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Aliases for SF3B5 Gene

Aliases for SF3B5 Gene

  • Splicing Factor 3b Subunit 5 2 3 5
  • Pre-MRNA-Splicing Factor SF3b 10 KDa Subunit 3 4
  • Splicing Factor 3b, Subunit 5, 10kDa 2 3
  • Splicing Factor 3B Subunit 5 3
  • SF3b10 3
  • SF3B10 4
  • SF3b5 4
  • Ysf3 3

External Ids for SF3B5 Gene

Previous GeneCards Identifiers for SF3B5 Gene

  • GC06M144351
  • GC06M144396
  • GC06M144457
  • GC06M141979
  • GC06M144416

Summaries for SF3B5 Gene

GeneCards Summary for SF3B5 Gene

SF3B5 (Splicing Factor 3b Subunit 5) is a Protein Coding gene. Among its related pathways are mRNA Splicing - Major Pathway and mRNA Splicing - Minor Pathway.

UniProtKB/Swiss-Prot for SF3B5 Gene

  • Involved in pre-mRNA splicing as a component of the splicing factor SF3B complex, a constituent of the spliceosome (PubMed:27720643, PubMed:28781166). SF3B complex is required for A complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. Sequence independent binding of SF3A/SF3B complex upstream of the branch site is essential, it may anchor U2 snRNP to the pre-mRNA (PubMed:12234937).

Gene Wiki entry for SF3B5 Gene

Additional gene information for SF3B5 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SF3B5 Gene

Genomics for SF3B5 Gene

GeneHancer (GH) Regulatory Elements for SF3B5 Gene

Promoters and enhancers for SF3B5 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
GH06J144094 Promoter/Enhancer 1.6 Ensembl ENCODE 650.7 +0.2 235 2.6 CLOCK MLX FEZF1 DMAP1 YY1 SLC30A9 E2F8 ZNF143 SP3 NFYC SF3B5 ADAT2 ENSG00000270890 LTV1 PLAGL1
GH06J144062 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE 13.2 +31.4 31417 2.9 SMAD1 ARID4B SIN3A ZNF2 IRF4 YY1 SLC30A9 POLR2B ZNF766 ZNF213 PLAGL1 SF3B5 STX11 PHACTR2 GC06P144049
GH06J144005 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE 11.5 +88.2 88197 3.2 HDGF PKNOX1 ATF1 ARNT SIN3A EGR1 FOS CREM SMAD5 ZBTB11 PLAGL1 ENSG00000276680 HYMAI SF3B5 PHACTR2 PHACTR2-AS1 GC06P143999
GH06J144123 Enhancer 1 Ensembl ENCODE dbSUPER 11.7 -28.4 -28400 0.9 BRD4 MEIS2 LEF1 PKNOX1 TEAD4 TAL1 CEBPB CBFA2T3 DPF2 E4F1 SF3B5 ENSG00000225311 PIR44650 LOC105378036 MRPL42P3
GH06J144054 Enhancer 0.8 Ensembl ENCODE 11.8 +40.2 40161 1.7 HDGF MEIS2 SRF PKNOX1 NR2F1 KLF5 ZNF148 TARDBP MLLT1 RUNX3 SF3B5 LTV1 STX11 PHACTR2 PLAGL1 GC06P144049
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SF3B5 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SF3B5 gene promoter:
  • Nkx5-1
  • RORalpha2
  • HNF-4alpha1
  • LCR-F1
  • ER-alpha
  • En-1
  • XBP-1
  • GCNF-2
  • GCNF-1
  • GCNF

Genomic Locations for SF3B5 Gene

Genomic Locations for SF3B5 Gene
chr6:144,094,881-144,095,617
(GRCh38/hg38)
Size:
737 bases
Orientation:
Minus strand
chr6:144,416,018-144,416,754
(GRCh37/hg19)
Size:
737 bases
Orientation:
Minus strand

