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Aliases for SF3B6 Gene

Aliases for SF3B6 Gene

  • Splicing Factor 3b Subunit 6 2 3 5
  • Splicing Factor 3b, Subunit 6, 14kDa 2 3 4
  • Spliceosome-Associated Protein, 14-KDa 3 4
  • Pre-MRNA Branch Site Protein P14 3 4
  • Splicing Factor 3B Subunit 6 3 4
  • SF3b 14 KDa Subunit 3 4
  • SF3B14a 3 4
  • SF3B14 3 4
  • SAP14 3 4
  • Spliceosome-Associated Protein, 14 KDa Subunit 3
  • Splicing Factor 3B, 14 KDa Subunit 3
  • Pre MRNA Branch Site Protein P14 2
  • CGI-110 3
  • HSPC175 3
  • SF3B14A 4
  • SAP14a 3
  • Ht006 3
  • P14 3

External Ids for SF3B6 Gene

Previous GeneCards Identifiers for SF3B6 Gene

  • GC02M024291

Summaries for SF3B6 Gene

Entrez Gene Summary for SF3B6 Gene

  • This gene encodes a 14 kDa protein subunit of the splicing factor 3b complex. Splicing factor 3b associates with both the U2 and U11/U12 small nuclear ribonucleoprotein complexes (U2 snRNP) of spliceosomes. This 14 kDa protein interacts directly with subunit 1 of the splicing factor 3b complex. This 14 kDa protein also interacts directly with the adenosine that carries out the first transesterification step of splicing at the pre-mRNA branch site. [provided by RefSeq, Jul 2008]

GeneCards Summary for SF3B6 Gene

SF3B6 (Splicing Factor 3b Subunit 6) is a Protein Coding gene. Among its related pathways are mRNA Splicing - Minor Pathway and mRNA Splicing - Major Pathway. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and nucleotide binding.

UniProtKB/Swiss-Prot for SF3B6 Gene

  • Involved in pre-mRNA splicing as a component of the splicing factor SF3B complex (PubMed:27720643). SF3B complex is required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA (PubMed:12234937). Directly contacts the pre-mRNA branch site adenosine for the first catalytic step of splicing (PubMed:16432215). Enters the spliceosome and associates with the pre-mRNA branch site as part of the 17S U2 or, in the case of the minor spliceosome, as part of the 18S U11/U12 snRNP complex, and thus may facilitate the interaction of these snRNP with the branch sites of U2 and U12 respectively (PubMed:16432215).

Gene Wiki entry for SF3B6 Gene

Additional gene information for SF3B6 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SF3B6 Gene

Genomics for SF3B6 Gene

GeneHancer (GH) Regulatory Elements for SF3B6 Gene

Promoters and enhancers for SF3B6 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02J024075 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 600.7 -0.4 -429 3.7 CC2D1A SP1 ZFX ELF3 MNT SIX5 NKRF POLR2A CEBPG RERE FAM228B GC02M024079 SF3B6 PIR43014 FAM228A ATAD2B TP53I3 PFN4 ITSN2 WDCP
GH02J024045 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 12.2 +28.1 28143 5.8 ZNF652 CC2D1A SP1 ELF3 SIX5 POLR2A ZNF121 CEBPG GTF2F1 ZSCAN21 WDCP FKBP1B FAM228B ATAD2B PFN4 SF3B6 MFSD2B TP53I3 UBXN2A ENSG00000271936
GH02J023924 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 10.6 +149.8 149843 4.4 SP1 ZFX CTCF MNT ZNF148 NKRF POLR2A MLLT1 CEBPG RERE UBXN2A ATAD2B FAM228B MFSD2B SF3B6 PFN4 FKBP1B RPS13P4 GC02P023754
GH02J023900 Promoter/Enhancer 1.3 Ensembl ENCODE 9.2 +175.0 175013 2.9 CEBPG ZNF384 SP7 SMARCA4 CREB1 DPF2 CEBPA PKNOX1 SMARCC1 SMARCC2 RPS13P4 UBXN2A ATAD2B FAM228B SF3B6 PFN4 GC02P023754
GH02J024110 Enhancer 0.8 Ensembl ENCODE 11.2 -34.9 -34910 1.6 MAFK NFE2L2 ZNF316 SP1 NFE2 EHMT2 MAFG FOSL2 PRDM10 ATF7 GC02M024111 PIR36243 FAM228B PFN4 TP53I3 SF3B6 MFSD2B ATAD2B UBXN2A FAM228A
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SF3B6 on UCSC Golden Path with GeneCards custom track

Genomic Locations for SF3B6 Gene

Genomic Locations for SF3B6 Gene
chr2:24,067,584-24,076,444
(GRCh38/hg38)
Size:
8,861 bases
Orientation:
Minus strand
chr2:24,290,454-24,299,314
(GRCh37/hg19)
Size:
8,861 bases
Orientation:
Minus strand

Genomic View for SF3B6 Gene

Genes around SF3B6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SF3B6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SF3B6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SF3B6 Gene

