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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
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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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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
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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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

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