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Aliases for SF3B4 Gene

Aliases for SF3B4 Gene

  • Splicing Factor 3b Subunit 4 2 3 5
  • Pre-MRNA-Splicing Factor SF3b 49 KDa Subunit 3 4
  • Splicing Factor 3b, Subunit 4, 49kDa 2 3
  • Splicing Factor 3b, Subunit 4, 49kD 2 3
  • Spliceosome-Associated Protein 49 3 4
  • SAP 49 3 4
  • SAP49 3 4
  • Spliceosome-Associated Protein (U2 SnRNP) 3
  • Spliceosomal Protein 3
  • SF3b49 3
  • SF3b50 3
  • Hsh49 3
  • AFD1 3

External Ids for SF3B4 Gene

Previous GeneCards Identifiers for SF3B4 Gene

  • GC01M147536
  • GC01M145637
  • GC01M146670
  • GC01M147111
  • GC01M146708
  • GC01M148161
  • GC01M149895
  • GC01M121275

Summaries for SF3B4 Gene

Entrez Gene Summary for SF3B4 Gene

  • This gene encodes one of four subunits of the splicing factor 3B. The protein encoded by this gene cross-links to a region in the pre-mRNA immediately upstream of the branchpoint sequence in pre-mRNA in the prespliceosomal complex A. It also may be involved in the assembly of the B, C and E spliceosomal complexes. In addition to RNA-binding activity, this protein interacts directly and highly specifically with subunit 2 of the splicing factor 3B. This protein contains two N-terminal RNA-recognition motifs (RRMs), consistent with the observation that it binds directly to pre-mRNA. [provided by RefSeq, Jul 2008]

GeneCards Summary for SF3B4 Gene

SF3B4 (Splicing Factor 3b Subunit 4) is a Protein Coding gene. Diseases associated with SF3B4 include Acrofacial Dysostosis 1, Nager Type and Hereditary Hearing Loss And Deafness. Among its related pathways are mRNA Splicing - Major Pathway and Gene Expression. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and nucleotide binding.

UniProtKB/Swiss-Prot for SF3B4 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. 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). May also be involved in the assembly of the E complex. SF3B4 has been found in complex B and C as well (PubMed:10882114). Belongs also to the minor U12-dependent spliceosome, which is involved in the splicing of rare class of nuclear pre-mRNA intron (PubMed:15146077).

Gene Wiki entry for SF3B4 Gene

Additional gene information for SF3B4 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SF3B4 Gene

Genomics for SF3B4 Gene

GeneHancer (GH) Regulatory Elements for SF3B4 Gene

Promoters and enhancers for SF3B4 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
GH01I149926 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 575.7 -0.5 -461 4.1 PKNOX1 SMAD1 ARNT ARID4B SIN3A FEZF1 DMAP1 YY1 SLC30A9 POLR2B SF3B4 GC01M149927 PIR45673 SETDB1 SV2A PRPF3 GOLPH3L UBE2D3P3 RPRD2 APH1A
GH01I149883 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 106.5 +41.6 41641 5.9 CLOCK MLX ZFP64 FEZF1 IRF4 YY1 ZNF213 E2F8 ZNF143 SP3 HIST2H2AB BOLA1 HIST2H2AC HIST2H2BE GC01M149896 PRPF3 SF3B4 UBE2D3P3 ARNT GOLPH3L
GH01I149156 Promoter/Enhancer 2.3 FANTOM5 Ensembl ENCODE dbSUPER 74.6 +768.0 768008 7.8 HDGF HNRNPUL1 PKNOX1 FOXA2 SMAD1 MLX ZFP64 ARID4B SIN3A DMAP1 LOC647481 SF3B4 HIST2H2BD VPS45 LOC101927468 HIST2H2AB HIST2H2BC ENSG00000227700 ENSG00000261716 PDE4DIP
GH01I150232 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 71.6 -306.8 -306792 4.8 CLOCK MLX DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 ANP32E GC01P150237 RNU2-17P SETDB1 PRPF3 PIP5K1A GABPB2 SF3B4 ARNT UBE2D3P3
GH01I150486 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 57.3 -559.3 -559296 1.7 CLOCK ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 TARS2 SETDB1 PRPF3 GABPB2 PIP5K1A SF3B4 PI4KB ZNF687 UBE2D3P3 RPRD2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SF3B4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SF3B4 gene promoter:

