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    HOXA3 homeobox A3 [ Homo sapiens (human) ]

    Gene ID: 3200, updated on 5-Mar-2024

    Summary

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    Official Symbol
    HOXA3provided by HGNC
    Official Full Name
    homeobox A3provided by HGNC
    Primary source
    HGNC:HGNC:5104
    See related
    Ensembl:ENSG00000105997 MIM:142954; AllianceGenome:HGNC:5104
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    HOX1; HOX1E
    Summary
    In vertebrates, the genes encoding the class of transcription factors called homeobox genes are found in clusters named A, B, C, and D on four separate chromosomes. Expression of these proteins is spatially and temporally regulated during embryonic development. This gene is part of the A cluster on chromosome 7 and encodes a DNA-binding transcription factor which may regulate gene expression, morphogenesis, and differentiation. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in kidney (RPKM 1.8), fat (RPKM 1.4) and 17 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    7p15.2
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (27107010..27152583, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (27242907..27288574, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (27146629..27192202, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 2148 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:27136009-27136581 Neighboring gene HOXA transcript antisense RNA, myeloid-specific 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:27142137-27142976 Neighboring gene homeobox A2 Neighboring gene Sharpr-MPRA regulatory region 6231 Neighboring gene NANOG hESC enhancer GRCh37_chr7:27152731-27153232 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:27155135-27155350 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:27161315-27162514 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:27163690-27164487 Neighboring gene HOXA cluster antisense RNA 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18042 Neighboring gene homeobox A4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:27179129-27179707 Neighboring gene HOXA cluster antisense RNA 3 Neighboring gene homeobox A5 Neighboring gene homeobox A6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:27194138-27194722 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:27200121-27200806 Neighboring gene homeobox A7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:27201681-27202180 Neighboring gene HOXA10-HOXA9 readthrough Neighboring gene NUP98-HOXA9 recombination region Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:27203692-27204569 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:27204570-27205446 Neighboring gene homeobox A9

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Downregulation of HOXA3 in lung adenocarcinoma and its relevant molecular mechanism analysed by RT-qPCR, TCGA and in silico analysis. Gan BL, et al. Int J Oncol, 2018 Oct. PMID 30066858, Free PMC Article
    2. Homeobox A3 and KDM6A cooperate in transcriptional control of aerobic glycolysis and glioblastoma progression. Yang R, et al. Neuro Oncol, 2023 Apr 6. PMID 36215227, Free PMC Article
    3. ARID1B/SUB1-activated lncRNA HOXA-AS2 drives the malignant behaviour of hepatoblastoma through regulation of HOXA3. Liu G, et al. J Cell Mol Med, 2021 Apr. PMID 33683826, Free PMC Article
    4. miR‑338‑3p suppresses the malignancy of T‑cell lymphoblastic lymphoma by downregulating HOXA3. Wang L, et al. Mol Med Rep, 2019 Sep. PMID 31322185, Free PMC Article
    5. The histone chaperone NAP1L3 is required for haematopoietic stem cell maintenance and differentiation. Heshmati Y, et al. Sci Rep, 2018 Jul 25. PMID 30046127, Free PMC Article

    See all (41) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. HOXA3 functions as the on-off switch to regulate the development of hESC-derived third pharyngeal pouch endoderm through EPHB2-mediated Wnt pathway.
      Title: HOXA3 functions as the on-off switch to regulate the development of hESC-derived third pharyngeal pouch endoderm through EPHB2-mediated Wnt pathway.
    2. Homeobox A3 and KDM6A cooperate in transcriptional control of aerobic glycolysis and glioblastoma progression.
      Title: Homeobox A3 and KDM6A cooperate in transcriptional control of aerobic glycolysis and glioblastoma progression.
    3. ARID1B/SUB1-activated lncRNA HOXA-AS2 drives the malignant behaviour of hepatoblastoma through regulation of HOXA3.
      Title: ARID1B/SUB1-activated lncRNA HOXA-AS2 drives the malignant behaviour of hepatoblastoma through regulation of HOXA3.
    4. Bioinformatics analysis of putative target mRNAs of miR3383p identified a direct binding site in the 3'untranslated of homeobox A3 (HOXA3).
      Title: miR‑338‑3p suppresses the malignancy of T‑cell lymphoblastic lymphoma by downregulating HOXA3.
    5. we demonstrate that HOXA3 and HOXA5 genes are markedly upregulated when NAP1L3 is suppressed in umbilical cord blood (UCB) haematopoietic stem cells (HSCs). Taken together, our findings establish an important role for NAP1L3 in haematopoietic stem cells homeostasis and haematopoietic differentiation.
      Title: The histone chaperone NAP1L3 is required for haematopoietic stem cell maintenance and differentiation.
    6. Study indicated that low HOXA3 expression may play a certain role in lung adenocarcinoma; however, its association with lung squamous cell carcinoma still requires further investigation.
      Title: Downregulation of HOXA3 in lung adenocarcinoma and its relevant molecular mechanism analysed by RT-qPCR, TCGA and in silico analysis.
    7. aim of this work was to search for mutations in thyroid developmental candidate genes HOXA3, HOXB3, HOXD3 and PITX2
      Title: The absence of mutations in homeobox candidate genes HOXA3, HOXB3, HOXD3 and PITX2 in familial and sporadic thyroid hemiagenesis.
    8. HOXA7, HOXB3, HOXA3, and HOXB13 expression levels changed during angiogenesis, sugessting these proteins might be involved in the angiogenesis of hMSCs.
      Title: HOX gene analysis of endothelial cell differentiation in human bone marrow-derived mesenchymal stem cells.
    9. Observational study of gene-disease association. (HuGE Navigator)
      Title: High-density association study of 383 candidate genes for volumetric BMD at the femoral neck and lumbar spine among older men.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association analyses identify variants in developmental genes associated with hypospadias.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC10155

