Retinaldehyde dehydrogenase 2 (RALDH2), a cytosolic NAD+-dependent aldehyde dehydrogenase of the ALDH1A subfamily (EC 1.2.1.36) that oxidizes all-trans-retinaldehyde to all-trans retinoic acid (RA), the bioactive vitamin A metabolite. It is the principal source of embryonic RA in the trunk. In Xenopus, aldh1a2 is expressed first in the gastrula Spemann-Mangold organizer and then shifts laterally and posteriorly into paraxial and lateral plate mesoderm of the trunk and tail, so that RA is generated in the tissues that supply posteriorizing signals to adjacent neurectoderm. RA made by this enzyme acts through RAR/RXR nuclear receptors to set posterior Hox gene expression, patterning the hindbrain and spinal cord, and supports heart, forelimb and foregut-derived organ development. Loss of the orthologous enzyme in zebrafish and mouse truncates the anteroposterior axis, abolishes pectoral fin or forelimb induction and reduces posterior Hox expression, defects that exogenous RA can rescue. The 511-residue protein has the canonical two-domain aldehyde dehydrogenase fold, with a Rossmann-type NAD-binding domain, a conserved catalytic cysteine, and no signal peptide, transmembrane segment or organellar targeting sequence.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004029 aldehyde dehydrogenase (NAD+) activity | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Phylogenetic inference of generic NAD+-dependent aldehyde dehydrogenase activity at a deep, pan-eukaryotic ALDH node. The assertion is true of aldh1a2, since GO:0001758 (retinal dehydrogenase (NAD+) activity) is a direct is_a descendant of this term, but it does not convey the retinaldehyde substrate specificity that defines the core function of this gene. Reason: The node placement is sound and the target sits squarely inside the clade. The WITH/FROM seeds behind PANTHER:PTN000192421 span human ALDH1A1, ALDH2 and ALDH9A1, bovine ALDH1A1, mouse Aldh1a1, Aldh1a3 and Aldh1l1, rat Aldh1a1, Aldh2 and Aldh9a1, yeast ALD4 and ALD5, Drosophila Aldh, E. coli BetB and maize rf2, a set whose only shared and defensible activity is generic NAD+-dependent aldehyde oxidation, so a retinal-specific term could not have been asserted at this node. The frog protein retains the complete ALDH catalytic machinery, verified residue-by-residue against the sequence and recorded as machine-checkable residue claims below, anchored on the family review interpro/panther/PTHR11699/PTHR11699-review.yaml (node assessment for PANTHER:PTN000192666). The general-base glutamate Glu279 sits in the invariant LKRVTL[E]LGGKSP block and is the record's single ACT_SITE feature (PROSITE-ProRule PRU10007; an earlier version of this review mislabelled that feature as a catalytic cysteine at 279), and the catalytic nucleophile Cys313 sits in the invariant FNQGQC[C] block, corresponding to human ALDH1A2 Cys320. There is therefore no evidence of catalytic loss. Retained as a true but uninformative ancestor of the core molecular function rather than as the core function itself. Propagation Review Root cause: NO FAILURE NON CORE Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000192421 · ancestral ALDH node in PTHR11699 (aldehyde dehydrogenase-related) SUPPORTS TRANSFER Deep pan-kingdom ALDH node; the target is inside the clade and retains the catalytic machinery (see residue_claims), so descent-based transfer of the generic activity holds. This node id comes from the GOA WITH/FROM (row dated 20250411); the current cached PAINT slice (snapshot 20260828) records the GO:0004029 IBD at PANTHER:PTN000192666 with an essentially matching, expanded seed list, consistent with a PANTHER re-release renumbering the node. The current node is assessed NEEDS_PRUNING in the family review interpro/panther/PTHR11699/PTHR11699-review.yaml, with the prune scoped to the NADP+-dependent ALDH1L/FDH clade (SF120/SF131); that assessment explicitly affirms inheritance on the ALDH1A branch containing this target. UniProtKB:P00352 · human ALDH1A1 SUPPORTS TRANSFER Cytosolic ALDH1A-subfamily retinaldehyde dehydrogenase and the closest characterized seed to the target. MGI:MGI:1861722 · mouse Aldh1a3 SUPPORTS TRANSFER ALDH1A-subfamily paralog of the target and itself a retinaldehyde dehydrogenase. UniProtKB:P05091 · human ALDH2 (mitochondrial) SUPPORTS TRANSFER Supports the generic NAD+ aldehyde dehydrogenase activity only; its mitochondrial localization and acetaldehyde preference do not transfer, which is why the node term is generic. UniProtKB:P17445 · E. coli betaine aldehyde dehydrogenase BetB SUPPORTS TRANSFER Bacterial seed fixing the assertion at the generic activity level; its substrate is unrelated to retinoids. FB:FBgn0012036 · Drosophila Aldh SUPPORTS TRANSFER Invertebrate seed, consistent with an ancestral and substrate-generic node placement. |