Genomic View for SF3B5 Gene

Genes around SF3B5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SF3B5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SF3B5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SF3B5 Gene

Proteins for SF3B5 Gene

  • Protein details for SF3B5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BWJ5-SF3B5_HUMAN
    Recommended name:
    Splicing factor 3B subunit 5
    Protein Accession:
    Q9BWJ5
    Secondary Accessions:
    • B2R568
    • Q7RTV1

    Protein attributes for SF3B5 Gene

    Size:
    86 amino acids
    Molecular mass:
    10135 Da
    Quaternary structure:
    • Component of the spliceosome B complex (PubMed:28781166). 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:28541300, PubMed:27720643). SF3B associates with the splicing factor SF3A and a 12S RNA unit to form the U2 small nuclear ribonucleoproteins complex (U2 snRNP) (PubMed:12234937). Within the SF3B complex interacts directly with SF3B1 (via HEAT domain) and SF3B3 (PubMed:27720643). 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 SF3B5 Gene

neXtProt entry for SF3B5 Gene

Post-translational modifications for SF3B5 Gene

  • Ubiquitination at posLast=7171, posLast=2828, and posLast=1717
  • Modification sites at PhosphoSitePlus

Other Protein References for SF3B5 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SF3B5 Gene

Domains & Families for SF3B5 Gene

Gene Families for SF3B5 Gene

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

Protein Domains for SF3B5 Gene

Suggested Antigen Peptide Sequences for SF3B5 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9BWJ5

UniProtKB/Swiss-Prot:

SF3B5_HUMAN :
  • Belongs to the SF3B5 family.
Family:
  • Belongs to the SF3B5 family.
genes like me logo Genes that share domains with SF3B5: view

Function for SF3B5 Gene

Molecular function for SF3B5 Gene

UniProtKB/Swiss-Prot Function:
Involved in pre-mRNA splicing as a component of the splicing factor SF3B complex, a constituent of the spliceosome (PubMed:27720643, PubMed:28781166). SF3B complex is required for A complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. Sequence independent binding of SF3A/SF3B complex upstream of the branch site is essential, it may anchor U2 snRNP to the pre-mRNA (PubMed:12234937).

Phenotypes From GWAS Catalog for SF3B5 Gene

Gene Ontology (GO) - Molecular Function for SF3B5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IEA --
genes like me logo Genes that share ontologies with SF3B5: view
genes like me logo Genes that share phenotypes with SF3B5: view

Animal Model Products

CRISPR Products

miRNA for SF3B5 Gene

miRTarBase miRNAs that target SF3B5

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SF3B5

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SF3B5 Gene

Localization for SF3B5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SF3B5 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 SF3B5 gene
Compartment Confidence
nucleus 5
extracellular 2
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SF3B5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 28781166
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IEA --
GO:0005686 U2 snRNP IBA --
GO:0005689 U12-type spliceosomal complex IDA 15146077
genes like me logo Genes that share ontologies with SF3B5: view

Pathways & Interactions for SF3B5 Gene

genes like me logo Genes that share pathways with SF3B5: view

Pathways by source for SF3B5 Gene

1 KEGG pathway for SF3B5 Gene

Gene Ontology (GO) - Biological Process for SF3B5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006397 mRNA processing IEA --
GO:0008380 RNA splicing IEA --
genes like me logo Genes that share ontologies with SF3B5: view

No data available for SIGNOR curated interactions for SF3B5 Gene

Drugs & Compounds for SF3B5 Gene

No Compound Related Data Available

Transcripts for SF3B5 Gene

mRNA/cDNA for SF3B5 Gene

(1) REFSEQ mRNAs :
(3) Additional mRNA sequences :
(451) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SF3B5 Gene

Splicing factor 3b, subunit 5, 10kDa:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SF3B5

Alternative Splicing Database (ASD) splice patterns (SP) for SF3B5 Gene

No ASD Table

Relevant External Links for SF3B5 Gene

GeneLoc Exon Structure for
SF3B5
ECgene alternative splicing isoforms for
SF3B5

Expression for SF3B5 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SF3B5 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SF3B5 Gene

