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    HOXA1 homeobox A1 [ Homo sapiens (human) ]

    Gene ID: 3198, updated on 10-Dec-2024

    Summary

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    Official Symbol
    HOXA1provided by HGNC
    Official Full Name
    homeobox A1provided by HGNC
    Primary source
    HGNC:HGNC:5099
    See related
    Ensembl:ENSG00000105991 MIM:142955; AllianceGenome:HGNC:5099
    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
    BSAS; HOX1; HOX1F
    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. The encoded protein may be involved in the placement of hindbrain segments in the proper location along the anterior-posterior axis during development. Two transcript variants encoding two different isoforms have been found for this gene, with only one of the isoforms containing the homeodomain region. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in urinary bladder (RPKM 4.0), skin (RPKM 1.0) and 13 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See HOXA1 in Genome Data Viewer
    Location:
    7p15.2
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (27092993..27096000, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (27228895..27231899, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (27132612..27135619, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene tropomyosin 3 pseudogene 4 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr7:27069907-27070612 Neighboring gene NHP2 ribonucleoprotein pseudogene 2 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:27131207-27132117 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:27133706-27134206 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:27134207-27134707 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

    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. Clinical characterization of the HOXA1 syndrome BSAS variant. Bosley TM, et al. Neurology, 2007 Sep 18. PMID 17875913, Free PMC Article
    2. Upregulation of HOXA1 promotes tumorigenesis and development of non‑small cell lung cancer: A comprehensive investigation based on reverse transcription-quantitative polymerase chain reaction and bioinformatics analysis. Zhang Y, et al. Int J Oncol, 2018 Jul. PMID 29658571, Free PMC Article
    3. HOXA1 enhances the cell proliferation, invasion and metastasis of prostate cancer cells. Wang H, et al. Oncol Rep, 2015 Sep. PMID 26135141
    4. HOXA1 Mutations are Not Commonly Associated with Non-Syndromic Deafness. Abu-Amero KK, et al. Can J Neurol Sci, 2014 Jul. PMID 24878468
    5. MicroRNA-99 family members suppress Homeobox A1 expression in epithelial cells. Chen D, et al. PLoS One, 2013. PMID 24312487, Free PMC Article

    See all (121) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. HOXA1 promotes aerobic glycolysis and cancer progression in cervical cancer.
      Title: HOXA1 promotes aerobic glycolysis and cancer progression in cervical cancer.
    2. HOXA1 silencing inhibits cisplatin resistance of oral squamous cell carcinoma cells via IkappaB/NF-kappaB signaling pathway.
      Title: HOXA1 silencing inhibits cisplatin resistance of oral squamous cell carcinoma cells via IκB/NF-κB signaling pathway.
    3. A poly-histidine motif of HOXA1 is involved in regulatory interactions with cysteine-rich proteins.
      Title: A poly-histidine motif of HOXA1 is involved in regulatory interactions with cysteine-rich proteins.
    4. Downregulation of homeobox A1 in human granulosa cells is involved in diminished ovarian reserve through promoting cell apoptosis and mitochondrial dysfunction.
      Title: Downregulation of homeobox A1 in human granulosa cells is involved in diminished ovarian reserve through promoting cell apoptosis and mitochondrial dysfunction.
    5. Circ_0058063 regulates the development of esophageal cancer through miR-377-3p/HOXA1 axis.
      Title: Circ_0058063 regulates the development of esophageal cancer through miR-377-3p/HOXA1 axis.
    6. HOXA1 promotes proliferation and metastasis of bladder cancer by enhancing SMAD3 transcription.
      Title: HOXA1 promotes proliferation and metastasis of bladder cancer by enhancing SMAD3 transcription.
    7. HOXA1, a breast cancer oncogene.
      Title: HOXA1, a breast cancer oncogene.
    8. Hsa_circ_0074032 promotes prostate cancer progression through elevating homeobox A1 expression by serving as a microRNA-198 decoy.
      Title: Hsa_circ_0074032 promotes prostate cancer progression through elevating homeobox A1 expression by serving as a microRNA-198 decoy.
    9. CircRASSF2 acts as a prognostic factor and promotes breast cancer progression by modulating miR-1205/HOXA1 axis.
      Title: CircRASSF2 acts as a prognostic factor and promotes breast cancer progression by modulating miR-1205/HOXA1 axis.
    10. MiR-10a-5p restrains the aggressive phenotypes of ovarian cancer cells by inhibiting HOXA1.
      Title: MiR-10a-5p restrains the aggressive phenotypes of ovarian cancer cells by inhibiting HOXA1.
    Submit: New GeneRIF Correction See all GeneRIFs (78)

    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

    Associated conditions

    Description Tests
    Human HOXA1 syndromes
    MedGen: C1832215 OMIM: 601536 GeneReviews: HOXA1-Related Disorders
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat HIV-1 Tat specifically associates with HOXA1 promoter to upregulate HOXA1 expression in T cells PubMed

    Go to the HIV-1, Human Interaction Database

    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

    • MGC45232

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables sequence-specific double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in abducens nerve formation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in anatomical structure morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in artery development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in artery morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in cochlea development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in cochlea morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in cognition IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in embryonic neurocranium morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in inner ear development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in neuromuscular process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in optokinetic behavior IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in outer ear morphogenesis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of behavior IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in semicircular canal formation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in sensory perception of sound IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chromatin ISA
    Inferred from Sequence Alignment
    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-A1
    Names
    HOX A1 homeodomain protein
    Hox 1.6-like protein
    homeo box A1
    homeobox 1F
    homeobox protein Hox-1F
    lab-like protein

    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.

    Genomic

    1. NG_011813.2 RefSeqGene

      Range
      5000..8007
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_005522.5 → NP_005513.2  homeobox protein Hox-A1 isoform a

      Status: REVIEWED

      Source sequence(s)
      AC004079
      Consensus CDS
      CCDS5401.1
      UniProtKB/Swiss-Prot
      A0A2R8Y4R9, A4D184, B2R8U7, O43363, P49639
      Related
      ENSP00000494260.2, ENST00000643460.2
      Conserved Domains (2) summary
      COG5576
      Location:176 → 286
      COG5576; Homeodomain-containing transcription factor [Transcription]
      pfam00046
      Location:233 → 286
      Homeobox; Homeobox domain

    2. NM_153620.3 → NP_705873.3  homeobox protein Hox-A1 isoform b

      Status: REVIEWED

      Source sequence(s)
      AC004079
      Consensus CDS
      CCDS5402.2
      UniProtKB/TrEMBL
      A4D185, E7ERT8
      Related
      ENSP00000347851.5, ENST00000355633.5

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    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
      27092993..27096000 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      27228895..27231899 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P49639.3 GenPept UniProtKB/Swiss-Prot:P49639

    Gene LinkOut

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

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