| GO:0006081 aldehyde metabolic process | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Phylogenetic inference of generic aldehyde metabolism. This is true of aldh1a2, whose physiological substrate retinaldehyde is an aldehyde, but it is the generic parent process rather than the retinoid-specific process the enzyme actually performs. Reason: This IBA is correctly rather than wrongly conservative and should be retained rather than swapped. The node PANTHER:PTN002619055 is seeded by the direct mouse ortholog Aldh1a2 (MGI:MGI:107928) together with human ALDH1A3, human ALDH2, rat Aldh2 and Drosophila Aldh. Because ALDH2 and Drosophila Aldh are not retinaldehyde dehydrogenases, the retinoid-specific process GO:0002138 could not be asserted at this node, and the PAINT curator's placement of the generic aldehyde-metabolism term is the correct call for the clade. The specific process is therefore proposed separately below as a new annotation supported by target-relevant experimental literature, rather than as a replacement for this row. An earlier version of this review used MODIFY with GO:0002138 as the replacement, which would have pushed a subfamily-specific process onto a node that does not support it. A family-level pass (interpro/panther/PTHR11699/PTHR11699-review.yaml) confirms this judgment. Note that the current cached PAINT slice (snapshot 20260409) records the IBD at PANTHER:PTN002619055 as GO:0046185 (aldehyde catabolic process) with human ALDH2 as the recorded seed, placed at Eumetazoa, i.e. the node assertion has been narrowed since the GOA row (dated 20250320) was generated; the node is assessed SOUND under either version, and the family review scopes GO:0006081 as RESIDUE_DETERMINED by the catalytic-cysteine site, which the target retains (see the residue claims on the GO:0004029 row). Propagation Review Root cause: NO FAILURE NON CORE Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN002619055 · ALDH node seeded by ALDH1A and ALDH2 members SUPPORTS TRANSFER Node contains both retinaldehyde-specific members (ALDH1A2, ALDH1A3) and non-retinoid members (ALDH2, Drosophila Aldh), so generic aldehyde metabolic process is the most specific term the node can carry. In the current cached PAINT slice (snapshot 20260409) this node asserts the narrowed term GO:0046185 with human ALDH2 as recorded seed; assessed SOUND in the family review interpro/panther/PTHR11699/PTHR11699-review.yaml. MGI:MGI:107928 · mouse Aldh1a2 (Raldh2) SUPPORTS TRANSFER Direct one-to-one ortholog of the target; its experimental annotations are the strongest descendant evidence behind the node placement. UniProtKB:P47895 · human ALDH1A3 (RALDH3) SUPPORTS TRANSFER Closest characterized paralog and also a retinaldehyde dehydrogenase; in Xenopus, aldh1a3 acts alongside aldh1a2 in embryonic RA production. UniProtKB:P05091 · human ALDH2 (mitochondrial) SUPPORTS TRANSFER Non-retinoid member whose presence in the node constrains the assertion to the generic term. RGD:69219 · rat Aldh2 SUPPORTS TRANSFER As for human ALDH2, supports generic aldehyde metabolism only. FB:FBgn0012036 · Drosophila Aldh SUPPORTS TRANSFER Invertebrate seed, consistent with an ancestral and substrate-generic process assertion. |
