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Taking over the Atlas
Dear Colleagues,
The Atlas, once more, is in great danger, and I will have to proceed to a collective economic lay-off of all the team involved in the Atlas before the begining of April 2015 (a foundation having suddenly withdrawn its commitment to support the Atlas). I ask you herein if any Scientific Society (a Society of Cytogenetics, of Clinical Genetics, of Hematology, or a Cancer Society, or any other...), any University and/or Hospital, any Charity, or any database would be interested in taking over the Atlas, in whole or in part. If taking charge of the whole lot is too big, a consortium of various actors could be the solution (I am myself trying to find partners). Could you please spread the information, contact the relevant authorities, and find partners.
Survival of the Atlas will be critically dependant upon your ability to find solutions (and urgently!).
Kind regards.
Jean-Loup Huret
Donations are also welcome

Donate (in Euros)

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SF3B4 (splicing factor 3b, subunit 4, 49kDa)

Identity

Other namesAFD1
Hsh49
SAP49
SF3b49
HGNC (Hugo) SF3B4
LocusID (NCBI) 10262
Location 1q21.2
Location_base_pair Starts at 149895209 and ends at 149900144 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)SF3B4   10771
Cards
Entrez_Gene (NCBI)SF3B4  10262  splicing factor 3b, subunit 4, 49kDa
GeneCards (Weizmann)SF3B4
Ensembl hg19 (Hinxton)ENSG00000143368 [Gene_View]  chr1:149895209-149900144 [Contig_View]  SF3B4 [Vega]
Ensembl hg38 (Hinxton)ENSG00000143368 [Gene_View]  chr1:149895209-149900144 [Contig_View]  SF3B4 [Vega]
ICGC DataPortalENSG00000143368
cBioPortalSF3B4
AceView (NCBI)SF3B4
Genatlas (Paris)SF3B4
WikiGenes10262
SOURCE (Princeton)SF3B4
Genomic and cartography
GoldenPath hg19 (UCSC)SF3B4  -     chr1:149895209-149900144 -  1q21.2   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)SF3B4  -     1q21.2   [Description]    (hg38-Dec_2013)
EnsemblSF3B4 - 1q21.2 [CytoView hg19]  SF3B4 - 1q21.2 [CytoView hg38]
Mapping of homologs : NCBISF3B4 [Mapview hg19]  SF3B4 [Mapview hg38]
OMIM154400   605593   
Gene and transcription
Genbank (Entrez)AI925089 AK097315 AK223322 AK310495 BC004273
RefSeq transcript (Entrez)NM_005850
RefSeq genomic (Entrez)AC_000133 NC_000001 NC_018912 NG_032777 NT_004487 NW_001838529 NW_004929293
Consensus coding sequences : CCDS (NCBI)SF3B4
Cluster EST : UnigeneHs.516160 [ NCBI ]
CGAP (NCI)Hs.516160
Alternative Splicing : Fast-db (Paris)GSHG0002479
Alternative Splicing GalleryENSG00000143368
Gene ExpressionSF3B4 [ NCBI-GEO ]     SF3B4 [ SEEK ]   SF3B4 [ MEM ]
SOURCE (Princeton)Expression in : [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ15427 (Uniprot)
NextProtQ15427  [Medical]
With graphics : InterProQ15427
Splice isoforms : SwissVarQ15427 (Swissvar)
Domaine pattern : Prosite (Expaxy)RRM (PS50102)   
Domains : Interpro (EBI)Nucleotide-bd_a/b_plait    RRM_dom   
Related proteins : CluSTrQ15427
Domain families : Pfam (Sanger)RRM_1 (PF00076)   
Domain families : Pfam (NCBI)pfam00076   
Domain families : Smart (EMBL)RRM (SM00360)  
DMDM Disease mutations10262
Blocks (Seattle)Q15427
PDB (SRS)1X5T    1X5U   
PDB (PDBSum)1X5T    1X5U   
PDB (IMB)1X5T    1X5U   
PDB (RSDB)1X5T    1X5U   
Human Protein AtlasENSG00000143368
Peptide AtlasQ15427
HPRD12028
IPIIPI00017339   IPI00644485   
Protein Interaction databases
DIP (DOE-UCLA)Q15427
IntAct (EBI)Q15427
FunCoupENSG00000143368
BioGRIDSF3B4
IntegromeDBSF3B4
STRING (EMBL)SF3B4
Ontologies - Pathways
QuickGOQ15427
Ontology : AmiGOnucleotide binding  RNA splicing, via transesterification reactions  mRNA splicing, via spliceosome  mRNA splicing, via spliceosome  protein binding  nucleoplasm  spliceosomal complex  U12-type spliceosomal complex  mRNA processing  RNA splicing  gene expression  poly(A) RNA binding  
Ontology : EGO-EBInucleotide binding  RNA splicing, via transesterification reactions  mRNA splicing, via spliceosome  mRNA splicing, via spliceosome  protein binding  nucleoplasm  spliceosomal complex  U12-type spliceosomal complex  mRNA processing  RNA splicing  gene expression  poly(A) RNA binding  
Pathways : KEGGSpliceosome   
Protein Interaction DatabaseSF3B4
DoCM (Curated mutations)SF3B4
Wikipedia pathwaysSF3B4
Gene fusion - rearrangements
Polymorphisms : SNP, variants
NCBI Variation ViewerSF3B4 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SF3B4
dbVarSF3B4
ClinVarSF3B4
1000_GenomesSF3B4 
Exome Variant ServerSF3B4
SNP (GeneSNP Utah)SF3B4
SNP : HGBaseSF3B4
Genetic variants : HAPMAPSF3B4
Genomic Variants (DGV)SF3B4 [DGVbeta]
Mutations
ICGC Data PortalENSG00000143368 
Somatic Mutations in Cancer : COSMICSF3B4 
CONAN: Copy Number AnalysisSF3B4 
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)LOVD - Leiden Open Variation Database
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)1:149895209-149900144
Mutations and Diseases : HGMDSF3B4
OMIM154400    605593   
MedgenSF3B4
NextProtQ15427 [Medical]
GENETestsSF3B4
Disease Genetic AssociationSF3B4
Huge Navigator SF3B4 [HugePedia]  SF3B4 [HugeCancerGEM]
snp3D : Map Gene to Disease10262
DGIdb (Drug Gene Interaction db)SF3B4
General knowledge
Homologs : HomoloGeneSF3B4
Homology/Alignments : Family Browser (UCSC)SF3B4
Phylogenetic Trees/Animal Genes : TreeFamSF3B4
Chemical/Protein Interactions : CTD10262
Chemical/Pharm GKB GenePA35689
Clinical trialSF3B4
Cancer Resource (Charite)ENSG00000143368
Other databases
Probes
Litterature
PubMed56 Pubmed reference(s) in Entrez
CoreMineSF3B4
GoPubMedSF3B4
iHOPSF3B4
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

Contributor(s)

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

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Sat Feb 14 18:31:15 CET 2015

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jlhuret@AtlasGeneticsOncology.org.