This gene is overexpressed in Fetal testis (6.2) and NK cells (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SF3B5 Gene



Protein tissue co-expression partners for SF3B5 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SF3B5 Gene:

SF3B5

SOURCE GeneReport for Unigene cluster for SF3B5 Gene:

Hs.110695

Evidence on tissue expression from TISSUES for SF3B5 Gene

  • Eye(4.5)
  • Lung(2.9)
  • Muscle(2.9)
  • Nervous system(2.8)
  • Kidney(2.1)
genes like me logo Genes that share expression patterns with SF3B5: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SF3B5 Gene

Orthologs for SF3B5 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SF3B5 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SF3B5 34 33
  • 100 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SF3B5 34
  • 97 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SF3B5 34 33
  • 96.51 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SF3B5 34 33
  • 92.64 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Sf3b5 16 34 33
  • 90.7 (n)
rat
(Rattus norvegicus)
Mammalia Sf3b5 33
  • 88.76 (n)
oppossum
(Monodelphis domestica)
Mammalia SF3B5 34
  • 83 (a)
OneToOne
chicken
(Gallus gallus)
Aves SF3B5 33
  • 90.7 (n)
lizard
(Anolis carolinensis)
Reptilia SF3B5 34
  • 97 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sf3b5 33
  • 81.78 (n)
Str.16 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.8383 33
zebrafish
(Danio rerio)
Actinopterygii sf3b5 34 33
  • 85.1 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG11985 34 33
  • 74.9 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011907 33
  • 72.55 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT4G14342 33
  • 59.13 (n)
rice
(Oryza sativa)
Liliopsida Os08g0278966 33
  • 57.54 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU02000 33
  • 57.32 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes sab10 33
  • 52.74 (n)
Species where no ortholog for SF3B5 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)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SF3B5 Gene

ENSEMBL:
Gene Tree for SF3B5 (if available)
TreeFam:
Gene Tree for SF3B5 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SF3B5: view image

Paralogs for SF3B5 Gene

No data available for Paralogs for SF3B5 Gene

Variants for SF3B5 Gene

Sequence variations from dbSNP and Humsavar for SF3B5 Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs1001572263 -- 144,096,618(-) GA/ upstream_transcript_variant
rs1001670384 -- 144,096,929(-) C/G upstream_transcript_variant
rs1003195279 -- 144,095,986(-) C/G/T upstream_transcript_variant
rs1003246359 -- 144,095,378(-) G/A coding_sequence_variant, synonymous_variant
rs1003249643 -- 144,096,303(-) G/A upstream_transcript_variant

Variation tolerance for SF3B5 Gene

Residual Variation Intolerance Score: 50.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.03; 0.75% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SF3B5 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SF3B5

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for SF3B5 Gene

Disorders for SF3B5 Gene

Additional Disease Information for SF3B5

No disorders were found for SF3B5 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SF3B5 Gene

Publications for SF3B5 Gene

  1. Characterization of novel SF3b and 17S U2 snRNP proteins, including a human Prp5p homologue and an SF3b DEAD-box protein. (PMID: 12234937) Will CL … Lührmann R (The EMBO journal 2002) 2 3 4 58
  2. Cryo-EM Structure of a Pre-catalytic Human Spliceosome Primed for Activation. (PMID: 28781166) Bertram K … Stark H (Cell 2017) 3 4 58
  3. The human 18S U11/U12 snRNP contains a set of novel proteins not found in the U2-dependent spliceosome. (PMID: 15146077) Will CL … Lührmann R (RNA (New York, N.Y.) 2004) 3 4 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. The DNA sequence and analysis of human chromosome 6. (PMID: 14574404) Mungall AJ … Beck S (Nature 2003) 3 4 58

Products for SF3B5 Gene

Sources for SF3B5 Gene

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