| GO:0001758 retinal dehydrogenase (NAD+) activity | IEA GO_REF:0000003 | ACCEPT | Summary: This is the core molecular function of aldh1a2. The enzyme catalyzes the NAD+-dependent oxidation of retinaldehyde to retinoate (EC 1.2.1.36), the activity that generates the bioactive retinoid signal. The EC-based mapping matches the EC number carried on the RefSeq and UniProt records for this protein, and the activity is directly demonstrated for the vertebrate RALDH2 enzyme in a Xenopus assay system. Supporting Evidence: PMID:10570467 injection of Xenopus embryos with mRNAs for either mouse Aldh1 or mouse Raldh2 stimulates RA synthesis at low and high levels, respectively PMID:10570467 This provides evidence that some members of the ALDH gene family can indeed perform RA synthesis in vivo file:XENTR/aldh1a2/aldh1a2-deep-research.md Biochemical studies have shown that Xenopus (and mouse/human) ALDH1A2 efficiently oxidizes retinaldehyde to retinoic acid in vitro |
| GO:0016491 oxidoreductase activity | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: Keyword and InterPro driven annotation to a very high-level oxidoreductase term. It is a true ancestor of GO:0001758 and is not incorrect, but it carries almost no information about what this enzyme does. Reason: GO:0016491 is an is_a ancestor of the core term GO:0001758, so the mapping is factually correct and there is no basis for removal; it is simply subsumed by the more specific EC-derived annotation. Retained as a non-core, uninformative parent rather than deleted, since automated pipelines legitimately assert ancestor terms and removing true ancestors is not a curation goal. |
| GO:0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO mapping from the aldehyde dehydrogenase C-terminal domain signature (IPR016163), which the frog protein carries. Correct and reasonably informative about the chemistry, but still an ancestor of the substrate-specific core term. Reason: The domain-to-term mapping is sound, since the protein has the ALDH C-terminal domain together with the PROSITE aldehyde dehydrogenase cysteine and glutamate active-site signatures, and GO:0016620 is an is_a ancestor of GO:0001758, so the term is true rather than wrong. It is kept as a non-core parent of the retinal-specific activity rather than removed. |
| GO:0002138 retinoic acid biosynthetic process | ISS file:XENTR/aldh1a2/aldh1a2-deep-research.md | NEW | Summary: aldh1a2 catalyzes the second, effectively committed step of retinoic acid biosynthesis, oxidizing retinaldehyde to all-trans retinoic acid. This is the specific biological process the enzyme performs, and the one that the generic IBA to aldehyde metabolic process under-calls. Reason: Proposed as the substrate-specific process term corresponding to the accepted molecular function GO:0001758. It is supported by direct demonstration that Raldh2 mRNA injection drives RA synthesis in Xenopus embryos, and by loss-of-function evidence in the zebrafish aldh1a2 (neckless) mutant, where the phenotype tracks a primary defect in retinoic acid signalling and is rescued by exogenous RA. The frog protein is a one-to-one ortholog of these characterized enzymes and retains the complete catalytic machinery. Supporting Evidence: PMID:10570467 injection of Xenopus embryos with mRNAs for either mouse Aldh1 or mouse Raldh2 stimulates RA synthesis at low and high levels, respectively PMID:11688558 it inactivates retinaldehyde dehydrogenase type 2, an enzyme involved in retinoic acid biosynthesis PMID:11688558 some of these defects in neckless mutants can be rescued by application of exogenous retinoic acid |
| GO:0009952 anterior/posterior pattern specification | ISS PMID:11688558 The zebrafish neckless mutation reveals a requirement for ra... | NEW | Summary: Retinoic acid generated by RALDH2 in trunk mesoderm acts as a posteriorizing signal that positions anteroposterior identity along the body axis. Loss of the enzyme in the zebrafish neckless mutant truncates the anteroposterior axis and delays and reduces expression of the anteroposterior marker hoxb4. Reason: Inferred from the orthologous zebrafish aldh1a2 loss-of-function phenotype together with the conserved Xenopus expression domain, in which aldh1a2 is expressed in the gastrula organizer and then in the trunk mesoderm that supplies posteriorizing RA. The zebrafish defects are rescued by exogenous RA, tying the patterning role to the enzyme's RA-producing activity rather than to an unrelated function. Supporting Evidence: PMID:15652703 Our findings demonstrate that RA synthesized in the somitic mesoderm is necessary for posterior neural transformation in the mouse and that Raldh2 provides the only source of RA for posterior development PMID:11688558 neckless embryos are characterised by a truncation of the anteroposterior axis anterior to the somites, defects in midline mesendodermal tissues and absence of pectoral fins PMID:11688558 expression of the retinoic acid receptor a and hoxb4 genes is delayed and significantly reduced PMID:35372345 Two embryonic retinaldehyde dehydrogenases, ALDH1A2 (RALDH2) and ALDH1A3 (RALDH3) are initially expressed in the organizer and subsequently mark the trunk and the migrating leading edge mesendoderm, respectively |
