Free for academic non-profit institutions. Other users need a Commercial license

Aliases for COL23A1 Gene

Aliases for COL23A1 Gene

  • Collagen Type XXIII Alpha 1 Chain 2 3 5
  • Collagen, Type XXIII, Alpha 1 2

External Ids for COL23A1 Gene

Previous GeneCards Identifiers for COL23A1 Gene

  • GC05M177733
  • GC05M177778
  • GC05M177597
  • GC05M177664
  • GC05M172390

Summaries for COL23A1 Gene

Entrez Gene Summary for COL23A1 Gene

  • 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]

GeneCards Summary for COL23A1 Gene

COL23A1 (Collagen Type XXIII Alpha 1 Chain) is a Protein Coding gene. Diseases associated with COL23A1 include Ichthyosis, Congenital, Autosomal Recessive 11 and Autosomal Recessive Congenital Ichthyosis. Among its related pathways are Phospholipase-C Pathway and Degradation of the extracellular matrix. An important paralog of this gene is COL22A1.

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for COL23A1 Gene

Genomics for COL23A1 Gene

Regulatory Elements for COL23A1 Gene

Enhancers for COL23A1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH05G178483 1.2 FANTOM5 Ensembl ENCODE 16.2 +106.7 106702 1.1 L3MBTL2 BHLHE40 MAX MYC MGA YY1 COL23A1 CLK4 PHYKPL LOC105377756 PIR48624
GH05G178476 1.2 FANTOM5 Ensembl ENCODE 16.2 +112.9 112868 1.8 BCOR NFIB MAFG ZMYM3 NFIC PBX2 FOXJ2 NFE2 KDM1A EMSY COL23A1 PIR32964 LOC105377756
GH05G178624 1.4 FANTOM5 ENCODE 11.6 -35.5 -35477 3.8 HDGF CREB3L1 AGO1 WRNIP1 ARID4B SIN3A FEZF1 ZNF2 YY1 ZNF766 ZNF354B CLK4 ZNF354C COL23A1 HNRNPAB GRM6 PHYKPL RN7SKP70
GH05G178392 0.8 Ensembl ENCODE 18.4 +197.4 197449 1.0 ZNF34 MAX ZNF781 MYC COL23A1 ENSG00000254035 ZFP2 ENSG00000272431 ENSG00000253698 ZNF454 CLK4 PIR33393 RN7SL646P
GH05G178449 1.3 Ensembl dbSUPER 10.6 +140.7 140748 1.6 PKNOX1 ATF1 ARNT E2F7 TCF12 ZNF766 CBX5 ELK1 GATA2 CAVIN1 COL23A1 CLK4 ENSG00000245688 PIR32964
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around COL23A1 on UCSC Golden Path with GeneCards custom track

Promoters for COL23A1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000191480 155 801 HDAC1 CTCF MXI1 KLF1 ARNT SAP30 SIN3A RBBP5 RAD21 ZFHX2

Genomic Location for COL23A1 Gene

Chromosome:
5
Start:
178,237,616 bp from pter
End:
178,590,555 bp from pter
Size:
352,940 bases
Orientation:
Minus strand

Genomic View for COL23A1 Gene

Genes around COL23A1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
COL23A1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for COL23A1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COL23A1 Gene

Proteins for COL23A1 Gene

  • Protein details for COL23A1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q86Y22-CONA1_HUMAN
    Recommended name:
    Collagen alpha-1(XXIII) chain
    Protein Accession:
    Q86Y22
    Secondary Accessions:
    • Q8IVR4
    • Q9NT93

    Protein attributes for COL23A1 Gene

    Size:
    540 amino acids
    Molecular mass:
    51944 Da
    Quaternary structure:
    • Homotrimer.

