transfer is phylogenetically grounded, as donkey A0A9L0JBM7, human O43364 and mouse P31245 are all members of PANTHER subfamily PTHR45664:SF3 (HOMEOBOX PROTEIN HOX-A2), and the donkey homeodomain is 100% identical to human.
High levels of Six2 are observed in the Hoxa2 loss-of-function mutant.
file:EQUAS/HOXA2/HOXA2-bioinformatics/RESULTS.md
human region 143-202: 60 of 60 residues aligned, 60 identical
GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding
IEA GO_REF:0000120
ACCEPT
Summary: RNA polymerase II cis-regulatory region sequence-specific DNA binding (combined IEA, from the mouse ortholog and PANTHER node PTN000674557). Mouse Hoxa2 binds the Six2 promoter (PMID:15634706), and Hox/Pbx sites in the Krox20 element C enhancer mediate direct activation (PMID:18787068).
Reason: Most specific DNA-binding term supported for the PTHR45664:SF3 subfamily; the donkey homeodomain, which carries all DNA-contacting residues, is identical to human.
Summary: DNA-binding transcription factor activity, RNA polymerase II-specific (combined IEA; homeobox signature and PANTHER node). HOXA2 is a homeodomain sequence-specific transcription factor that both represses (Six2) and, with Pbx/Meis, activates (Krox20) target genes.
Reason: Core molecular function of a HOX protein. Because HOXA2 acts as both repressor and activator depending on target and cofactor context, this general RNA Pol II TF activity term is the appropriate core term alongside the repressor child term.
Summary: DNA-binding transcription repressor activity, RNA polymerase II-specific (Ensembl Compara from mouse Hoxa2, based on PMID:15634706).
Reason: Mouse Hoxa2 binds the Six2 promoter and its loss derepresses Six2, so it acts as a direct repressor of this RNA Pol II target. HOXA2 also activates other targets, so this is one of two valid specific activities rather than an exclusive one. Same PANTHER subfamily (PTHR45664:SF3) as the donor.
Summary: DNA binding (combined IEA from homeobox signatures). True, but entailed by the accepted RNA polymerase II cis-regulatory region sequence-specific DNA binding term.
Reason: HOXA2 binds DNA via its homeodomain; GO:0000978 (accepted in this review) is a descendant of GO:0003677, so the generic term adds nothing.
Summary: Nucleus (combined IEA including mouse ortholog transfer and SubCell mapping). Mouse Hoxa-2 protein is detected in nuclei by immunohistochemistry (PMID:10536059).
Reason: A sequence-specific transcription factor acting on chromatin; nuclear localization is shown for the mouse ortholog in the same PANTHER subfamily and is curated for human HOXA2.
Sequence-specific transcription factor which is part of a
GO:0006357 regulation of transcription by RNA polymerase II
IEA GO_REF:0000118
ACCEPT
Summary: Regulation of transcription by RNA polymerase II, from TreeGrafter (PANTHER node PTN000674557). HOXA2 directly regulates RNA Pol II target genes, repressing some (Six2) and activating others (Krox20 element C) with Pbx/Meis cofactors.
Reason: Consistent with the RNA Pol II-specific TF activity. TreeGrafter places the donkey sequence in PTHR45664:SF3, the same subfamily as the experimentally characterised mouse and human HOXA2, so the PANTHER node inheritance is sound.
Summary: Sequence-specific DNA binding (Ensembl Compara from mouse Hoxa2, PMID:15634706). True, but an ancestor of the accepted GO:0000978.
Reason: GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding (accepted here) is_a GO:0043565 (checked against OLS hierarchical ancestors), and already conveys sequence specificity. The earlier review accepted this row on the grounds that it conveyed specificity; that reasoning does not hold, so the action is changed to TOO_GENERAL. The claim itself is true.
Summary: Embryonic skeletal system development (Ensembl Compara from mouse Hoxa2, PMID:25889273). Hoxa2 specifies second-arch skeletal identity in cranial neural crest cells; loss of function transforms hyoid into mandibular/middle-ear elements, and ectopic expression transforms first-arch elements into second-arch-like structures.
Reason: As a selector transcription factor acting cell-autonomously in skeletogenic cranial neural crest mesenchyme (required in NCCs, and after their migration), HOXA2 directly regulates the morphogenetic programme of these skeletal elements; this is the defining developmental role of the HOXA2 subfamily in mammals, supported by independent knockout, conditional and gain-of-function studies.
Ectopic Hoxa2 expression results in the transformation of the proximal Meckel's cartilage and of the malleus, two ventral PA1 CNCCs derivatives, into a supernumerary styloid process (SP)
Summary: Pharyngeal system development (Ensembl Compara from mouse Hoxa2, PMID:25889273). Hoxa2 is the selector gene for second pharyngeal arch identity.