| GO:0030902 hindbrain development | ISS PMID:11688558 The zebrafish neckless mutation reveals a requirement for ra... | NEW | Summary: RALDH2-derived retinoic acid produced in paraxial mesoderm signals non-cell-autonomously to the adjacent neural tube to pattern the posterior hindbrain, acting through hox gene expression. In the zebrafish aldh1a2 mutant, hoxb4 and retinoic acid receptor expression in the nervous system are delayed and reduced. Reason: Supported by the zebrafish ortholog loss-of-function phenotype and by mosaic analysis showing that the neural effect is non-cell-autonomous, meaning the enzyme acts by supplying a diffusible RA signal from mesoderm to neurectoderm. The authors state the conclusion as a conserved vertebrate role, and the Xenopus expression domain of organizer followed by trunk mesoderm matches. Note that the cached abstract documents altered posterior hox and RAR expression rather than a described loss of rhombomere identity, so the summary is limited to what is reported. Supporting Evidence: PMID:11688558 our results demonstrate a conserved role for retinaldehyde dehydrogenase type 2 in patterning the posterior cranial mesoderm of the vertebrate embryo PMID:11688558 expression of the retinoic acid receptor a and hoxb4 genes is delayed and significantly reduced |
| GO:0021915 neural tube development | ISS PMID:11688558 The zebrafish neckless mutation reveals a requirement for ra... | NEW | Summary: Retinoic acid made by RALDH2 in paraxial mesoderm is required for signalling to the adjacent neural tube, where it helps set posterior neural identity. Reason: The zebrafish study provides direct evidence that endogenous retinoic acid mediates signalling from paraxial mesoderm to the neural tube, and mosaic analysis shows that the effect on neural hoxb4 expression is non-cell-autonomous. In Xenopus, aldh1a2 is expressed in the mesoderm surrounding the neural tube at tailbud stages, consistent with the same relationship. Proposed as a non-core, RA-dependent developmental role rather than as a core function. Supporting Evidence: PMID:11688558 provide definitive evidence for an involvement of endogenous retinoic acid in signalling between the paraxial mesoderm and neural tube file:XENTR/aldh1a2/aldh1a2-deep-research.md in tailbud-stage Xenopus embryos, aldh1a2 is expressed around developing somites and in mesoderm surrounding the neural tube |
| GO:0060173 limb development | ISS PMID:16774994 Induction and prepatterning of the zebrafish pectoral fin bu... | NEW | Summary: RALDH2-derived retinoic acid from flanking somites is required permissively for induction of the forelimb field. Zebrafish aldh1a2 (neckless) mutants lack pectoral fins, and fin induction is restored by exogenous retinoic acid. Reason: Inferred from the orthologous zebrafish enzyme, where the requirement is mapped precisely, in that RA acts during the six- to eight-somite stages for pectoral fin induction, and transplantation shows somite-derived RA production is both required and sufficient for fin bud initiation. The pectoral fin is the teleost forelimb homolog, so the transferable claim is the general limb and appendage initiation role rather than a fin-specific one. An earlier version of this review cited only the title of PMID:11688558, which concerns hindbrain patterning and does not support a limb claim; the supporting text has been replaced with the relevant fin-induction and fin-absence statements. Supporting Evidence: PMID:16774994 By rescuing pectoral fin induction in the aldh1a2/neckless mutant with exogenous RA and by blocking RA signaling in wild-type embryos, we find that RA acts as a permissive signal that is required during the six- to eight-somite stages for pectoral fin induction PMID:16774994 Cell-transplantation experiments show that RA production is not only crucially required from flanking somites, but is sufficient to permit fin bud initiation when the trunk mesoderm is genetically ablated PMID:11688558 neckless embryos are characterised by a truncation of the anteroposterior axis anterior to the somites, defects in midline mesendodermal tissues and absence of pectoral fins |