    Alternative splice isoforms for COL23A1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for COL23A1 Gene

Post-translational modifications for COL23A1 Gene

  • Undergoes proteolytic cleavage by furin protease to yield a 60 kDa soluble form that forms a homotrimer and exhibits a low affinity interaction with heparin.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for COL23A1 Gene

Domains & Families for COL23A1 Gene

Gene Families for COL23A1 Gene

Protein Domains for COL23A1 Gene

Suggested Antigen Peptide Sequences for COL23A1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with COL23A1: view

No data available for UniProtKB/Swiss-Prot for COL23A1 Gene

Function for COL23A1 Gene

Gene Ontology (GO) - Molecular Function for COL23A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with COL23A1: view
genes like me logo Genes that share phenotypes with COL23A1: view

Animal Model Products

  • Taconic Biosciences Mouse Models for COL23A1

CRISPR Products

Inhibitory RNA Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for COL23A1 Gene

Localization for COL23A1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COL23A1 Gene

Cell membrane; Single-pass type II membrane protein; Extracellular side.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for COL23A1 gene
Compartment Confidence
plasma membrane 5
endoplasmic reticulum 4
extracellular 2
mitochondrion 1
nucleus 1
cytosol 1

Gene Ontology (GO) - Cellular Components for COL23A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005581 collagen trimer IEA --
GO:0005788 endoplasmic reticulum lumen TAS --
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with COL23A1: view

Pathways & Interactions for COL23A1 Gene

genes like me logo Genes that share pathways with COL23A1: view

Gene Ontology (GO) - Biological Process for COL23A1 Gene

None

No data available for SIGNOR curated interactions for COL23A1 Gene

Drugs & Compounds for COL23A1 Gene

No Compound Related Data Available

Transcripts for COL23A1 Gene

mRNA/cDNA for COL23A1 Gene

(11) REFSEQ mRNAs :
(3) Additional mRNA sequences :
(2) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for COL23A1 Gene

Collagen, type XXIII, alpha 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for COL23A1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21
SP1:
SP2: -
SP3:
SP4:
SP5: -

Relevant External Links for COL23A1 Gene

GeneLoc Exon Structure for
COL23A1
ECgene alternative splicing isoforms for
COL23A1

Expression for COL23A1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for COL23A1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for COL23A1 Gene

This gene is overexpressed in Thyroid (x15.4) and Heart - Left Ventricle (x5.4).

Protein differential expression in normal tissues from HIPED for COL23A1 Gene

This gene is overexpressed in Adipocyte (28.4), Pancreatic juice (17.6), Peripheral blood mononuclear cells (15.0), and Heart (8.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for COL23A1 Gene



Protein tissue co-expression partners for COL23A1 Gene

NURSA nuclear receptor signaling pathways regulating expression of COL23A1 Gene:

COL23A1

SOURCE GeneReport for Unigene cluster for COL23A1 Gene:

Hs.660026

Evidence on tissue expression from TISSUES for COL23A1 Gene

  • Nervous system(4.1)
genes like me logo Genes that share expression patterns with COL23A1: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for COL23A1 Gene

Orthologs for COL23A1 Gene

This gene was present in the common ancestor of animals.

Orthologs for COL23A1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia COL23A1 34 35
  • 95.19 (n)
dog
(Canis familiaris)
Mammalia COL23A1 34 35
  • 88.21 (n)
cow
(Bos Taurus)
Mammalia COL23A1 34 35
  • 87.04 (n)
mouse
(Mus musculus)
Mammalia Col23a1 34 16 35
  • 86.34 (n)
rat
(Rattus norvegicus)
Mammalia Col23a1 34
  • 85.75 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia COL23A1 35
  • 84 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia COL23A1 35
  • 82 (a)
OneToOne
chicken
(Gallus gallus)
Aves COL23A1 34 35
  • 68.82 (n)
lizard
(Anolis carolinensis)
Reptilia COL23A1 35
  • 51 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii LOC101886266 34
  • 61.51 (n)
si:dkey-117n7.4 35
  • 27 (a)
ManyToMany
zgc:113232 35
  • 25 (a)
ManyToMany
si:ch211-106n13.3 35
  • 11 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea col-135 35
  • 27 (a)
OneToMany
Species where no ortholog for COL23A1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for COL23A1 Gene

ENSEMBL:
Gene Tree for COL23A1 (if available)
TreeFam:
Gene Tree for COL23A1 (if available)

Paralogs for COL23A1 Gene

(3) SIMAP similar genes for COL23A1 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with COL23A1: view

