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

Gene ID: 30813, updated on 8-Jan-2020

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
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

Genomic context

See VSX1 in Genome Data Viewer
Location:
20p11.21
Exon count:
7
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 20 NC_000020.11 (25069940..25082379, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (25051521..25063015, complement)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 1257, pseudogene Neighboring gene adipocyte plasma membrane associated protein Neighboring gene acyl-CoA synthetase short chain family member 1 Neighboring gene V-set domain containing T cell activation inhibitor 1 pseudogene 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
neuron development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
neuron maturation IEA
Inferred from Electronic Annotation
more info
 
regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
response to stimulus IEA
Inferred from Electronic Annotation
more info
 
retinal bipolar neuron differentiation IEA
Inferred from Electronic Annotation
more info
 
visual perception IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cellular_component ND
No biological Data available
more info
 
nuclear chromatin ISA
Inferred from Sequence Alignment
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

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)

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_001256271.1NP_001243200.1  visual system homeobox 1 isoform c

    See identical proteins and their annotated locations for NP_001243200.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 3' UTR and has coding region, compared to variant 1. The resulting protein (isoform c) has a distinct C-terminus and is shorter than isoform a.
    Source sequence(s)
    AF176797, AL080312, BM680858, DQ854811
    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_001256272.1NP_001243201.1  visual system homeobox 1 isoform d

    See identical proteins and their annotated locations for NP_001243201.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 3' UTR and coding region, compared to variant 1. The resulting protein (isoform d) has a distinct C-terminus and is shorter than isoform a.
    Source sequence(s)
    AF176797, AL080312, BM680858, DQ854812
    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_014588.6NP_055403.2  visual system homeobox 1 isoform a

    See identical proteins and their annotated locations for NP_055403.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AF176797, DQ854807
    Consensus CDS
    CCDS13168.1
    UniProtKB/Swiss-Prot
    Q9NZR4
    Related
    ENSP00000365899.3, ENST00000376709.8
    Conserved Domains (2) summary
    pfam00046
    Location:167220
    Homeobox; Homeobox domain
    cl26247
    Location:47149
    DNA_pol3_delta2; DNA polymerase III, delta subunit
  4. NM_199425.2NP_955457.1  visual system homeobox 1 isoform b

    See identical proteins and their annotated locations for NP_955457.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 3' UTR and coding region compared to variant 1, resulting in a shorter isoform (b) that has a distinct C-terminus compared to isoform a.
    Source sequence(s)
    AF176797, AL080312, DQ854808
    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_045948.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 3' UTR and coding region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF176797, AL080312, BM680858, DQ854809
  2. NR_045951.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) differs in the 3' UTR and coding region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF176797, AL080312, BM680858, DQ854810
  3. NR_165181.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL080312
  4. NR_165182.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL080312
  5. NR_165183.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL080312
  6. NR_165184.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL080312

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p13 Primary Assembly

    Range
    25069940..25082379 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017027838.1XP_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_017027837.1XP_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
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