| GO:0003007 heart morphogenesis | ISS PMID:34643182 Tbx5 drives Aldh1a2 expression to regulate a RA-Hedgehog-Wnt... | NEW | Summary: aldh1a2 is expressed in foregut lateral plate mesoderm/posterior second heart field, where Tbx5 directly maintains its expression via a conserved intronic enhancer. Aldh1a2-derived retinoic acid is required for posterior second heart field patterning, and both Tbx5 loss (which depletes aldh1a2) and direct Aldh1a2 knockdown disrupt this cardiac program, with partial rescue by exogenous RA. Reason: Supported by direct Xenopus experiments in the now-cached primary paper (Rankin et al. 2021, eLife). Tbx5 loss-of-function in both X. laevis (morpholino) and X. tropicalis (CRISPR/Cas9) strongly reduces aldh1a2 transcript and protein in the foregut lateral plate mesoderm, targeted Aldh1a2 morpholino knockdown phenocopies pharmacological RA synthesis inhibition with loss of posterior second heart field markers and expansion of anterior second heart field gene expression, and exogenous RA partially rescues the Tbx5-MO, Aldh1a2-MO and DEAB phenotypes. This places the enzyme causally upstream of second heart field patterning rather than merely correlated with it. An earlier version of this review cited the paper by PMC id only with deep-research paraphrases; the PMC id was resolved to PMID:34643182 via the NCBI ID converter and the quotes below are verbatim from the cached full text. Retained as a proposed non-core developmental role. Supporting Evidence: PMID:34643182 Both X. laevis Tbx5-MO morphant and X. trop tbx5 CRISPR/CAS9 mutant embryos exhibited a loss or strong reduction of aldh1a2 transcripts and Aldh1a2 protein in the foregut lpm at NF34 PMID:34643182 We suppressed endogenous RA synthesis by addition of the Aldh enzyme inhibitor DEAB between NF20 and NF34, the time when aldh1a2 expression was Tbx5-dependent. This phenocopied the Tbx5 LOF with loss of pSHF and pulmonary markers and an expansion of aSHF gene expression PMID:34643182 Importantly, we could partially rescue the Tbx5-MO, Aldh1a2-MO, and DEAB phenotypes with exogenous RA between NF20 and NF34, using a physiological concentration of 25 nM PMID:34643182 Specifically, Tbx5 directly maintains expression of Aldh1a2 in pSHF via an evolutionarily conserved intronic enhancer |
| GO:0030324 lung development | ISS PMID:34643182 Tbx5 drives Aldh1a2 expression to regulate a RA-Hedgehog-Wnt... | NEW | Summary: Aldh1a2-derived retinoic acid, maintained downstream of Tbx5 in foregut lateral plate mesoderm, is required for induction of Nkx2-1+ pulmonary progenitors in the adjacent foregut endoderm. Direct Aldh1a2 morpholino knockdown in Xenopus disrupts the RA-dependent cardiopulmonary signalling cascade and blocks pulmonary specification. Reason: Proposed as a non-core organogenesis role on direct Xenopus evidence from the now-cached primary paper (Rankin et al. 2021, eLife). Targeted Aldh1a2 morpholino injection, like DEAB inhibition of RA synthesis, results in failed induction of Nkx2-1+ pulmonary progenitors, and exogenous RA rescues the associated gene-expression changes; mechanistically, Tbx5/Aldh1a2-dependent RA directly activates shh transcription in the foregut endoderm, initiating the Hedgehog-Wnt2/2b cascade that induces pulmonary fate. An earlier version of this review cited the paper by PMC id only with deep-research paraphrases and a truncated quote; the PMC id was resolved to PMID:34643182 via the NCBI ID converter and the quotes below are verbatim from the cached full text. Supporting Evidence: PMID:34643182 Immunostaining of NF34 embryos for Aldh1a2 (red), Nkx2-1 (green), and Sox2 (blue) confirms that Aldh1a2-MO injection or DEAB treatment disrupts the RA>Tbx5>Aldh1a2>RA positive feedback loop (diagrammed in (D)) and results in failed induction of Nkx2-1+ pulmonary progenitors PMID:34643182 We find that Tbx5/Aldh1a2-dependent RA signaling directly activates shh transcription in the adjacent foregut endoderm through a conserved MACS1 enhancer. Hedgehog signaling coordinates with Tbx5 in the mesoderm to activate expression of wnt2/2b, which induces pulmonary fate in the foregut endoderm |
