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    Vit vitrin [ Mus musculus (house mouse) ]

    Gene ID: 74199, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Vitprovided by MGI
    Official Full Name
    vitrinprovided by MGI
    Primary source
    MGI:MGI:1921449
    See related
    Ensembl:ENSMUSG00000024076 AllianceGenome:MGI:1921449
    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
    AKH; akhirin; 1700052E02Rik; 1700110E08Rik; 2810429K11Rik
    Summary
    Enables glycosaminoglycan binding activity. Involved in spinal cord development. Acts upstream of or within extracellular matrix organization and positive regulation of cell-substrate adhesion. Located in interstitial matrix. Is expressed in several structures, including cranium; ganglia; sensory organ; ventral grey horn; and ventricular layer. Orthologous to human VIT (vitrin). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in testis adult (RPKM 3.9), subcutaneous fat pad adult (RPKM 2.5) and 16 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Vit in Genome Data Viewer
    Location:
    17 49.38 cM; 17 E3
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 17 NC_000083.7 (78815480..78934838)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 17 NC_000083.6 (78508051..78627409)

    Chromosome 17 - NC_000083.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 53961 Neighboring gene histone deacetylase 1, pseudogene Neighboring gene predicted gene, 32573 Neighboring gene STARR-seq mESC enhancer starr_43270 Neighboring gene striatin, calmodulin binding protein Neighboring gene STARR-positive B cell enhancer ABC_E1201 Neighboring gene ubiquitin-conjugating enzyme E2C pseudogene

    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. Akhirin regulates the proliferation and differentiation of neural stem cells/progenitor cells at neurogenic niches in mouse brain. Anam MB, et al. Dev Growth Differ, 2020 Feb. PMID 31943155
    2. iSyTE: integrated Systems Tool for Eye gene discovery. Lachke SA, et al. Invest Ophthalmol Vis Sci, 2012 Mar. PMID 22323457, Free PMC Article
    3. Akhirin regulates the proliferation and differentiation of neural stem cells in intact and injured mouse spinal cord. Abdulhaleem FA, et al. Dev Neurobiol, 2015 May. PMID 25331329
    4. VIT-1: the second member of a new branch of the von Willebrand factor A domain superfamily. Mayne R, et al. Biochem Soc Trans, 1999 Dec. PMID 10830112
    5. The protomap is propagated to cortical plate neurons through an Eomes-dependent intermediate map. Elsen GE, et al. Proc Natl Acad Sci U S A, 2013 Mar 5. PMID 23431145, Free PMC Article

    See all (26) 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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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables glycosaminoglycan binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within extracellular matrix organization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of cell-substrate adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within positive regulation of cell-substrate adhesion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in spinal cord development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in extracellular matrix IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in interstitial matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in interstitial matrix IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    vitrin

    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_001197028.1 → NP_001183957.1  vitrin isoform 2

      See identical proteins and their annotated locations for NP_001183957.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame splice junction compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AI835120, AK051606, AK158117
      Consensus CDS
      CCDS89157.1
      UniProtKB/TrEMBL
      A0A3B2WCI9
      Related
      ENSMUSP00000156543.2, ENSMUST00000232859.2
      Conserved Domains (3) summary
      cd01472
      Location:444 → 604
      vWA_collagen; von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins. This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form ...
      pfam03815
      Location:22 → 111
      LCCL; LCCL domain
      cl00057
      Location:243 → 406
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

    2. NM_028813.2 → NP_083089.1  vitrin isoform 1 precursor

      See identical proteins and their annotated locations for NP_083089.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AI835120, AK158117, BC034120
      Consensus CDS
      CCDS37696.1
      UniProtKB/Swiss-Prot
      Q3TZ47, Q8BQ41, Q8K047, Q8VHI5, Q9CYZ1
      Related
      ENSMUSP00000024880.10, ENSMUST00000024880.11
      Conserved Domains (3) summary
      cd01472
      Location:466 → 626
      vWA_collagen; von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins. This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form ...
      pfam03815
      Location:44 → 133
      LCCL; LCCL domain
      cl00057
      Location:265 → 428
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

    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_000083.7 Reference GRCm39 C57BL/6J

      Range
      78815480..78934838
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006525028.4 → XP_006525091.1  vitrin isoform X1

      Conserved Domains (3) summary
      cd01472
      Location:465 → 625
      vWA_collagen; von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins. This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form ...
      pfam03815
      Location:44 → 133
      LCCL; LCCL domain
      cl00057
      Location:264 → 427
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

    2. XM_006525029.5 → XP_006525092.1  vitrin isoform X2

      Conserved Domains (3) summary
      cd01472
      Location:408 → 568
      vWA_collagen; von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins. This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form ...
      pfam03815
      Location:2 → 75
      LCCL; LCCL domain
      cl00057
      Location:207 → 370
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8VHI5.2 GenPept UniProtKB/Swiss-Prot:Q8VHI5

    Gene LinkOut

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

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