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 ... See more...

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
  • SF3B14a 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
  • CGI-110 2 3
  • SAP14a 2 3
  • SF3B14 3 4
  • Ht006 2 3
  • SAP14 3 4
  • P14 2 3
  • Spliceosome-Associated Protein, 14 KDa Subunit 3
  • Splicing Factor 3B, 14 KDa Subunit 3
  • Pre MRNA Branch Site Protein P14 2
  • HSPC175 3
  • SF3B14A 4
  • SF3B6 5

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. Diseases associated with SF3B6 include Amyotrophic Lateral Sclerosis 1. Among its related pathways are mRNA Splicing - Minor Pathway and Gene Expression. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and nucleotide binding.

UniProtKB/Swiss-Prot Summary 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 , Rfam classification and piRNA Summary for SF3B6 Gene

Genomics for SF3B6 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SF3B6 Gene
- 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 the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SF3B6

Genomic Locations for SF3B6 Gene

Genomic Locations for SF3B6 Gene
chr2:24,067,586-24,076,373
(GRCh38/hg38)
Size:
8,788 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 Lys7, Lys29, and Lys41
  • 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

Protein Domains for SF3B6 Gene

InterPro:
Blocks:
  • RNA-binding region RNP-1 (RNA recognition motif)
ProtoNet:

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).

Phenotypes From GWAS Catalog for SF3B6 Gene

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 IEA,HDA 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

No data available for Enzyme Numbers (IUBMB) , 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
extracellular 1
mitochondrion 1

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 IEA,IDA 27720643
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IEA --
GO:0005684 U2-type spliceosomal complex IBA 21873635
GO:0005686 U2 snRNP IBA 21873635
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 IEA,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 NCBI additional mRNA sequence :
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

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

Expression for SF3B6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SF3B6

Evidence on tissue expression from TISSUES for SF3B6 Gene

  • Blood(4.4)
  • Nervous system(4.3)
  • Skin(2.9)
  • Gall bladder(2.3)
  • Thyroid gland(2.3)
  • Lung(2.1)
  • Intestine(2)
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
Chimpanzee
(Pan troglodytes)
Mammalia SF3B14 30
  • 100 (n)
-- 31
  • 100 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia -- 31
  • 100 (a)
OneToOne
SF3B14 30
  • 97.07 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 100 (a)
OneToOne
Cow
(Bos Taurus)
Mammalia SF3B14 30 31
  • 97.6 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia -- 31
  • 93 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia 0610009D07Rik 30 31
  • 92 (n)
OneToOne
Sf3b6 17
Rat
(Rattus norvegicus)
Mammalia LOC100365504 30
  • 91.47 (n)
Chicken
(Gallus gallus)
Aves -- 31
  • 100 (a)
OneToOne
SF3B14 30
  • 85.6 (n)
Lizard
(Anolis carolinensis)
Reptilia -- 31
  • 100 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia sf3b14 30
  • 82.13 (n)
Str.5936 30
African clawed frog
(Xenopus laevis)
Amphibia MGC68842 30
Zebrafish
(Danio rerio)
Actinopterygii sf3b14 31
  • 100 (a)
OneToOne
sf3b6 30
  • 81.87 (n)
wufb78f04 30
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10259 30
Fruit Fly
(Drosophila melanogaster)
Insecta CG13298 30 31
  • 67.83 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002780 30
  • 66.39 (n)
Worm
(Caenorhabditis elegans)
Secernentea C50D2.5 30 31
  • 61.87 (n)
OneToOne
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT5G12190 30
  • 57.3 (n)
Soybean
(Glycine max)
eudicotyledons Gma.8283 30
Rice
(Oryza sativa)
Liliopsida Os03g0811700 30
  • 61.02 (n)
Os.5336 30
Barley
(Hordeum vulgare)
Liliopsida Hv.3044 30
Wheat
(Triticum aestivum)
Liliopsida Ta.3276 30
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.5237 30
Species where no ortholog for SF3B6 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Squirt (Ciona savignyi)
  • 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, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SF3B6 Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
746917 Benign: not provided 24,067,780(-) G/A SYNONYMOUS_VARIANT
777563 Benign: not provided 24,068,453(-) G/A SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for SF3B6 Gene

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

MalaCards: The human disease database

(1) MalaCards diseases for SF3B6 Gene - From: DISEASES

Disorder Aliases PubMed IDs
amyotrophic lateral sclerosis 1
  • als1
- elite association - COSMIC cancer census association via MalaCards
Search SF3B6 in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with SF3B6: view

No data available for 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
  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
  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
  4. Molecular Architecture of SF3b and Structural Consequences of Its Cancer-Related Mutations. (PMID: 27720643) Cretu C … Pena V (Molecular cell 2016) 3 4
  5. Structural model of the p14/SF3b155 · branch duplex complex. (PMID: 21062891) Schellenberg MJ … MacMillan AM (RNA (New York, N.Y.) 2011) 3 4

Products for SF3B6 Gene

Sources for SF3B6 Gene