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SMARCAL1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a-like 1)

Identity

Other namesHARP
HHARP
HGNC (Hugo) SMARCAL1
LocusID (NCBI) 50485
Location 2q35
Location_base_pair Starts at 217277473 and ends at 217347774 bp from pter ( according to hg19-Feb_2009)
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)SMARCAL1   11102
Cards
Entrez_Gene (NCBI)SMARCAL1  50485  SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a-like 1
GeneCards (Weizmann)SMARCAL1
Ensembl hg19 (Hinxton)ENSG00000138375 [Gene_View]  chr2:217277473-217347774 [Contig_View]  SMARCAL1 [Vega]
Ensembl hg38 (Hinxton)ENSG00000138375 [Gene_View]  chr2:217277473-217347774 [Contig_View]  SMARCAL1 [Vega]
ICGC DataPortalENSG00000138375
cBioPortalSMARCAL1
AceView (NCBI)SMARCAL1
Genatlas (Paris)SMARCAL1
WikiGenes50485
SOURCE (Princeton)SMARCAL1
Genomic and cartography
GoldenPath hg19 (UCSC)SMARCAL1  -     chr2:217277473-217347774 +  2q35   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)SMARCAL1  -     2q35   [Description]    (hg38-Dec_2013)
EnsemblSMARCAL1 - 2q35 [CytoView hg19]  SMARCAL1 - 2q35 [CytoView hg38]
Mapping of homologs : NCBISMARCAL1 [Mapview hg19]  SMARCAL1 [Mapview hg38]
OMIM242900   606622   
Gene and transcription
Genbank (Entrez)AF082179 AF432223 AI701066 AK000117 AK023780
RefSeq transcript (Entrez)NM_001127207 NM_014140
RefSeq genomic (Entrez)AC_000134 NC_000002 NC_018913 NG_009771 NT_005403 NW_001838863 NW_004929305
Consensus coding sequences : CCDS (NCBI)SMARCAL1
Cluster EST : UnigeneHs.516674 [ NCBI ]
CGAP (NCI)Hs.516674
Alternative Splicing : Fast-db (Paris)GSHG0017173
Alternative Splicing GalleryENSG00000138375
Gene ExpressionSMARCAL1 [ NCBI-GEO ]     SMARCAL1 [ SEEK ]   SMARCAL1 [ MEM ]
SOURCE (Princeton)Expression in : [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9NZC9 (Uniprot)
NextProtQ9NZC9  [Medical]
With graphics : InterProQ9NZC9
Splice isoforms : SwissVarQ9NZC9 (Swissvar)
Catalytic activity : Enzyme3.6.4.- [ Enzyme-Expasy ]   3.6.4.-3.6.4.- [ IntEnz-EBI ]   3.6.4.- [ BRENDA ]   3.6.4.- [ KEGG ]   
Domaine pattern : Prosite (Expaxy)HARP (PS51467)    HELICASE_ATP_BIND_1 (PS51192)    HELICASE_CTER (PS51194)   
Domains : Interpro (EBI)HARP_dom    Helicase_ATP-bd    Helicase_C    P-loop_NTPase    SNF2_N   
Related proteins : CluSTrQ9NZC9
Domain families : Pfam (Sanger)HARP (PF07443)    Helicase_C (PF00271)    SNF2_N (PF00176)   
Domain families : Pfam (NCBI)pfam07443    pfam00271    pfam00176   
Domain families : Smart (EMBL)DEXDc (SM00487)  HELICc (SM00490)  
DMDM Disease mutations50485
Blocks (Seattle)Q9NZC9
Human Protein AtlasENSG00000138375
Peptide AtlasQ9NZC9
HPRD05969
IPIIPI00386311   IPI00924929   IPI00927078   IPI00927311   IPI00925870   IPI00926097   IPI00924517   IPI00924761   IPI00925468   
Protein Interaction databases
DIP (DOE-UCLA)Q9NZC9
IntAct (EBI)Q9NZC9
FunCoupENSG00000138375
BioGRIDSMARCAL1
IntegromeDBSMARCAL1
STRING (EMBL)SMARCAL1
Ontologies - Pathways
QuickGOQ9NZC9
Ontology : AmiGODNA strand renaturation  DNA strand renaturation  DNA binding  helicase activity  protein binding  ATP binding  nucleus  DNA replication factor A complex  ATP catabolic process  ATP catabolic process  DNA metabolic process  regulation of transcription from RNA polymerase II promoter  cellular response to DNA damage stimulus  DNA-dependent ATPase activity  chromatin modification  replication fork processing  site of double-strand break  annealing helicase activity  annealing helicase activity  
Ontology : EGO-EBIDNA strand renaturation  DNA strand renaturation  DNA binding  helicase activity  protein binding  ATP binding  nucleus  DNA replication factor A complex  ATP catabolic process  ATP catabolic process  DNA metabolic process  regulation of transcription from RNA polymerase II promoter  cellular response to DNA damage stimulus  DNA-dependent ATPase activity  chromatin modification  replication fork processing  site of double-strand break  annealing helicase activity  annealing helicase activity  
Protein Interaction DatabaseSMARCAL1
DoCM (Curated mutations)SMARCAL1
Wikipedia pathwaysSMARCAL1
Gene fusion - rearrangements
Polymorphisms : SNP, variants
NCBI Variation ViewerSMARCAL1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SMARCAL1
dbVarSMARCAL1
ClinVarSMARCAL1
1000_GenomesSMARCAL1 
Exome Variant ServerSMARCAL1
SNP (GeneSNP Utah)SMARCAL1
SNP : HGBaseSMARCAL1
Genetic variants : HAPMAPSMARCAL1
Genomic VariantsSMARCAL1  SMARCAL1 [DGVbeta]
Mutations
ICGC Data PortalENSG00000138375 
Somatic Mutations in Cancer : COSMICSMARCAL1 
CONAN: Copy Number AnalysisSMARCAL1 
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
LOVD (Leiden Open Variation Database)**PUBLIC** CCHMC Molecular Genetics Laboratory Mutation Database
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)2:217277473-217347774
Mutations and Diseases : HGMDSMARCAL1
OMIM242900    606622   
MedgenSMARCAL1
NextProtQ9NZC9 [Medical]
GENETestsSMARCAL1
Disease Genetic AssociationSMARCAL1
Huge Navigator SMARCAL1 [HugePedia]  SMARCAL1 [HugeCancerGEM]
snp3D : Map Gene to Disease50485
DGIdb (Drug Gene Interaction db)SMARCAL1
General knowledge
Homologs : HomoloGeneSMARCAL1
Homology/Alignments : Family Browser (UCSC)SMARCAL1
Phylogenetic Trees/Animal Genes : TreeFamSMARCAL1
Chemical/Protein Interactions : CTD50485
Chemical/Pharm GKB GenePA35952
Clinical trialSMARCAL1
Cancer Resource (Charite)ENSG00000138375
Other databases
Probes
Litterature
PubMed40 Pubmed reference(s) in Entrez
CoreMineSMARCAL1
GoPubMedSMARCAL1
iHOPSMARCAL1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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Contributor(s)

Written09-2002Dessen P, Le Minor S
Updated12-2014Dessen P

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Sun Dec 21 01:31:55 CET 2014

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