Proteins for SF3B6 Gene

  • Protein details for SF3B6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y3B4-SF3B6_HUMAN
    Recommended name:
    Splicing factor 3B subunit 6
    Protein Accession:
    Q9Y3B4
    Secondary Accessions:
    • Q53TM1

    Protein attributes for SF3B6 Gene

    Size:
    125 amino acids
    Molecular mass:
    14585 Da
    Quaternary structure:
    • Component of splicing factor SF3B complex which is composed of at least eight subunits; SF3B1, SF3B2, SF3B3, SF3B4, SF3B5, SF3B6, PHF5A and DDX42 (PubMed:12234937, PubMed:12738865, PubMed:16432215, PubMed:27720643, PubMed:28541300). Within the SF3B complex interacts directly with SF3B1 (PubMed:21062891, PubMed:16432215, Ref.20). The SF3B complex composed of SF3B1, SF3B2, SF3B3, SF3B4, SF3B5, SF3B6 and PHF5A interacts with U2AF2 (PubMed:27720643). Component of the U11/U12 snRNPs that are part of the U12-type spliceosome (PubMed:15146077).

    Three dimensional structures from OCA and Proteopedia for SF3B6 Gene

neXtProt entry for SF3B6 Gene

Post-translational modifications for SF3B6 Gene

  • Ubiquitination at posLast=77 and isoforms=41
  • Modification sites at PhosphoSitePlus

Other Protein References for SF3B6 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SF3B6 Gene

Domains & Families for SF3B6 Gene

Gene Families for SF3B6 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for SF3B6 Gene

GenScript: Design optimal peptide antigens:
  • SF3b 14 kDa subunit (PM14_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9Y3B4

UniProtKB/Swiss-Prot:

SF3B6_HUMAN :
  • Belongs to the SF3B6 family.
Family:
  • Belongs to the SF3B6 family.
genes like me logo Genes that share domains with SF3B6: view

Function for SF3B6 Gene

Molecular function for SF3B6 Gene

UniProtKB/Swiss-Prot Function:
Involved in pre-mRNA splicing as a component of the splicing factor SF3B complex (PubMed:27720643). SF3B complex is required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA (PubMed:12234937). Directly contacts the pre-mRNA branch site adenosine for the first catalytic step of splicing (PubMed:16432215). Enters the spliceosome and associates with the pre-mRNA branch site as part of the 17S U2 or, in the case of the minor spliceosome, as part of the 18S U11/U12 snRNP complex, and thus may facilitate the interaction of these snRNP with the branch sites of U2 and U12 respectively (PubMed:16432215).

Gene Ontology (GO) - Molecular Function for SF3B6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding HDA,IEA 22658674
GO:0003729 mRNA binding IDA 16432215
GO:0005515 protein binding IPI 16432215
genes like me logo Genes that share ontologies with SF3B6: view
genes like me logo Genes that share phenotypes with SF3B6: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SF3B6

Clone Products

  • Addgene plasmids for SF3B6
  • Applied Biological Materials (abm): Clones for SF3B6 - Now 50% OFF >
  • * SF3B6 as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * SF3B6 tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for SF3B6 Gene

Localization for SF3B6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SF3B6 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SF3B6 gene
Compartment Confidence
nucleus 5
mitochondrion 0

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SF3B6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IEA 27720643
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IEA --
GO:0005686 U2 snRNP IBA 21873635
GO:0005689 U12-type spliceosomal complex IBA,IDA 15146077
genes like me logo Genes that share ontologies with SF3B6: view

Pathways & Interactions for SF3B6 Gene

genes like me logo Genes that share pathways with SF3B6: view

Pathways by source for SF3B6 Gene

Gene Ontology (GO) - Biological Process for SF3B6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0001825 blastocyst formation IEA --
GO:0006397 mRNA processing IEA --
GO:0008380 RNA splicing IEA --
genes like me logo Genes that share ontologies with SF3B6: view

No data available for SIGNOR curated interactions for SF3B6 Gene

Drugs & Compounds for SF3B6 Gene

No Compound Related Data Available

Transcripts for SF3B6 Gene

mRNA/cDNA for SF3B6 Gene

(1) REFSEQ mRNAs :
(9) Additional mRNA sequences :
(143) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SF3B6

Clone Products

  • Addgene plasmids for SF3B6
  • Applied Biological Materials (abm): Clones for SF3B6 - Now 50% OFF >
  • * SF3B6 as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * SF3B6 tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All

Alternative Splicing Database (ASD) splice patterns (SP) for SF3B6 Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2a · 2b · 2c ^ 3a · 3b ^ 4a · 4b · 4c
SP1: - -
SP2: - - -
SP3: - - - -
SP4: -
SP5:

Relevant External Links for SF3B6 Gene

GeneLoc Exon Structure for
SF3B6
ECgene alternative splicing isoforms for
SF3B6

Expression for SF3B6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SF3B6 Gene

