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COL21A1 (collagen type XXI alpha 1 chain)

Identity

Alias_namescollagen
Other aliasCOLA1L
FP633
HGNC (Hugo) COL21A1
LocusID (NCBI) 81578
Atlas_Id 55082
Location 6p12.1  [Link to chromosome band 6p12]
Location_base_pair Starts at 56056590 and ends at 56247580 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
BMP5 (6p12.1) / COL21A1 (6p12.1)COL21A1 (6p12.1) / EFCAB1 (8q11.21)COL21A1 (6p12.1) / TFEB (6p21.1)
BMP5 6p12.1 / COL21A1 6p12.1COL21A1 6p12.1 / EFCAB1 8q11.21

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

 


Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 3 ]
  BMP5/COL21A1 (6p12)
t(6;6)(p12;p21) COL21A1/TFEB
t(6;8)(p12;q11) COL21A1/EFCAB1


External links

Nomenclature
HGNC (Hugo)COL21A1   17025
Cards
Entrez_Gene (NCBI)COL21A1  81578  collagen type XXI alpha 1 chain
AliasesCOLA1L; FP633
GeneCards (Weizmann)COL21A1
Ensembl hg19 (Hinxton)ENSG00000124749 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000124749 [Gene_View]  ENSG00000124749 [Sequence]  chr6:56056590-56247580 [Contig_View]  COL21A1 [Vega]
ICGC DataPortalENSG00000124749
TCGA cBioPortalCOL21A1
AceView (NCBI)COL21A1
Genatlas (Paris)COL21A1
WikiGenes81578
SOURCE (Princeton)COL21A1
Genetics Home Reference (NIH)COL21A1
Genomic and cartography
GoldenPath hg38 (UCSC)COL21A1  -     chr6:56056590-56247580 -  6p12.1   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)COL21A1  -     6p12.1   [Description]    (hg19-Feb_2009)
EnsemblCOL21A1 - 6p12.1 [CytoView hg19]  COL21A1 - 6p12.1 [CytoView hg38]
Mapping of homologs : NCBICOL21A1 [Mapview hg19]  COL21A1 [Mapview hg38]
OMIM610002   
Gene and transcription
Genbank (Entrez)AF330693 AF370383 AF414088 AK096444 AK126586
RefSeq transcript (Entrez)NM_001318751 NM_001318752 NM_001318753 NM_001318754 NM_030820
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)COL21A1
Cluster EST : UnigeneHs.47629 [ NCBI ]
CGAP (NCI)Hs.47629
Alternative Splicing GalleryENSG00000124749
Gene ExpressionCOL21A1 [ NCBI-GEO ]   COL21A1 [ EBI - ARRAY_EXPRESS ]   COL21A1 [ SEEK ]   COL21A1 [ MEM ]
Gene Expression Viewer (FireBrowse)COL21A1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)81578
GTEX Portal (Tissue expression)COL21A1
Human Protein AtlasENSG00000124749-COL21A1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ96P44   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ96P44  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ96P44
Splice isoforms : SwissVarQ96P44
PhosPhoSitePlusQ96P44
Domaine pattern : Prosite (Expaxy)VWFA (PS50234)   
Domains : Interpro (EBI)Collagen    ConA-like_dom_sf    Laminin_G    VWF_A    vWFA_dom_sf   
Domain families : Pfam (Sanger)Collagen (PF01391)    VWA (PF00092)   
Domain families : Pfam (NCBI)pfam01391    pfam00092   
Domain families : Smart (EMBL)TSPN (SM00210)  VWA (SM00327)  
Conserved Domain (NCBI)COL21A1
DMDM Disease mutations81578
Blocks (Seattle)COL21A1
SuperfamilyQ96P44
Human Protein Atlas [tissue]ENSG00000124749-COL21A1 [tissue]
Peptide AtlasQ96P44
HPRD09884
IPIIPI00102435   IPI00435960   IPI00644733   IPI00852868   IPI00852849   IPI00977174   
Protein Interaction databases
DIP (DOE-UCLA)Q96P44
