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    Vstm5 V-set and transmembrane domain containing 5 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 500947, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Vstm5provided by RGD
    Official Full Name
    V-set and transmembrane domain containing 5provided by RGD
    Primary source
    RGD:1563328
    See related
    EnsemblRapid:ENSRNOG00000010480 AllianceGenome:RGD:1563328
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to be involved in several processes, including filopodium assembly; positive regulation of excitatory synapse assembly; and protein homooligomerization. Predicted to be located in membrane. Predicted to be active in axon; dendrite; and plasma membrane. Orthologous to human VSTM5 (V-set and transmembrane domain containing 5). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Kidney (RPKM 44.1), Brain (RPKM 34.9) and 3 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Vstm5 in Genome Data Viewer
    Location:
    8q12
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 8 NC_086026.1 (20361474..20381844)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 8 NC_051343.1 (12080019..12100443)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 8 NC_005107.4 (13796009..13816125)

    Chromosome 8 - NC_086026.1Genomic Context describing neighboring genes Neighboring gene U1 spliceosomal RNA Neighboring gene small nucleolar RNA SNORA55 Neighboring gene mediator complex subunit 17 Neighboring gene uncharacterized LOC102552229

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Putative Cell Adhesion Membrane Protein Vstm5 Regulates Neuronal Morphology and Migration in the Central Nervous System. Lee AR, et al. J Neurosci, 2016 Sep 28. PMID 27683913, Free PMC Article
    2. Expression of the immunoglobulin superfamily cell adhesion molecules in the developing spinal cord and dorsal root ganglion. Gu Z, et al. PLoS One, 2015. PMID 25826454, Free PMC Article
    3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Process Evidence Code Pubs
    involved_in filopodium assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in filopodium assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in filopodium assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of excitatory synapse assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of excitatory synapse assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of excitatory synapse assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein homooligomerization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein homooligomerization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in ventral spinal cord development ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in axon IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in axon ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in axon ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in dendrite IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in dendrite ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in dendrite ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    V-set and transmembrane domain-containing protein 5
    Names
    hypothetical gene supported by BC088439

    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_001144870.1 → NP_001138342.1  V-set and transmembrane domain-containing protein 5 precursor

      See identical proteins and their annotated locations for NP_001138342.1

      Status: VALIDATED

      Source sequence(s)
      BC088439, DY310175
      UniProtKB/Swiss-Prot
      Q5M7U7
      UniProtKB/TrEMBL
      A6JNB3
      Related
      ENSRNOP00000013927.5, ENSRNOT00000013927.8
      Conserved Domains (2) summary
      cl00817
      Location:11 → 72
      MM_CoA_mutase; Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM)-like family; contains proteins similar to MCM, and the large subunit of Streptomyces coenzyme B12-dependent isobutyryl-CoA mutase (ICM). MCM catalyzes the isomerization of ...
      cl11960
      Location:64 → 138
      Ig; Immunoglobulin domain

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086026.1 Reference GRCr8

      Range
      20361474..20381844
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039081905.2 → XP_038937833.1  V-set and transmembrane domain-containing protein 5 isoform X1

      Conserved Domains (3) summary
      cd00096
      Location:63 → 67
      Ig; Ig strand C [structural motif]
      cl00817
      Location:11 → 72
      MM_CoA_mutase; Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM)-like family; contains proteins similar to MCM, and the large subunit of Streptomyces coenzyme B12-dependent isobutyryl-CoA mutase (ICM). MCM catalyzes the isomerization of ...
      cl11960
      Location:62 → 137
      Ig; Immunoglobulin domain
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5M7U7.2 GenPept UniProtKB/Swiss-Prot:Q5M7U7

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
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