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COL25A1 (collagen type XXV alpha 1 chain)

Identity

Alias_namescollagen
Other aliasAMY
CFEOM5
CLAC
CLAC-P
CLACP
HGNC (Hugo) COL25A1
LocusID (NCBI) 84570
Atlas_Id 40124
Location 4q25  [Link to chromosome band 4q25]
Location_base_pair Starts at 108823883 and ends at 109302367 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
COL25A1 (4q25) / CCDC109B (4q25)PPP3CA (4q24) / COL25A1 (4q25)COL25A1 4q25 / CCDC109B 4q25
PPP3CA 4q24 / COL25A1 4q25

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


External links

Nomenclature
HGNC (Hugo)COL25A1   18603
Cards
Entrez_Gene (NCBI)COL25A1  84570  collagen type XXV alpha 1 chain
AliasesAMY; CFEOM5; CLAC; CLAC-P; 
CLACP
GeneCards (Weizmann)COL25A1
Ensembl hg19 (Hinxton)ENSG00000188517 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000188517 [Gene_View]  chr4:108823883-109302367 [Contig_View]  COL25A1 [Vega]
ICGC DataPortalENSG00000188517
TCGA cBioPortalCOL25A1
AceView (NCBI)COL25A1
Genatlas (Paris)COL25A1
WikiGenes84570
SOURCE (Princeton)COL25A1
Genetics Home Reference (NIH)COL25A1
Genomic and cartography
GoldenPath hg38 (UCSC)COL25A1  -     chr4:108823883-109302367 -  4q25   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)COL25A1  -     4q25   [Description]    (hg19-Feb_2009)
EnsemblCOL25A1 - 4q25 [CytoView hg19]  COL25A1 - 4q25 [CytoView hg38]
Mapping of homologs : NCBICOL25A1 [Mapview hg19]  COL25A1 [Mapview hg38]
OMIM610004   616219   
Gene and transcription
Genbank (Entrez)AF293340 AF293341 AK095098 BC030649 BC036669
RefSeq transcript (Entrez)NM_001256074 NM_032518 NM_198721
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)COL25A1
Cluster EST : UnigeneHs.658842 [ NCBI ]
CGAP (NCI)Hs.658842
Alternative Splicing GalleryENSG00000188517
Gene ExpressionCOL25A1 [ NCBI-GEO ]   COL25A1 [ EBI - ARRAY_EXPRESS ]   COL25A1 [ SEEK ]   COL25A1 [ MEM ]
Gene Expression Viewer (FireBrowse)COL25A1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)84570
GTEX Portal (Tissue expression)COL25A1
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9BXS0   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9BXS0  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9BXS0
Splice isoforms : SwissVarQ9BXS0
PhosPhoSitePlusQ9BXS0
Domains : Interpro (EBI)CLAC-P    Collagen   
Domain families : Pfam (Sanger)Collagen (PF01391)   
Domain families : Pfam (NCBI)pfam01391   
Conserved Domain (NCBI)COL25A1
DMDM Disease mutations84570
Blocks (Seattle)COL25A1
SuperfamilyQ9BXS0
Human Protein AtlasENSG00000188517
Peptide AtlasQ9BXS0
HPRD09886
IPIIPI00186946   IPI00942774   IPI00743622   IPI00953070   IPI01010812   IPI00852938   IPI00968157   IPI00966207   
Protein Interaction databases
DIP (DOE-UCLA)Q9BXS0
IntAct (EBI)Q9BXS0
FunCoupENSG00000188517
BioGRIDCOL25A1
STRING (EMBL)COL25A1
ZODIACCOL25A1
Ontologies - Pathways
QuickGOQ9BXS0
Ontology : AmiGObeta-amyloid binding  extracellular region  extracellular region  collagen trimer  extracellular space  endoplasmic reticulum lumen  plasma membrane  integral component of plasma membrane  heparin binding  integral component of membrane  collagen catabolic process  axonogenesis involved in innervation  
Ontology : EGO-EBIbeta-amyloid binding  extracellular region  extracellular region  collagen trimer  extracellular space  endoplasmic reticulum lumen  plasma membrane  integral component of plasma membrane  heparin binding  integral component of membrane  collagen catabolic process  axonogenesis involved in innervation  
NDEx NetworkCOL25A1
Atlas of Cancer Signalling NetworkCOL25A1
Wikipedia pathwaysCOL25A1
Orthology - Evolution
OrthoDB84570
GeneTree (enSembl)ENSG00000188517
Phylogenetic Trees/Animal Genes : TreeFamCOL25A1
HOVERGENQ9BXS0
HOGENOMQ9BXS0
Homologs : HomoloGeneCOL25A1
Homology/Alignments : Family Browser (UCSC)COL25A1
Gene fusions - Rearrangements
Fusion: TCGACOL25A1 4q25 CCDC109B 4q25 BRCA
Fusion: TCGAPPP3CA 4q24 COL25A1 4q25 BRCA
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerCOL25A1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)COL25A1
dbVarCOL25A1
ClinVarCOL25A1
1000_GenomesCOL25A1 
Exome Variant ServerCOL25A1
ExAC (Exome Aggregation Consortium)COL25A1 (select the gene name)
Genetic variants : HAPMAP84570
Genomic Variants (DGV)COL25A1 [DGVbeta]
DECIPHERCOL25A1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisCOL25A1 
Mutations
ICGC Data PortalCOL25A1 
TCGA Data PortalCOL25A1 
Broad Tumor PortalCOL25A1
OASIS PortalCOL25A1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICCOL25A1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDCOL25A1
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch COL25A1
DgiDB (Drug Gene Interaction Database)COL25A1
DoCM (Curated mutations)COL25A1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)COL25A1 (select a term)
intoGenCOL25A1
Cancer3DCOL25A1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM610004    616219   
Orphanet1039    12141   
MedgenCOL25A1
Genetic Testing Registry COL25A1
NextProtQ9BXS0 [Medical]
TSGene84570
GENETestsCOL25A1
Target ValidationCOL25A1
Huge Navigator COL25A1 [HugePedia]
snp3D : Map Gene to Disease84570
BioCentury BCIQCOL25A1
ClinGenCOL25A1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD84570
Chemical/Pharm GKB GenePA134912284
Clinical trialCOL25A1
Miscellaneous
canSAR (ICR)COL25A1 (select the gene name)
Probes
Litterature
PubMed20 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineCOL25A1
EVEXCOL25A1
GoPubMedCOL25A1
iHOPCOL25A1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Wed Jun 7 12:29:07 CEST 2017

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