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
    Inferred from Sequence Alignment
    more info
    		  
    enables HMG box domain binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in angiogenesis IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in animal organ formation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in anterior/posterior pattern specification IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in blood vessel remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cartilage development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in embryonic skeletal system morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in gene expression IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in glossopharyngeal nerve morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in parathyroid gland development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of stem cell proliferation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in specification of animal organ position IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in stem cell proliferation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in thymus development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in thyroid gland development IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of chromatin ISA
    Inferred from Sequence Alignment
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    homeobox protein Hox-A3
    Names
    Hox-1.5-like protein
    homeo box 1E
    homeo box A3
    homeobox protein Hox-1E

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001384335.1 → NP_001371264.1  homeobox protein Hox-A3

      Status: REVIEWED

      Source sequence(s)
      AC004079, AC004080, AC010990
      Consensus CDS
      CCDS5404.1
      UniProtKB/Swiss-Prot
      A4D181, O43365
      UniProtKB/TrEMBL
      B3KPN8
      Conserved Domains (2) summary
      pfam00046
      Location:195 → 248
      Homeobox; Homeobox domain
      pfam13293
      Location:378 → 441
      DUF4074; Domain of unknown function (DUF4074)

    2. NM_001384336.1 → NP_001371265.1  homeobox protein Hox-A3

      Status: REVIEWED

      Source sequence(s)
      AC004079, AC004080, AC010990
      Consensus CDS
      CCDS5404.1
      UniProtKB/Swiss-Prot
      A4D181, O43365
      UniProtKB/TrEMBL
      B3KPN8
      Conserved Domains (2) summary
      pfam00046
      Location:195 → 248
      Homeobox; Homeobox domain
      pfam13293
      Location:378 → 441
      DUF4074; Domain of unknown function (DUF4074)

    3. NM_001384337.1 → NP_001371266.1  homeobox protein Hox-A3

      Status: REVIEWED

      Source sequence(s)
      AC004079, AC004080, AC010990
      Consensus CDS
      CCDS5404.1
      UniProtKB/Swiss-Prot
      A4D181, O43365
      UniProtKB/TrEMBL
      B3KPN8
      Conserved Domains (2) summary
      pfam00046
      Location:195 → 248
      Homeobox; Homeobox domain
      pfam13293
      Location:378 → 441
      DUF4074; Domain of unknown function (DUF4074)

    4. NM_001384338.1 → NP_001371267.1  homeobox protein Hox-A3

      Status: REVIEWED

      Source sequence(s)
      AC004079, AC004080, AC010990
      Consensus CDS
      CCDS5404.1
      UniProtKB/Swiss-Prot
      A4D181, O43365
      UniProtKB/TrEMBL
      B3KPN8
      Conserved Domains (2) summary
      pfam00046
      Location:195 → 248
      Homeobox; Homeobox domain
      pfam13293
      Location:378 → 441
      DUF4074; Domain of unknown function (DUF4074)

    5. NM_001384339.1 → NP_001371268.1  homeobox protein Hox-A3

      Status: REVIEWED

      Source sequence(s)
      AC004079, AC004080, AC010990
      Consensus CDS
      CCDS5404.1
      UniProtKB/Swiss-Prot
      A4D181, O43365
      UniProtKB/TrEMBL
      B3KPN8
      Conserved Domains (2) summary
      pfam00046
      Location:195 → 248
      Homeobox; Homeobox domain
      pfam13293
      Location:378 → 441
      DUF4074; Domain of unknown function (DUF4074)

    6. NM_001384340.1 → NP_001371269.1  homeobox protein Hox-A3

      Status: REVIEWED

      Source sequence(s)
      AC004079, AC004080, AC010990
      Consensus CDS
      CCDS5404.1
      UniProtKB/Swiss-Prot
      A4D181, O43365
      UniProtKB/TrEMBL
      B3KPN8
      Related
      ENSP00000324884.2, ENST00000317201.7
      Conserved Domains (2) summary
      pfam00046
      Location:195 → 248
      Homeobox; Homeobox domain
      pfam13293
      Location:378 → 441
      DUF4074; Domain of unknown function (DUF4074)