| GO:0005829 cytosol | ISS file:XENTR/aldh1a2/aldh1a2-deep-research.md | NEW | Summary: The enzyme is a soluble cytosolic protein in retinoic acid-producing cells, consistent with the "cytosolic retinal dehydrogenase activity" synonym of its molecular function term. The protein has no signal peptide, transmembrane segment or organellar targeting sequence. Reason: Proposed as the single, informative cellular-component term for this soluble enzyme. It rests on the absence of targeting or membrane-anchoring features in the frog protein, whose UniProt record annotates only the aldehyde dehydrogenase domain and the catalytic residue, together with the established soluble and non-mitochondrial character of ALDH1A-subfamily enzymes, which contrasts with the mitochondrial ALDH2 branch of the same family. An earlier version of this review also proposed the parent term GO:0005737 (cytoplasm) as a separate NEW annotation; that was redundant parent-plus-child over-proposal (the same argument used to drop GO:0042573 in favour of GO:0002138), so only this child term is retained. No direct immunolocalization has been performed on the Xenopus tropicalis protein, so this remains an inference from sequence and family context rather than a demonstrated localization. Supporting Evidence: file:XENTR/aldh1a2/aldh1a2-deep-research.md In RA-producing cells (such as specific embryonic mesodermal cells), ALDH1A2 localizes to the cytosol file:XENTR/aldh1a2/aldh1a2-deep-research.md consistent with its role as a soluble metabolic enzyme |
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Download this section (compressed HTML)Q: Is retinoic acid production in the Xenopus tropicalis trunk supplied by aldh1a2 alone, or is there functional redundancy with aldh1a1 and aldh1a3 that masks the aldh1a2 loss-of-function phenotype?
Q: What cis-regulatory elements drive the shift of aldh1a2 expression from the Spemann-Mangold organizer to trunk paraxial and lateral plate mesoderm, and is the Tbx5 intronic enhancer conserved in X. tropicalis?
Q: Does aldh1a2 protein localize exclusively to the cytosol in frog embryonic mesoderm, or is there evidence of association with membranes or other compartments?
Q: How is the balance between aldh1a2-mediated retinoic acid synthesis and cyp26-mediated degradation used to shape the posterior retinoic acid gradient in the frog embryo?
Q: Which of the organogenesis phenotypes attributed to aldh1a2 are direct consequences of local retinoic acid supply, and which are secondary to the earlier axial patterning defect?
Experiment: CRISPR/Cas9 F0 knockout of aldh1a2 in X. tropicalis with scoring of axial, hindbrain, somite, heart and limb bud phenotypes, and rescue by staged all-trans retinoic acid administration to establish which defects are retinoic acid dependent and when
Experiment: LC-MS/MS quantification of all-trans retinoic acid and retinaldehyde in dissected anterior versus trunk regions of wild-type and aldh1a2-depleted embryos, to test whether the enzyme is the rate-limiting source of trunk retinoic acid
Experiment: Double and triple depletion of aldh1a2, aldh1a1 and aldh1a3 to test for redundancy in embryonic retinoic acid production, given that aldh1a3 rather than aldh1a2 was shown to be the enzyme required for head formation
Experiment: Enzymatic characterization of recombinant X. tropicalis aldh1a2 with retinaldehyde and a panel of non-retinoid aldehydes, to determine whether the substrate preference matches the retinal-specific EC 1.2.1.36 assignment or is broader
Experiment: Immunostaining and subcellular fractionation of frog embryonic mesoderm to test the inferred cytosolic localization directly, together with ChIP or reporter assays for Tbx5 occupancy at the X. tropicalis aldh1a2 locus
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