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    COL5A3 collagen type V alpha 3 chain [ Homo sapiens (human) ]

    Gene ID: 50509, updated on 28-Oct-2024

    Summary

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    Official Symbol
    COL5A3provided by HGNC
    Official Full Name
    collagen type V alpha 3 chainprovided by HGNC
    Primary source
    HGNC:HGNC:14864
    See related
    Ensembl:ENSG00000080573 MIM:120216; AllianceGenome:HGNC:14864
    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
    Summary
    This gene encodes an alpha chain for one of the low abundance fibrillar collagens. Fibrillar collagen molecules are trimers that can be composed of one or more types of alpha chains. Type V collagen is found in tissues containing type I collagen and appears to regulate the assembly of heterotypic fibers composed of both type I and type V collagen. This gene product is closely related to type XI collagen and it is possible that the collagen chains of types V and XI constitute a single collagen type with tissue-specific chain combinations. Mutations in this gene are thought to be responsible for the symptoms of a subset of patients with Ehlers-Danlos syndrome type III. Messages of several sizes can be detected in northern blots but sequence information cannot confirm the identity of the shorter messages. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in placenta (RPKM 20.1), fat (RPKM 19.6) and 20 other tissues See more
    Orthologs
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    Genomic context

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    See COL5A3 in Genome Data Viewer
    Location:
    19p13.2
    Exon count:
    67
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (9959561..10010504, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (10085749..10136694, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (10070237..10121180, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10047 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10048 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:9958151-9958702 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:9958703-9959252 Neighboring gene peptidylprolyl cis/trans isomerase, NIMA-interacting 1 Neighboring gene olfactomedin 2 Neighboring gene uncharacterized LOC124904636 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10049 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10050 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:10046447-10047041 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:10047708-10048210 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr19:10062835-10063428 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:10063429-10064021 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:10109314-10109542 Neighboring gene Sharpr-MPRA regulatory region 3549 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:10112173-10112674 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:10112675-10113174 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_50731 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr19:10128438-10129637 Neighboring gene CRISPRi-validated cis-regulatory element chr19.1735 Neighboring gene retinol dehydrogenase 8 Neighboring gene microRNA 5589

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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

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    Related articles in PubMed

    1. Isolation and native characterization of cysteine-rich collagens from bovine placental tissues and uterus and their relationship to types IV and V collagens. Abedin MZ, et al. Biosci Rep, 1982 Jul. PMID 7115902
    2. Another look at collagen V and XI molecules. Fichard A, et al. Matrix Biol, 1995 Jul. PMID 8535602
    3. Basic fibroblast growth factor decreases type V/XI collagen expression in cultured bovine aortic smooth muscle cells. Kypreos KE, et al. J Cell Biochem, 1998 Feb 1. PMID 9443080
    4. Control of heterotypic fibril formation by collagen V is determined by chain stoichiometry. Chanut-Delalande H, et al. J Biol Chem, 2001 Jun 29. PMID 11423559
    5. The transcription factor CCAAT-binding factor CBF/NF-Y and two repressors regulate the core promoter of the human pro-alpha3(V) collagen gene (COL5A3). Nagato H, et al. J Biol Chem, 2004 Nov 5. PMID 15316020

    See all (26) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. This study identified significant interaction between two new genes, COL5A3 and MMP9, which may be accounted for by a degradation of COL5A3 by MMP9 influencing eczema susceptibility
      Title: The COL5A3 and MMP9 genes interact in eczema susceptibility.
    2. Absence of obvious disease-causing mutations and null alleles in a cohort of 13 patients with h-EDS is consistent with exclusion of COL5A3 as a candidate gene for this disease.
      Title: Absence of apparent disease causing mutations in COL5A3 in 13 patients with hypermobility Ehlers-Danlos syndrome.
    3. analysis of processing of the Pro-alpha1(V)Pro-alpha2(V)Pro-alpha3(V) procollagen heterotrimer
      Title: Biosynthetic processing of the Pro-alpha1(V)Pro-alpha2(V)Pro-alpha3(V) procollagen heterotrimer.
    4. CBF/NF-Y and two repressors regulate the core promoter of the human pro-alpha3(V) collagen gene
      Title: The transcription factor CCAAT-binding factor CBF/NF-Y and two repressors regulate the core promoter of the human pro-alpha3(V) collagen gene (COL5A3).
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    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 GOA

    Function Evidence Code Pubs
    enables collagen binding NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    enables extracellular matrix structural constituent NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    enables extracellular matrix structural constituent conferring tensile strength HDA PubMed 
    enables extracellular matrix structural constituent conferring tensile strength IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables extracellular matrix structural constituent conferring tensile strength RCA
    inferred from Reviewed Computational Analysis
    more info
    		 PubMed 
    enables heparin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables proteoglycan binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell-matrix adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in collagen fibril organization NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in skin development NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of collagen type V trimer NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in collagen-containing extracellular matrix HDA PubMed 
    is_active_in collagen-containing extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum lumen TAS
    Traceable Author Statement
    more info
    		  
    located_in extracellular region TAS
    Traceable Author Statement
    more info
    		  
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    collagen alpha-3(V) chain
    Names
    collagen, type V, alpha 3
    pro-(alpha)3(V) collagen

    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.

    Genomic

    1. NG_046943.1 RefSeqGene

      Range
      5035..55978
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_015719.4 → NP_056534.2  collagen alpha-3(V) chain preproprotein

      See identical proteins and their annotated locations for NP_056534.2

      Status: REVIEWED

      Source sequence(s)
      AC008742, AF177941, BQ006883
      Consensus CDS
      CCDS12222.1
      UniProtKB/Swiss-Prot
      P25940, Q9NZQ6
      UniProtKB/TrEMBL
      Q59GD4
      Related
      ENSP00000264828.3, ENST00000264828.4
      Conserved Domains (3) summary
      pfam01391
      Location:572 → 631
      Collagen; Collagen triple helix repeat (20 copies)
      pfam01410
      Location:1515 → 1743
      COLFI; Fibrillar collagen C-terminal domain
      cl22861
      Location:31 → 210
      LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      9959561..10010504 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011528042.3 → XP_011526344.1  collagen alpha-3(V) chain isoform X1

      UniProtKB/TrEMBL
      Q59GD4
      Conserved Domains (3) summary
      pfam01391
      Location:571 → 630
      Collagen; Collagen triple helix repeat (20 copies)
      pfam01410
      Location:1514 → 1742
      COLFI; Fibrillar collagen C-terminal domain
      cl22861
      Location:31 → 209
      LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

    2. XM_017026849.2 → XP_016882338.1  collagen alpha-3(V) chain isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      10085749..10136694 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054321132.1 → XP_054177107.1  collagen alpha-3(V) chain isoform X1

    2. XM_054321133.1 → XP_054177108.1  collagen alpha-3(V) chain isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P25940.3 GenPept UniProtKB/Swiss-Prot:P25940

    Gene LinkOut

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