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    Vrtn vertebrae development associated [ Mus musculus (house mouse) ]

    Gene ID: 432677, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Vrtnprovided by MGI
    Official Full Name
    vertebrae development associatedprovided by MGI
    Primary source
    MGI:MGI:3588197
    See related
    Ensembl:ENSMUSG00000071235 AllianceGenome:MGI:3588197
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    7420416P09Rik
    Summary
    Predicted to enable DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in chromatin and nucleus. Orthologous to human VRTN (vertebrae development associated). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Restricted expression toward ovary adult (RPKM 2.3) See more
    Orthologs
    human all
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    Genomic context

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    See Vrtn in Genome Data Viewer
    Location:
    12 D1; 12 39.32 cM
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 12 NC_000078.7 (84687793..84698229)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 12 NC_000078.6 (84641019..84651455)

    Chromosome 12 - NC_000078.7Genomic Context describing neighboring genes Neighboring gene visual system homeobox 2 Neighboring gene STARR-seq mESC enhancer starr_32746 Neighboring gene STARR-seq mESC enhancer starr_32747 Neighboring gene ATP-binding cassette, sub-family D member 4 Neighboring gene STARR-seq mESC enhancer starr_32748 Neighboring gene STARR-seq mESC enhancer starr_32749 Neighboring gene synapse differentiation inducing 1 like Neighboring gene STARR-positive B cell enhancer mm9_chr12:86096267-86096568 Neighboring gene NPC intracellular cholesterol transporter 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. VRTN is Required for the Development of Thoracic Vertebrae in Mammals. Duan Y, et al. Int J Biol Sci, 2018. PMID 29904281, Free PMC Article
    2. An Oct4-centered protein interaction network in embryonic stem cells. van den Berg DLC, et al. Cell Stem Cell, 2010 Apr 2. PMID 20362541, Free PMC Article
    3. Lysosomal Signaling Licenses Embryonic Stem Cell Differentiation via Inactivation of Tfe3. Villegas F, et al. Cell Stem Cell, 2019 Feb 7. PMID 30595499
    4. Genome-wide expression profiling of mid-gestation placenta and embryo using a 15,000 mouse developmental cDNA microarray. Tanaka TS, et al. Proc Natl Acad Sci U S A, 2000 Aug 1. PMID 10922068, Free PMC Article
    5. Large-scale gene trapping in C57BL/6N mouse embryonic stem cells. Hansen GM, et al. Genome Res, 2008 Oct. PMID 18799693, Free PMC Article

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Clone Names

    • MGC117755

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    vertnin
    Names
    vertebrae development homolog (pig)

    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_001033776.2 → NP_001028948.1  vertnin

      See identical proteins and their annotated locations for NP_001028948.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.
      Source sequence(s)
      AC159641
      Consensus CDS
      CCDS26048.1
      UniProtKB/Swiss-Prot
      Q3SYK4
      Related
      ENSMUSP00000093207.5, ENSMUST00000095551.5
      Conserved Domains (1) summary
      cl21459
      Location:274 → 305
      HTH; Helix-turn-helix domains

    2. NM_001168588.1 → NP_001162060.1  vertnin

      See identical proteins and their annotated locations for NP_001162060.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2 and 3 encode the same protein.
      Source sequence(s)
      AC159641
      Consensus CDS
      CCDS26048.1
      UniProtKB/Swiss-Prot
      Q3SYK4
      Related
      ENSMUSP00000132050.2, ENSMUST00000167227.8
      Conserved Domains (1) summary
      cl21459
      Location:274 → 305
      HTH; Helix-turn-helix domains

    3. NM_001168589.2 → NP_001162061.1  vertnin

      See identical proteins and their annotated locations for NP_001162061.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.
      Source sequence(s)
      AC159641
      Consensus CDS
      CCDS26048.1
      UniProtKB/Swiss-Prot
      Q3SYK4
      Related
      ENSMUSP00000128808.3, ENSMUST00000166772.9
      Conserved Domains (1) summary
      cl21459
      Location:274 → 305
      HTH; Helix-turn-helix domains

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000078.7 Reference GRCm39 C57BL/6J

      Range
      84687793..84698229
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q3SYK4.1 GenPept UniProtKB/Swiss-Prot:Q3SYK4

    Gene LinkOut

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

    Chemical Information
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