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    COL19A1 collagen type XIX alpha 1 chain [ Homo sapiens (human) ]

    Gene ID: 1310, updated on 27-Nov-2024

    Summary

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    Official Symbol
    COL19A1provided by HGNC
    Official Full Name
    collagen type XIX alpha 1 chainprovided by HGNC
    Primary source
    HGNC:HGNC:2196
    See related
    Ensembl:ENSG00000082293 MIM:120165; AllianceGenome:HGNC:2196
    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
    COL9A1L; D6S228E
    Summary
    This gene encodes the alpha chain of type XIX collagen, a member of the FACIT collagen family (fibril-associated collagens with interrupted helices). Although the function of this collagen is not known, other members of this collagen family are found in association with fibril-forming collagens such as type I and II, and serve to maintain the integrity of the extracellular matrix. The transcript produced from this gene has an unusually large 3' UTR which has not been completely sequenced. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in lymph node (RPKM 1.1), appendix (RPKM 0.8) and 14 other tissues See more
    Orthologs
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    Genomic context

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    See COL19A1 in Genome Data Viewer
    Location:
    6q13
    Exon count:
    53
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (69866556..70212468)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (71046687..71393027)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (70576448..70922171)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene MPRA-validated peak5886 silencer Neighboring gene LMBR1 domain containing 1 Neighboring gene uncharacterized LOC124901337 Neighboring gene nucleophosmin 1 pseudogene 37 Neighboring gene glyceraldehyde 3 phosphate dehydrogenase pseudogene 42 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:70505853-70506409 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:70506410-70506965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24728 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24729 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17315 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17316 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17314 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:70597939-70598122 Neighboring gene NANOG hESC enhancer GRCh37_chr6:70623798-70624319 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:70627263-70628462 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:70845103-70845604 Neighboring gene ribosomal protein L37 pseudogene 15 Neighboring gene MPRA-validated peak5887 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24730 Neighboring gene collagen type IX alpha 1 chain Neighboring gene uncharacterized LOC105377848 Neighboring gene Sharpr-MPRA regulatory region 4194

    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
    • 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. Type XIX collagen: A new partner in the interactions between tumor cells and their microenvironment. Oudart JB, et al. Matrix Biol, 2017 Jan. PMID 27491275
    2. Synteny between the loci for a novel FACIT-like collagen locus (D6S228E) and alpha 1 (IX) collagen (COL9A1) on 6q12-q14 in humans. Yoshioka H, et al. Genomics, 1992 Jul. PMID 1639419
    3. The mRNA for alpha 1(XIX) collagen chain, a new member of FACITs, contains a long unusual 3' untranslated region and displays many unique splicing variants. Inoguchi K, et al. J Biochem, 1995 Jan. PMID 7775380
    4. The triple-helical region of human type XIX collagen consists of multiple collagenous subdomains and exhibits limited sequence homology to alpha 1(XVI). Myers JC, et al. J Biol Chem, 1994 Jul 15. PMID 8034603
    5. Type XIX collagen purified from human umbilical cord is characterized by multiple sharp kinks delineating collagenous subdomains and by intermolecular aggregates via globular, disulfide-linked, and heparin-binding amino termini. Myers JC, et al. J Biol Chem, 2003 Aug 22. PMID 12788917

    See all (22) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Naturally occurring interruptions in nonfibrillar collagen play key roles in molecular flexibility, collagen degradation, and ligand binding. This study focused on a G5G type natural interruption sequence G-POALO-G from human type XIX collagen, a homotrimer collagen, as this sequence possesses distinct properties compared with those of a pathological similar Gly mutation sequence in collagen mimic peptides.
      Title: Unique Conformation in a Natural Interruption Sequence of Type XIX Collagen Revealed by Its High-Resolution Crystal Structure.
    2. Type XIX collagen is a new partner in the interactions between tumor cells and their microenvironment. (Review)
      Title: Type XIX collagen: A new partner in the interactions between tumor cells and their microenvironment.
    3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    4. The NC2 domain of collagen XIX and probably of other FACITs is responsible for chain selection and trimerization
      Title: Trimerization and triple helix stabilization of the collagen XIX NC2 domain.
    5. collagen IX has unique cell adhesion properties when compared with other collagens, and it provides a novel mechanism for cell adhesion to cartilaginous matrix
      Title: The fibril-associated collagen IX provides a novel mechanism for cell adhesion to cartilaginous matrix.
    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

    EBI GWAS Catalog

    Description
    Genome-wide association of lipid-lowering response to statins in combined study populations.
    EBI GWAS Catalog
    Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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 extracellular matrix structural constituent NAS
    Non-traceable Author Statement
    more info
    		 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 protein-macromolecule adaptor activity NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell adhesion NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cell-cell adhesion NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in extracellular matrix organization NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in skeletal muscle tissue development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in skeletal system development TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of collagen 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 matrix NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    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-1(XIX) chain
    Names
    a1 chain of type XIX collagen
    collagen XIX, alpha-1 polypeptide
    collagen alpha 1 (Y) chain
    collagen, type XIX, alpha 1

    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_001858.6 → NP_001849.2  collagen alpha-1(XIX) chain precursor

      See identical proteins and their annotated locations for NP_001849.2

      Status: REVIEWED

      Source sequence(s)
      AL160262, BC113364, D38163, KF510956
      Consensus CDS
      CCDS4970.1
      UniProtKB/Swiss-Prot
      Q00559, Q05850, Q12885, Q13676, Q14993, Q14DH1, Q5JUF0, Q5T424, Q9H572, Q9NPZ2, Q9NQP2
      Related
      ENSP00000480474.1, ENST00000620364.5
      Conserved Domains (2) summary
      pfam01391
      Location:597 → 659
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:50 → 233
      TSPN; Thrombospondin N-terminal -like domains

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      69866556..70212468
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047418188.1 → XP_047274144.1  collagen alpha-1(XIX) chain isoform X6

    2. XM_011535437.3 → XP_011533739.1  collagen alpha-1(XIX) chain isoform X1

      Conserved Domains (3) summary
      pfam01391
      Location:622 → 684
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:75 → 258
      TSPN; Thrombospondin N-terminal -like domains
      pfam03157
      Location:299 → 691
      Glutenin_hmw; High molecular weight glutenin subunit

    3. XM_017010253.2 → XP_016865742.1  collagen alpha-1(XIX) chain isoform X2

    4. XM_017010254.2 → XP_016865743.1  collagen alpha-1(XIX) chain isoform X3

    5. XM_017010257.2 → XP_016865746.1  collagen alpha-1(XIX) chain isoform X4

    6. XM_047418187.1 → XP_047274143.1  collagen alpha-1(XIX) chain isoform X5

    7. XM_017010259.2 → XP_016865748.1  collagen alpha-1(XIX) chain isoform X7

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      71046687..71393027
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054354243.1 → XP_054210218.1  collagen alpha-1(XIX) chain isoform X6

    2. XM_054354238.1 → XP_054210213.1  collagen alpha-1(XIX) chain isoform X1

    3. XM_054354239.1 → XP_054210214.1  collagen alpha-1(XIX) chain isoform X2

    4. XM_054354240.1 → XP_054210215.1  collagen alpha-1(XIX) chain isoform X3

    5. XM_054354241.1 → XP_054210216.1  collagen alpha-1(XIX) chain isoform X4

    6. XM_054354242.1 → XP_054210217.1  collagen alpha-1(XIX) chain isoform X5

    7. XM_054354244.1 → XP_054210219.1  collagen alpha-1(XIX) chain isoform X7

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q14993.3 GenPept UniProtKB/Swiss-Prot:Q14993

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