Variants for COL23A1 Gene

Sequence variations from dbSNP and Humsavar for COL23A1 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
rs1000006999 -- 178,366,215(+) TGCAA(C/T)TCTGC intron-variant, nc-transcript-variant
rs1000010297 -- 178,455,080(+) GGATT(A/C)AGGAC intron-variant
rs1000022030 -- 178,561,888(+) GGACC(A/G)GGAGA intron-variant
rs1000031708 -- 178,328,348(+) TCCAA(C/G)GGGCC intron-variant
rs1000041509 -- 178,355,224(+) TGCAG(C/T)GAGCT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for COL23A1 Gene

Variant ID Type Subtype PubMed ID
dgv10190n54 CNV loss 21841781
dgv10191n54 CNV loss 21841781
dgv10192n54 CNV loss 21841781
dgv10193n54 CNV loss 21841781
dgv10194n54 CNV loss 21841781
dgv1061e199 CNV deletion 23128226
dgv155e180 CNV deletion 20482838
dgv1680e212 CNV loss 25503493
dgv220n6 CNV deletion 16902084
dgv3235n106 CNV tandem duplication 24896259
dgv3236n106 CNV deletion 24896259
dgv3237n106 CNV deletion 24896259
dgv965e201 CNV deletion 23290073
dgv966e201 CNV deletion 23290073
dgv967e201 CNV deletion 23290073
dgv968e201 CNV deletion 23290073
dgv969e201 CNV deletion 23290073
dgv970e201 CNV deletion 23290073
esv1002980 CNV deletion 20482838
esv1008487 CNV deletion 20482838
esv1225849 CNV insertion 17803354
esv1755731 CNV deletion 17803354
esv1763768 CNV insertion 17803354
esv1948375 CNV deletion 18987734
esv2246259 CNV deletion 18987734
esv22470 CNV gain 19812545
esv22927 CNV gain+loss 19812545
esv2321766 CNV deletion 18987734
esv2333420 CNV deletion 18987734
esv2429795 CNV deletion 19546169
esv24398 CNV loss 19812545
esv2565934 CNV insertion 19546169
esv2605116 CNV deletion 19546169
esv2636926 CNV deletion 19546169
esv2658022 CNV deletion 23128226
esv2663093 CNV deletion 23128226
esv2731218 CNV deletion 23290073
esv2731219 CNV deletion 23290073
esv2731220 CNV deletion 23290073
esv2731221 CNV deletion 23290073
esv2731222 CNV deletion 23290073
esv2731223 CNV deletion 23290073
esv2731224 CNV deletion 23290073
esv2731225 CNV deletion 23290073
esv2731226 CNV deletion 23290073
esv2731227 CNV deletion 23290073
esv2731234 CNV deletion 23290073
esv2731240 CNV deletion 23290073
esv2731241 CNV deletion 23290073
esv2731242 CNV deletion 23290073
esv2731243 CNV deletion 23290073
esv2731244 CNV deletion 23290073
esv2731245 CNV deletion 23290073
esv2731246 CNV deletion 23290073
esv2731247 CNV deletion 23290073
esv2731248 CNV deletion 23290073
esv2731249 CNV deletion 23290073
esv2731260 CNV deletion 23290073
esv2731261 CNV deletion 23290073
esv2860680 CNV duplication 24192839
esv3220 CNV loss 18987735
esv3289384 CNV deletion 24192839
esv3289495 CNV deletion 24192839
esv3335979 CNV duplication 20981092
esv3348197 CNV duplication 20981092
esv3378133 CNV duplication 20981092
esv3409758 CNV insertion 20981092
esv3445094 CNV duplication 20981092
esv3567078 CNV deletion 23714750
esv3567083 CNV deletion 23714750
esv3607711 CNV loss 21293372
esv3607712 CNV loss 21293372
esv3607713 CNV loss 21293372
esv3607714 CNV gain 21293372
esv3607715 CNV loss 21293372
esv3607716 CNV loss 21293372
esv3607717 CNV loss 21293372
esv4301 CNV loss 18987735
esv4689 CNV loss 18987735
esv5342 CNV loss 18987735
esv6640 CNV loss 19470904
esv988470 CNV insertion 20482838
esv989570 OTHER inversion 20482838
nsv1019404 CNV gain 25217958
nsv1029822 CNV gain 25217958
nsv1073519 CNV deletion 25765185
nsv1073520 CNV deletion 25765185
nsv1074355 CNV deletion 25765185
nsv1074356 CNV deletion 25765185
nsv1078247 CNV insertion 25765185
nsv1111307 CNV tandem duplication 24896259
nsv1111308 CNV tandem duplication 24896259
nsv1111309 CNV tandem duplication 24896259
nsv1114763 CNV deletion 24896259
nsv1117427 CNV tandem duplication 24896259
nsv1120062 OTHER inversion 24896259
nsv1132944 CNV insertion 24896259
nsv1141818 CNV insertion 24896259
nsv1142006 OTHER inversion 24896259
nsv1144127 CNV deletion 24896259
nsv1144128 CNV deletion 24896259
nsv1148397 CNV deletion 26484159
nsv1149950 CNV deletion 26484159
nsv1153874 CNV deletion 26484159
nsv280 CNV insertion 15895083
nsv327226 CNV deletion 16902084
nsv327363 CNV deletion 16902084
nsv327487 CNV deletion 16902084
nsv328155 CNV deletion 16902084
nsv329434 CNV deletion 16902084
nsv436480 CNV deletion 17901297
nsv441978 CNV loss 18776908
nsv462568 CNV loss 19166990
nsv462569 CNV loss 19166990
nsv462570 CNV gain 19166990
nsv462571 CNV loss 19166990
nsv471059 CNV loss 18288195
nsv509106 CNV insertion 20534489
nsv509107 CNV insertion 20534489
nsv513279 CNV loss 21212237
nsv513280 CNV loss 21212237
nsv5153 CNV insertion 18451855
nsv517167 CNV loss 19592680
nsv522162 CNV loss 19592680
nsv526499 CNV loss 19592680
nsv527792 CNV loss 19592680
nsv527857 CNV loss 19592680
nsv600397 CNV loss 21841781
nsv600398 CNV loss 21841781
nsv600399 CNV loss 21841781
nsv600400 CNV loss 21841781
nsv600416 CNV loss 21841781
nsv600423 CNV gain 21841781
nsv600424 CNV loss 21841781
nsv600425 CNV loss 21841781
nsv600426 CNV loss 21841781
nsv600427 CNV loss 21841781
nsv820848 CNV deletion 20802225
nsv950732 CNV deletion 24416366
nsv950733 CNV deletion 24416366

