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    VSX1 visual system homeobox 1 [ Homo sapiens (human) ]

    Gene ID: 30813, updated on 2-May-2024

    Summary

    Official Symbol
    VSX1provided by HGNC
    Official Full Name
    visual system homeobox 1provided by HGNC
    Primary source
    HGNC:HGNC:12723
    See related
    Ensembl:ENSG00000100987 MIM:605020; AllianceGenome:HGNC:12723
    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
    PPD; KTCN; PPCD; RINX; KTCN1; PPCD1; CAASDS
    Summary
    The protein encoded by this gene contains a paired-like homeodomain and binds to the core of the locus control region of the red/green visual pigment gene cluster. The encoded protein may regulate expression of the cone opsin genes early in development. Mutations in this gene can cause posterior polymorphous corneal dystrophy and keratoconus. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See VSX1 in Genome Data Viewer
    Location:
    20p11.21
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (25070880..25082141, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (25127147..25146758, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (25051516..25062777, complement)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene acyl-CoA synthetase short chain family member 1 Neighboring gene Sharpr-MPRA regulatory region 14776 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12738 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17658 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17659 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12739 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:25038651-25039256 Neighboring gene uncharacterized LOC124904882 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr20:25052223-25052743 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:25062766-25063295 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:25064059-25064663 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:25064664-25065269 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:25085805-25086741 Neighboring gene VTCN1 pseudogene 1 Neighboring gene uncharacterized LOC284798

    Genomic regions, transcripts, and products

    Expression

    • 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

    Related articles in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in neuron development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in neuron maturation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in retinal bipolar neuron differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in visual perception IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    is_active_in cellular_component ND
    No biological Data available
    more info
     
    part_of chromatin ISA
    Inferred from Sequence Alignment
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    visual system homeobox 1
    Names
    homeodomain protein RINX
    retinal inner nuclear layer homeobox protein
    transcription factor VSX1
    visual system homeobox 1 homolog, CHX10-like

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_008101.3 RefSeqGene

      Range
      5041..11719
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001256271.2NP_001243200.1  visual system homeobox 1 isoform c

      See identical proteins and their annotated locations for NP_001243200.1

      Status: REVIEWED

      Source sequence(s)
      AL080312
      Consensus CDS
      CCDS58766.1
      UniProtKB/Swiss-Prot
      Q9NZR4
      Related
      ENSP00000387720.2, ENST00000444511.6
      Conserved Domains (1) summary
      pfam00046
      Location:167209
      Homeobox; Homeobox domain
    2. NM_001256272.2NP_001243201.1  visual system homeobox 1 isoform d

      See identical proteins and their annotated locations for NP_001243201.1

      Status: REVIEWED

      Source sequence(s)
      AL080312
      Consensus CDS
      CCDS58767.1
      UniProtKB/Swiss-Prot
      Q9NZR4
      Related
      ENSP00000401690.3, ENST00000429762.7
      Conserved Domains (1) summary
      pfam00046
      Location:167220
      Homeobox; Homeobox domain
    3. NM_001378633.1NP_001365562.1  visual system homeobox 1 isoform e

      Status: REVIEWED

      Source sequence(s)
      AL080312
    4. NM_014588.6NP_055403.2  visual system homeobox 1 isoform a

      See identical proteins and their annotated locations for NP_055403.2

      Status: REVIEWED

      Source sequence(s)
      AF176797, DQ854807
      Consensus CDS
      CCDS13168.1
      UniProtKB/Swiss-Prot
      B9EGJ4, D1MF28, Q0GM60, Q0GM61, Q0GM62, Q0GM63, Q0GM64, Q0GM65, Q5TF40, Q5TF41, Q9HCU3, Q9NU27, Q9NZR4
      Related
      ENSP00000365899.3, ENST00000376709.9
      Conserved Domains (2) summary
      pfam00046
      Location:167220
      Homeobox; Homeobox domain
      cl26247
      Location:47149
      DNA_pol3_delta2; DNA polymerase III, delta subunit
    5. NM_199425.3NP_955457.1  visual system homeobox 1 isoform b

      See identical proteins and their annotated locations for NP_955457.1

      Status: REVIEWED

      Source sequence(s)
      AL080312
      Consensus CDS
      CCDS13169.1
      UniProtKB/Swiss-Prot
      Q9NZR4
      Related
      ENSP00000365897.3, ENST00000376707.4
      Conserved Domains (1) summary
      pfam00046
      Location:167210
      Homeobox; Homeobox domain

    RNA

    1. NR_045948.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL080312
    2. NR_045951.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL080312
    3. NR_165181.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL080312
    4. NR_165182.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL080312
    5. NR_165183.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL080312

    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_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      25070880..25082141 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017027838.2XP_016883327.1  visual system homeobox 1 isoform X2

      UniProtKB/Swiss-Prot
      Q9NZR4
      Related
      ENSP00000387069.2, ENST00000409958.6
      Conserved Domains (1) summary
      pfam00046
      Location:167209
      Homeobox; Homeobox domain
    2. XM_017027837.2XP_016883326.1  visual system homeobox 1 isoform X1

      UniProtKB/Swiss-Prot
      Q9NZR4
      Related
      ENSP00000386612.2, ENST00000409285.6
      Conserved Domains (1) summary
      pfam00046
      Location:167220
      Homeobox; Homeobox domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      25127147..25146758 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054323401.1XP_054179376.1  visual system homeobox 1 isoform X3