IntAct (EBI)Q96P44
FunCoupENSG00000124749
BioGRIDCOL21A1
STRING (EMBL)COL21A1
ZODIACCOL21A1
Ontologies - Pathways
QuickGOQ96P44
Ontology : AmiGOgrowth plate cartilage chondrocyte morphogenesis  extracellular region  collagen trimer  extracellular space  endoplasmic reticulum lumen  cytosol  extracellular matrix structural constituent conferring tensile strength  extracellular matrix  collagen-containing extracellular matrix  collagen-containing extracellular matrix  
Ontology : EGO-EBIgrowth plate cartilage chondrocyte morphogenesis  extracellular region  collagen trimer  extracellular space  endoplasmic reticulum lumen  cytosol  extracellular matrix structural constituent conferring tensile strength  extracellular matrix  collagen-containing extracellular matrix  collagen-containing extracellular matrix  
Pathways : KEGGProtein digestion and absorption    Proteoglycans in cancer   
NDEx NetworkCOL21A1
Atlas of Cancer Signalling NetworkCOL21A1
Wikipedia pathwaysCOL21A1
Orthology - Evolution
OrthoDB81578
GeneTree (enSembl)ENSG00000124749
Phylogenetic Trees/Animal Genes : TreeFamCOL21A1
HOVERGENQ96P44
HOGENOMQ96P44
Homologs : HomoloGeneCOL21A1
Homology/Alignments : Family Browser (UCSC)COL21A1
Gene fusions - Rearrangements
Fusion : MitelmanBMP5/COL21A1 [6p12.1/6p12.1]  [t(6;6)(p12;p12)]  
Fusion : MitelmanCOL21A1/EFCAB1 [6p12.1/8q11.21]  [t(6;8)(p12;q11)]  
Fusion PortalBMP5 6p12.1 COL21A1 6p12.1 LUAD
Fusion PortalCOL21A1 6p12.1 EFCAB1 8q11.21 HNSC
Fusion : QuiverCOL21A1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerCOL21A1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)COL21A1
dbVarCOL21A1
ClinVarCOL21A1
1000_GenomesCOL21A1 
Exome Variant ServerCOL21A1
ExAC (Exome Aggregation Consortium)ENSG00000124749
GNOMAD BrowserENSG00000124749
Varsome BrowserCOL21A1
Genetic variants : HAPMAP81578
Genomic Variants (DGV)COL21A1 [DGVbeta]
DECIPHERCOL21A1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisCOL21A1 
Mutations
ICGC Data PortalCOL21A1 
TCGA Data PortalCOL21A1 
Broad Tumor PortalCOL21A1
OASIS PortalCOL21A1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICCOL21A1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDCOL21A1
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 COL21A1
DgiDB (Drug Gene Interaction Database)COL21A1
DoCM (Curated mutations)COL21A1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)COL21A1 (select a term)
intoGenCOL21A1
Cancer3DCOL21A1(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM610002   
Orphanet
DisGeNETCOL21A1
MedgenCOL21A1
Genetic Testing Registry COL21A1
NextProtQ96P44 [Medical]
TSGene81578
GENETestsCOL21A1
Target ValidationCOL21A1
Huge Navigator COL21A1 [HugePedia]
snp3D : Map Gene to Disease81578
BioCentury BCIQCOL21A1
ClinGenCOL21A1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD81578
Chemical/Pharm GKB GenePA26714
Clinical trialCOL21A1
Miscellaneous
canSAR (ICR)COL21A1 (select the gene name)
Probes
Litterature
PubMed15 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineCOL21A1
EVEXCOL21A1
GoPubMedCOL21A1
iHOPCOL21A1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Tue Nov 6 10:59:25 CET 2018

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