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    COL23A1 collagen type XXIII alpha 1 chain [ Homo sapiens (human) ]

    Gene ID: 91522, updated on 2-Nov-2024

    Summary

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    Official Symbol
    COL23A1provided by HGNC
    Official Full Name
    collagen type XXIII alpha 1 chainprovided by HGNC
    Primary source
    HGNC:HGNC:22990
    See related
    Ensembl:ENSG00000050767 MIM:610043; AllianceGenome:HGNC:22990
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    COL23A1 is a member of the transmembrane collagens, a subfamily of the nonfibrillar collagens that contain a single pass hydrophobic transmembrane domain (Banyard et al., 2003 [PubMed 12644459]).[supplied by OMIM, Mar 2008]
    Expression
    Biased expression in thyroid (RPKM 9.3), heart (RPKM 2.2) and 10 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See COL23A1 in Genome Data Viewer
    Location:
    5q35.3
    Exon count:
    32
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (178237618..178590393, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (178787901..179142365, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (177664619..178017394, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16714 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16715 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16716 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16717 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23742 Neighboring gene germ cell-less 2, spermatogenesis associated Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:177659427-177659965 Neighboring gene uncharacterized LOC112267937 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23743 Neighboring gene heterogeneous nuclear ribonucleoprotein A/B Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:177664463-177665136 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:177665137-177665810 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23744 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23745 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177673006-177673555 Neighboring gene 5-phosphohydroxy-L-lysine phospho-lyase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16720 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:177683188-177683378 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177713093-177713638 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:177713639-177714182 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:177714183-177714727 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177733440-177733951 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177739610-177740112 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177758265-177758871 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177776902-177777442 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177777443-177777982 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:177777983-177778523 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:177778524-177779063 Neighboring gene uncharacterized LOC105377757 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177790336-177791328 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177793313-177794304 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:177794322-177794906 Neighboring gene mitochondrial ribosomal protein L50 pseudogene 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177800891-177801390 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:177807438-177808244 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177809466-177810284 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177810285-177811102 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177811103-177811920 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177811921-177812737 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177813862-177814680 Neighboring gene RNA, 7SL, cytoplasmic 646, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:177845119-177846008 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:177864141-177864644 Neighboring gene uncharacterized LOC124901148 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177890827-177891326 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177892321-177893201 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:177896312-177896463 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177929903-177930403 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177929402-177929902 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:177951804-177953003 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177953380-177954128 Neighboring gene Sharpr-MPRA regulatory region 11707 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:177981034-177981592 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177988600-177989128 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177989129-177989656 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177989809-177990318 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:178009527-178010026 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:178015840-178016740 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16721 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:178052997-178053677 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:178057087-178058286 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:178070356-178071555 Neighboring gene RN7SK pseudogene 70 Neighboring gene CDC like kinase 4 Neighboring gene vomeronasal 2 receptor 2 pseudogene

    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. Collagen XXIII: a potential biomarker for the detection of primary and recurrent non-small cell lung cancer. Spivey KA, et al. Cancer Epidemiol Biomarkers Prev, 2010 May. PMID 20447926, Free PMC Article
    2. Shedding of collagen XXIII is mediated by furin and depends on the plasma membrane microenvironment. Veit G, et al. J Biol Chem, 2007 Sep 14. PMID 17627939
    3. Type XXIII collagen, a new transmembrane collagen identified in metastatic tumor cells. Banyard J, et al. J Biol Chem, 2003 Jun 6. PMID 12644459
    4. Collagen XXIII, novel ligand for integrin alpha2beta1 in the epidermis. Veit G, et al. J Biol Chem, 2011 Aug 5. PMID 21652699, Free PMC Article
    5. Expression of type XXIII collagen mRNA and protein. Koch M, et al. J Biol Chem, 2006 Jul 28. PMID 16728390

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. data suggest that extracellular membrane-bound CAIV, but not cytosolic CAII, augments transport activity of MCT2 in a non-catalytic manner, possibly by facilitating a proton pathway other than His-88
      Title: Collagen XXIII, novel ligand for integrin alpha2beta1 in the epidermis.
    2. High COL23A1 expression is associated with recurrent non-small cell lung cancer.
      Title: Collagen XXIII: a potential biomarker for the detection of primary and recurrent non-small cell lung cancer.
    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. Observational study of gene-disease association. (HuGE Navigator)
      Title: Association of genetic variants with hemorrhagic stroke in Japanese individuals.
    5. newly synthesized collagen XXIII either is cleaved inside the Golgi/trans-Golgi network or reaches the cell surface, where it becomes protected from processing by being localized in lipid rafts.
      Title: Shedding of collagen XXIII is mediated by furin and depends on the plasma membrane microenvironment.
    6. analysis of collagen XXIII mRNA and protein
      Title: Expression of type XXIII collagen mRNA and protein.
    7. identification and cloning; a new member of the transmembrane collagen family, showing structural homology with the transmembrane collagens XIII and XXV
      Title: Type XXIII collagen, a new transmembrane collagen identified in metastatic tumor cells.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genetic variants associated with disordered eating.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    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)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • DKFZp434K0621