Variation tolerance for COL23A1 Gene

Residual Variation Intolerance Score: 77.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.09; 80.45% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for COL23A1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
COL23A1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COL23A1 Gene

Disorders for COL23A1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for COL23A1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
ichthyosis, congenital, autosomal recessive 11
  • autosomal recessive congenital ichthyosis 11
autosomal recessive congenital ichthyosis
  • arci
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for COL23A1

Genetic Association Database (GAD)
COL23A1
Human Genome Epidemiology (HuGE) Navigator
COL23A1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
COL23A1
genes like me logo Genes that share disorders with COL23A1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for COL23A1 Gene

Publications for COL23A1 Gene

  1. Type XXIII collagen, a new transmembrane collagen identified in metastatic tumor cells. (PMID: 12644459) Banyard J. … Zetter B.R. (J. Biol. Chem. 2003) 2 3 4 64
  2. Assessment of a polymorphism of SDK1 with hypertension in Japanese Individuals. (PMID: 19851296) Oguri M. … Yamada Y. (Am. J. Hypertens. 2010) 3 46 64
  3. Association of genetic variants with hemorrhagic stroke in Japanese individuals. (PMID: 20198315) Yoshida T. … Yamada Y. (Int. J. Mol. Med. 2010) 3 46 64
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  5. Association of gene polymorphisms with chronic kidney disease in Japanese individuals. (PMID: 19724895) Yoshida T. … Yamada Y. (Int. J. Mol. Med. 2009) 3 46 64

Products for COL23A1 Gene

Sources for COL23A1 Gene

Content
Loading form....