    7. NM_001384341.1 → NP_001371270.1  homeobox protein Hox-A3

      Status: REVIEWED

      Source sequence(s)
      AC004079, AC010990
      Consensus CDS
      CCDS5404.1
      UniProtKB/Swiss-Prot
      A4D181, O43365
      UniProtKB/TrEMBL
      B3KPN8
      Conserved Domains (2) summary
      pfam00046
      Location:195 → 248
      Homeobox; Homeobox domain
      pfam13293
      Location:378 → 441
      DUF4074; Domain of unknown function (DUF4074)

    8. NM_001384342.1 → NP_001371271.1  homeobox protein Hox-A3

      Status: REVIEWED

      Source sequence(s)
      AC004079, AC010990
      Consensus CDS
      CCDS5404.1
      UniProtKB/Swiss-Prot
      A4D181, O43365
      UniProtKB/TrEMBL
      B3KPN8
      Conserved Domains (2) summary
      pfam00046
      Location:195 → 248
      Homeobox; Homeobox domain
      pfam13293
      Location:378 → 441
      DUF4074; Domain of unknown function (DUF4074)

    9. NM_001384343.1 → NP_001371272.1  homeobox protein Hox-A3

      Status: REVIEWED

      Source sequence(s)
      AC004079, AC010990
      Consensus CDS
      CCDS5404.1
      UniProtKB/Swiss-Prot
      A4D181, O43365
      UniProtKB/TrEMBL
      B3KPN8
      Conserved Domains (2) summary
      pfam00046
      Location:195 → 248
      Homeobox; Homeobox domain
      pfam13293
      Location:378 → 441
      DUF4074; Domain of unknown function (DUF4074)

    10. NM_001384344.1 → NP_001371273.1  homeobox protein Hox-A3

      Status: REVIEWED

      Source sequence(s)
      AC004079, AC010990
      Consensus CDS
      CCDS5404.1
      UniProtKB/Swiss-Prot
      A4D181, O43365
      UniProtKB/TrEMBL
      B3KPN8
      Conserved Domains (2) summary
      pfam00046
      Location:195 → 248
      Homeobox; Homeobox domain
      pfam13293
      Location:378 → 441
      DUF4074; Domain of unknown function (DUF4074)

    11. NM_001384345.1 → NP_001371274.1  homeobox protein Hox-A3

      Status: REVIEWED

      Source sequence(s)
      AC004079
      Consensus CDS
      CCDS5404.1
      UniProtKB/Swiss-Prot
      A4D181, O43365
      UniProtKB/TrEMBL
      B3KPN8
      Conserved Domains (2) summary
      pfam00046
      Location:195 → 248
      Homeobox; Homeobox domain
      pfam13293
      Location:378 → 441
      DUF4074; Domain of unknown function (DUF4074)

    12. NM_001384346.1 → NP_001371275.1  homeobox protein Hox-A3

      Status: REVIEWED

      Source sequence(s)
      AC004079
      Consensus CDS
      CCDS5404.1
      UniProtKB/Swiss-Prot
      A4D181, O43365
      UniProtKB/TrEMBL
      B3KPN8
      Conserved Domains (2) summary
      pfam00046
      Location:195 → 248
      Homeobox; Homeobox domain
      pfam13293
      Location:378 → 441
      DUF4074; Domain of unknown function (DUF4074)

    13. NM_030661.5 → NP_109377.1  homeobox protein Hox-A3

      See identical proteins and their annotated locations for NP_109377.1

      Status: REVIEWED

      Source sequence(s)
      AC004079
      Consensus CDS
      CCDS5404.1
      UniProtKB/Swiss-Prot
      A4D181, O43365
      UniProtKB/TrEMBL
      B3KPN8
      Related
      ENSP00000379640.3, ENST00000396352.8
      Conserved Domains (2) summary
      pfam00046
      Location:195 → 248
      Homeobox; Homeobox domain
      pfam13293
      Location:378 → 441
      DUF4074; Domain of unknown function (DUF4074)

    14. NM_153631.3 → NP_705895.1  homeobox protein Hox-A3

      See identical proteins and their annotated locations for NP_705895.1

      Status: REVIEWED

      Source sequence(s)
      AC004079, AC004080, AC010990
      Consensus CDS
      CCDS5404.1
      UniProtKB/Swiss-Prot
      A4D181, O43365
      UniProtKB/TrEMBL
      B3KPN8
      Related
      ENSP00000484411.1, ENST00000612286.5
      Conserved Domains (2) summary
      pfam00046
      Location:195 → 248
      Homeobox; Homeobox domain
      pfam13293
      Location:378 → 441
      DUF4074; Domain of unknown function (DUF4074)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      27107010..27152583 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      27242907..27288574 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_153632.2: Suppressed sequence

      Description
      NM_153632.2: This RefSeq was permanently suppressed because it represents a poorly supported variant with non-consensus splice sites.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O43365.1 GenPept UniProtKB/Swiss-Prot:O43365

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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