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables identical protein binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in basement membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cell surface IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of collagen trimer IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in collagen-containing extracellular matrix HDA PubMed 
    located_in endoplasmic reticulum lumen TAS
    Traceable Author Statement
    more info
    		  
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    collagen alpha-1(XXIII) chain
    Names
    collagen, type XXIII, alpha 1
    procollagen, type XXIII, alpha 1

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_173465.4 → NP_775736.2  collagen alpha-1(XXIII) chain

      See identical proteins and their annotated locations for NP_775736.2

      Status: VALIDATED

      Source sequence(s)
      AW014891, AY898961
      Consensus CDS
      CCDS4436.1
      UniProtKB/Swiss-Prot
      Q86Y22, Q8IVR4, Q9NT93
      Related
      ENSP00000375069.3, ENST00000390654.8
      Conserved Domains (1) summary
      pfam01391
      Location:466 → 520
      Collagen; Collagen triple helix repeat (20 copies)

    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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      178237618..178590393 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011534691.3 → XP_011532993.1  collagen alpha-1(XXIII) chain isoform X7

      Conserved Domains (1) summary
      pfam01391
      Location:427 → 484
      Collagen; Collagen triple helix repeat (20 copies)

    2. XM_011534690.3 → XP_011532992.1  collagen alpha-1(XXIII) chain isoform X5

      Conserved Domains (1) summary
      pfam01391
      Location:445 → 502
      Collagen; Collagen triple helix repeat (20 copies)

    3. XM_011534688.3 → XP_011532990.1  collagen alpha-1(XXIII) chain isoform X2

      Conserved Domains (1) summary
      pfam01391
      Location:454 → 511
      Collagen; Collagen triple helix repeat (20 copies)

    4. XM_006714934.4 → XP_006714997.1  collagen alpha-1(XXIII) chain isoform X3

      Conserved Domains (1) summary
      pfam01391
      Location:454 → 511
      Collagen; Collagen triple helix repeat (20 copies)

    5. XM_006714935.4 → XP_006714998.1  collagen alpha-1(XXIII) chain isoform X4

      Conserved Domains (1) summary
      pfam01391
      Location:451 → 508
      Collagen; Collagen triple helix repeat (20 copies)

    6. XM_047417869.1 → XP_047273825.1  collagen alpha-1(XXIII) chain isoform X8

    7. XM_006714936.4 → XP_006714999.1  collagen alpha-1(XXIII) chain isoform X6

      Conserved Domains (1) summary
      pfam01391
      Location:442 → 499
      Collagen; Collagen triple helix repeat (20 copies)

    8. XM_006714933.4 → XP_006714996.1  collagen alpha-1(XXIII) chain isoform X1

      Conserved Domains (1) summary
      pfam01391
      Location:463 → 520
      Collagen; Collagen triple helix repeat (20 copies)

    9. XM_011534692.3 → XP_011532994.1  collagen alpha-1(XXIII) chain isoform X9

      Conserved Domains (1) summary
      pfam01391
      Location:369 → 426
      Collagen; Collagen triple helix repeat (20 copies)

    10. XM_017010018.2 → XP_016865507.1  collagen alpha-1(XXIII) chain isoform X10

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      178787901..179142365 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054353777.1 → XP_054209752.1  collagen alpha-1(XXIII) chain isoform X7

    2. XM_054353775.1 → XP_054209750.1  collagen alpha-1(XXIII) chain isoform X5

    3. XM_054353772.1 → XP_054209747.1  collagen alpha-1(XXIII) chain isoform X2

    4. XM_054353773.1 → XP_054209748.1  collagen alpha-1(XXIII) chain isoform X3

    5. XM_054353774.1 → XP_054209749.1  collagen alpha-1(XXIII) chain isoform X4

    6. XM_054353778.1 → XP_054209753.1  collagen alpha-1(XXIII) chain isoform X8

    7. XM_054353776.1 → XP_054209751.1  collagen alpha-1(XXIII) chain isoform X6

    8. XM_054353771.1 → XP_054209746.1  collagen alpha-1(XXIII) chain isoform X1

    9. XM_054353779.1 → XP_054209754.1  collagen alpha-1(XXIII) chain isoform X9

    10. XM_054353780.1 → XP_054209755.1  collagen alpha-1(XXIII) chain isoform X10

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q86Y22.1 GenPept UniProtKB/Swiss-Prot:Q86Y22

    Gene LinkOut

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

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