Protein differential expression in normal tissues from HIPED for SF3B6 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (14.0) and Nasal epithelium (11.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SF3B6 Gene



Protein tissue co-expression partners for SF3B6 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SF3B6 Gene:

SF3B6

Evidence on tissue expression from TISSUES for SF3B6 Gene

  • Blood(4.3)
  • Nervous system(4.3)
  • Gall bladder(2.3)
  • Skin(2.3)
  • Thyroid gland(2.3)
genes like me logo Genes that share expression patterns with SF3B6: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SF3B6 Gene

Orthologs for SF3B6 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SF3B6 Gene

Organism Taxonomy Gene Similarity Type Details
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 100 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia -- 35
  • 100 (a)
OneToOne
SF3B14 34
  • 100 (n)
dog
(Canis familiaris)
Mammalia -- 35
  • 100 (a)
OneToOne
SF3B14 34
  • 97.07 (n)
cow
(Bos Taurus)
Mammalia SF3B14 35 34
  • 97.6 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 93 (a)
OneToOne
mouse
(Mus musculus)
Mammalia 0610009D07Rik 35 34
  • 92 (n)
OneToOne
Sf3b6 17
rat
(Rattus norvegicus)
Mammalia LOC100365504 34
  • 91.47 (n)
chicken
(Gallus gallus)
Aves -- 35
  • 100 (a)
OneToOne
SF3B14 34
  • 85.6 (n)
lizard
(Anolis carolinensis)
Reptilia -- 35
  • 100 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sf3b14 34
  • 82.13 (n)
Str.5936 34
African clawed frog
(Xenopus laevis)
Amphibia MGC68842 34
zebrafish
(Danio rerio)
Actinopterygii sf3b14 35
  • 100 (a)
OneToOne
sf3b6 34
  • 81.87 (n)
wufb78f04 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10259 34
fruit fly
(Drosophila melanogaster)
Insecta CG13298 35 34
  • 67.83 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002780 34
  • 66.39 (n)
worm
(Caenorhabditis elegans)
Secernentea C50D2.5 35 34
  • 61.87 (n)
OneToOne
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G12190 34
  • 57.3 (n)
soybean
(Glycine max)
eudicotyledons Gma.8283 34
rice
(Oryza sativa)
Liliopsida Os03g0811700 34
  • 61.02 (n)
Os.5336 34
barley
(Hordeum vulgare)
Liliopsida Hv.3044 34
wheat
(Triticum aestivum)
Liliopsida Ta.3276 34
sea squirt
(Ciona savignyi)
Ascidiacea Cin.5237 34
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.5237 34
Species where no ortholog for SF3B6 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for SF3B6 Gene

ENSEMBL:
Gene Tree for SF3B6 (if available)
TreeFam:
Gene Tree for SF3B6 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SF3B6: view image

Paralogs for SF3B6 Gene

Pseudogenes.org Pseudogenes for SF3B6 Gene

genes like me logo Genes that share paralogs with SF3B6: view

No data available for Paralogs for SF3B6 Gene

Variants for SF3B6 Gene

Sequence variations from dbSNP and Humsavar for SF3B6 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs1000316940 -- 24,073,376(-) A/C intron_variant
rs1000389653 -- 24,067,596(-) A/G 3_prime_UTR_variant
rs1000656844 -- 24,069,393(-) A/C intron_variant
rs1002113394 -- 24,067,948(-) A/G intron_variant
rs1002422000 -- 24,067,440(-) G/A downstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for SF3B6 Gene

Variant ID Type Subtype PubMed ID
nsv997445 CNV gain 25217958
nsv997725 CNV gain 25217958

Variation tolerance for SF3B6 Gene

Residual Variation Intolerance Score: 56.2% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SF3B6 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SF3B6

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SF3B6 Gene

Disorders for SF3B6 Gene

Additional Disease Information for SF3B6

No disorders were found for SF3B6 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SF3B6 Gene

Publications for SF3B6 Gene

  1. Molecular architecture of the multiprotein splicing factor SF3b. (PMID: 12738865) Golas MM … Stark H (Science (New York, N.Y.) 2003) 2 3 4 23 58
  2. A novel U2 and U11/U12 snRNP protein that associates with the pre-mRNA branch site. (PMID: 11500380) Will CL … Query CC (The EMBO journal 2001) 2 3 4 23 58
  3. Splicing modulators act at the branch point adenosine binding pocket defined by the PHF5A-SF3b complex. (PMID: 28541300) Teng T … Zhu P (Nature communications 2017) 3 4 58
  4. Molecular Architecture of SF3b and Structural Consequences of Its Cancer-Related Mutations. (PMID: 27720643) Cretu C … Pena V (Molecular cell 2016) 3 4 58
  5. Structural model of the p14/SF3b155 · branch duplex complex. (PMID: 21062891) Schellenberg MJ … MacMillan AM (RNA (New York, N.Y.) 2011) 3 4 58

Products for SF3B6 Gene

Sources for SF3B6 Gene

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