Reason: Core developmental role of the ortholog, executed by HOXA2 itself as a transcription factor in second-arch neural crest mesenchyme (selector gene for second-arch identity).
ectopic Hoxa2 expression is sufficient for the morphological and molecular transformation of the first PA (PA1) CNCC derivatives into the second PA (PA2)-like structures
Summary: Muscle structure development (Ensembl Compara from a mouse IDA row citing PMID:25889273, a Hoxa2 overexpression study in cranial neural crest).
Reason: The cached abstract of PMID:25889273 describes skeletal transformations of neural crest derivatives after ectopic Hoxa2 expression and says nothing about muscle; the full text is not available locally. Pharyngeal-arch muscles derive from mesoderm, not from the Hoxa2-expressing neural crest, so any effect of Hoxa2 on muscle patterning is expected to be non-cell-autonomous, via the crest-derived connective tissue. That makes muscle structure development a downstream consequence of HOXA2's activity in another cell population rather than a process HOXA2 performs. Not removed, because the mouse curator saw the full text; the earlier KEEP_AS_NON_CORE is tightened to over-annotation for the electronic transfer to donkey.
Here we show that ectopic expression of Hoxa2 in Hox-negative CNCCs results in distinct phenotypes in different CNCC subpopulations.
GO:1990837 sequence-specific double-stranded DNA binding
IEA GO_REF:0000107
TOO GENERAL
Summary: Sequence-specific double-stranded DNA binding (Ensembl Compara from a human HOXA2 IDA row citing PMID:28473536, a methylation-SELEX survey of 542 human TFs).
Reason: True for HOXA2 (homeodomain-mediated binding measured in a systematic SELEX survey; the donkey homeodomain is identical), but GO:0000978 accepted here is a descendant of GO:1990837 (checked against OLS hierarchical ancestors), so this term is entailed.
By analysis of 542 human TFs with methylation-sensitive SELEX
file:EQUAS/HOXA2/HOXA2-bioinformatics/RESULTS.md
human region 143-202: 60 of 60 residues aligned, 60 identical
Core Functions
Homeodomain transcription factor that binds RNA polymerase II cis-regulatory sequences in the nucleus and represses (e.g. Six2) or, with PBX/MEIS cofactors, activates (e.g. Krox20) target genes, conferring second pharyngeal arch identity on cranial neural crest mesenchyme.
Q: Does HOXA2 regulate pharyngeal-arch muscle patterning cell-autonomously or only through crest-derived connective tissue, and should muscle structure development be propagated to orthologs from PMID:25889273?
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.
Assessment of 3 ProtNLM2 GO predictions for donkey HOXA2 (A0A9L0JBM7). All three terms (DNA binding, DNA-binding transcription factor activity RNA polymerase II-specific, nucleus) are already in donkey GOA and are biologically supported by transfer from experimentally characterised mouse and human HOXA2, which share PANTHER subfamily PTHR45664:SF3 with the donkey protein, whose homeodomain is identical to human. The TF activity and nucleus terms are correct but not novel (CNN). DNA binding is correct but less specific than RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), which the donkey gene already carries and its gene review accepts (LSP). No non-GO ProtNLM2 outputs (function text or location) were emitted for this accession.
LSP — Less precise than existing annotation Review score: 2/2
Prediction method: ProtNLM2 · Version: UniProt API snapshot 2026-10-14
Review rationale: HOXA2 binds DNA through its homeodomain, which is 100% identical between donkey and human, so the prediction is correct. Donkey GOA already contains DNA binding and, more specifically, RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978) and sequence-specific double-stranded DNA binding (GO:1990837), both grounded in ortholog experiments. Because a supported, more specific annotation exists (GO:0000978 is a descendant of GO:0003677 and is accepted in the gene review, which marks DNA binding as too general), the prediction is less precise.
Prediction method: ProtNLM2 · Version: UniProt API snapshot 2026-10-14
Review rationale: HOXA2 is a sequence-specific homeodomain transcription factor; mouse Hoxa2 has IDA support for repressing and activating RNA polymerase II targets. The exact term is already in donkey GOA (combined IEA) and is the core function accepted by the gene review; the donkey protein shares PANTHER subfamily PTHR45664:SF3 and an identical homeodomain with the characterised orthologs. Correct but not novel; the repressor child term GO:0001227 is also present in GOA, but HOXA2 also activates targets, so the general TF term is appropriate rather than less precise.
Prediction method: ProtNLM2 · Version: UniProt API snapshot 2026-10-14
Review rationale: Nuclear localization is experimentally shown for mouse Hoxa2 (immunodetection in embryonic neural tube nuclei), and its regulated exit from the nucleus via the KPC2 interactor implies a nuclear steady state; human HOXA2 is curated as nuclear. The donkey protein is in the same PANTHER subfamily (PTHR45664:SF3) with an identical homeodomain, so the transfer is justified. The exact term is already in donkey GOA and is accepted as a core location by the gene review. Correct but not novel.