Atlas of Genetics and Cytogenetics in Oncology and Haematology

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SMCO4 (single-pass membrane protein with coiled-coil domains 4)

Identity

Alias (NCBI)C11orf75
FN5
HGNC (Hugo) SMCO4
HGNC Alias symbFN5
HGNC Previous nameC11orf75
HGNC Previous namechromosome 11 open reading frame 75
LocusID (NCBI) 56935
Atlas_Id 73544
Location 11q21  [Link to chromosome band 11q21]
Location_base_pair Starts at 93478473 and ends at 93543380 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)
SETBP1 (18q12.3) / SMCO4 (11q21)SMCO4 (11q21) / BCL7B (7q11.23)SMCO4 (11q21) / CHODL (21q21.1)
SMCO4 (11q21) / FAM129B (9q33.3)SMCO4 (11q21) / FDFT1 (8p23.1)

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) [ 2 ]
  t(8;11)(p23;q21) SMCO4/FDFT1
t(9;11)(q34;q21) SMCO4/FAM129B

External links

Nomenclature
HGNC (Hugo)SMCO4   24810
Cards
Entrez_Gene (NCBI)SMCO4    single-pass membrane protein with coiled-coil domains 4
AliasesC11orf75; FN5
GeneCards (Weizmann)SMCO4
Ensembl hg19 (Hinxton)ENSG00000166002 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000166002 [Gene_View]  ENSG00000166002 [Sequence]  chr11:93478473-93543380 [Contig_View]  SMCO4 [Vega]
ICGC DataPortalENSG00000166002
TCGA cBioPortalSMCO4
AceView (NCBI)SMCO4
Genatlas (Paris)SMCO4
SOURCE (Princeton)SMCO4
Genetics Home Reference (NIH)SMCO4
Genomic and cartography
GoldenPath hg38 (UCSC)SMCO4  -     chr11:93478473-93543380 -  11q21   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SMCO4  -     11q21   [Description]    (hg19-Feb_2009)
GoldenPathSMCO4 - 11q21 [CytoView hg19]  SMCO4 - 11q21 [CytoView hg38]
ImmunoBaseENSG00000166002
genome Data Viewer NCBISMCO4 [Mapview hg19]  
OMIM609477   
Gene and transcription
Genbank (Entrez)AF197137 BC031564
RefSeq transcript (Entrez)NM_020179
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SMCO4
Alternative Splicing GalleryENSG00000166002
Gene ExpressionSMCO4 [ NCBI-GEO ]   SMCO4 [ EBI - ARRAY_EXPRESS ]   SMCO4 [ SEEK ]   SMCO4 [ MEM ]
Gene Expression Viewer (FireBrowse)SMCO4 [ Firebrowse - Broad ]
GenevisibleExpression of SMCO4 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)56935
GTEX Portal (Tissue expression)SMCO4
Human Protein AtlasENSG00000166002-SMCO4 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9NRQ5   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9NRQ5  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9NRQ5
Splice isoforms : SwissVarQ9NRQ5
PhosPhoSitePlusQ9NRQ5
Domains : Interpro (EBI)DUF4519   
Domain families : Pfam (Sanger)DUF4519 (PF15012)   
Domain families : Pfam (NCBI)pfam15012   
Conserved Domain (NCBI)SMCO4
Blocks (Seattle)SMCO4
SuperfamilyQ9NRQ5
Human Protein Atlas [tissue]ENSG00000166002-SMCO4 [tissue]
Peptide AtlasQ9NRQ5
HPRD17008
IPIIPI00024602   IPI00983515   IPI00982340   
Protein Interaction databases
DIP (DOE-UCLA)Q9NRQ5
IntAct (EBI)Q9NRQ5
BioGRIDSMCO4
STRING (EMBL)SMCO4
ZODIACSMCO4
Ontologies - Pathways
QuickGOQ9NRQ5
Ontology : AmiGOmolecular_function  protein binding  cellular_component  biological_process  integral component of membrane  
Ontology : EGO-EBImolecular_function  protein binding  cellular_component  biological_process  integral component of membrane  
NDEx NetworkSMCO4
Atlas of Cancer Signalling NetworkSMCO4
Wikipedia pathwaysSMCO4
Orthology - Evolution
OrthoDB56935
GeneTree (enSembl)ENSG00000166002
Phylogenetic Trees/Animal Genes : TreeFamSMCO4
HOGENOMQ9NRQ5
Homologs : HomoloGeneSMCO4
Homology/Alignments : Family Browser (UCSC)SMCO4
Gene fusions - Rearrangements
Fusion : QuiverSMCO4
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSMCO4 [hg38]
dbVarSMCO4
ClinVarSMCO4
MonarchSMCO4
1000_GenomesSMCO4 
Exome Variant ServerSMCO4
GNOMAD BrowserENSG00000166002
Varsome BrowserSMCO4
Genomic Variants (DGV)SMCO4 [DGVbeta]
DECIPHERSMCO4 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSMCO4 
Mutations
ICGC Data PortalSMCO4 
TCGA Data PortalSMCO4 
Broad Tumor PortalSMCO4
OASIS PortalSMCO4 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSMCO4  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DSMCO4
Mutations and Diseases : HGMDSMCO4
BioMutasearch SMCO4
DgiDB (Drug Gene Interaction Database)SMCO4
DoCM (Curated mutations)SMCO4 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SMCO4 (select a term)
intoGenSMCO4
Cancer3DSMCO4(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM609477   
Orphanet
DisGeNETSMCO4
MedgenSMCO4
Genetic Testing Registry SMCO4
NextProtQ9NRQ5 [Medical]
GENETestsSMCO4
Target ValidationSMCO4
Huge Navigator SMCO4 [HugePedia]
ClinGenSMCO4
Clinical trials, drugs, therapy
MyCancerGenomeSMCO4
Protein Interactions : CTD
Pharm GKB GenePA144596494
Clinical trialSMCO4
Miscellaneous
canSAR (ICR)SMCO4 (select the gene name)
HarmonizomeSMCO4
DataMed IndexSMCO4
Probes
Litterature
PubMed7 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSMCO4
EVEXSMCO4
GoPubMedSMCO4
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

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indexed on : Sat Dec 5 17:27:35 CET 2020
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