Genomic Locations for SF3B4 Gene

Genomic Locations for SF3B4 Gene
chr1:149,923,317-149,928,344
(GRCh38/hg38)
Size:
5,028 bases
Orientation:
Minus strand
chr1:149,895,209-149,900,236
(GRCh37/hg19)

Genomic View for SF3B4 Gene

Genes around SF3B4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SF3B4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SF3B4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SF3B4 Gene

Proteins for SF3B4 Gene

  • Protein details for SF3B4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q15427-SF3B4_HUMAN
    Recommended name:
    Splicing factor 3B subunit 4
    Protein Accession:
    Q15427
    Secondary Accessions:
    • Q5SZ63

    Protein attributes for SF3B4 Gene

    Size:
    424 amino acids
    Molecular mass:
    44386 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:27720643, PubMed:28541300). SF3B associates with the splicing factor SF3A and a 12S RNA unit to form the U2 small nuclear ribonucleoproteins complex (U2 snRNP) (PubMed:12234937). Interacts directly with SF3B2. Found in a complex with PRMT9, SF3B2 and SF3B4 (PubMed:25737013). 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 SF3B4 Gene

neXtProt entry for SF3B4 Gene

Post-translational modifications for SF3B4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SF3B4 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SF3B4 Gene

Domains & Families for SF3B4 Gene

Gene Families for SF3B4 Gene

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

Suggested Antigen Peptide Sequences for SF3B4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q15427

UniProtKB/Swiss-Prot:

SF3B4_HUMAN :
  • Belongs to the SF3B4 family.
Family:
  • Belongs to the SF3B4 family.
genes like me logo Genes that share domains with SF3B4: view

Function for SF3B4 Gene

Molecular function for SF3B4 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. 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). May also be involved in the assembly of the E complex. SF3B4 has been found in complex B and C as well (PubMed:10882114). Belongs also to the minor U12-dependent spliceosome, which is involved in the splicing of rare class of nuclear pre-mRNA intron (PubMed:15146077).

Phenotypes From GWAS Catalog for SF3B4 Gene

Gene Ontology (GO) - Molecular Function for SF3B4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding HDA,IEA 22658674
GO:0005515 protein binding IPI 16189514
genes like me logo Genes that share ontologies with SF3B4: view
genes like me logo Genes that share phenotypes with SF3B4: view

Human Phenotype Ontology for SF3B4 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

miRNA for SF3B4 Gene

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for SF3B4 Gene

Localization for SF3B4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SF3B4 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 SF3B4 gene
Compartment Confidence
nucleus 5
cytosol 2
golgi apparatus 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SF3B4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IDA 9731529
GO:0005689 U12-type spliceosomal complex IDA 15146077
genes like me logo Genes that share ontologies with SF3B4: view

Pathways & Interactions for SF3B4 Gene

genes like me logo Genes that share pathways with SF3B4: view

Pathways by source for SF3B4 Gene

1 KEGG pathway for SF3B4 Gene

Gene Ontology (GO) - Biological Process for SF3B4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000375 RNA splicing, via transesterification reactions TAS 7958871
GO:0000398 mRNA splicing, via spliceosome TAS,IC --
GO:0006397 mRNA processing TAS 7958871
GO:0008380 RNA splicing TAS 7958871
GO:0048026 positive regulation of mRNA splicing, via spliceosome IEA --
genes like me logo Genes that share ontologies with SF3B4: view

No data available for SIGNOR curated interactions for SF3B4 Gene

Drugs & Compounds for SF3B4 Gene

No Compound Related Data Available

Transcripts for SF3B4 Gene

mRNA/cDNA for SF3B4 Gene

Unigene Clusters for SF3B4 Gene

Splicing factor 3b, subunit 4, 49kDa:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SF3B4 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5a · 5b · 5c ^ 6 ^ 7a · 7b
SP1: -
SP2: -
SP3:
SP4:

Relevant External Links for SF3B4 Gene

GeneLoc Exon Structure for
SF3B4
ECgene alternative splicing isoforms for
SF3B4

Expression for SF3B4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SF3B4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SF3B4 Gene

This gene is overexpressed in Pancreas (15.0) and Peripheral blood mononuclear cells (10.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SF3B4 Gene



Protein tissue co-expression partners for SF3B4 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SF3B4 Gene:

SF3B4

SOURCE GeneReport for Unigene cluster for SF3B4 Gene:

Hs.516160

Evidence on tissue expression from TISSUES for SF3B4 Gene

  • Skin(4.6)
  • Nervous system(3.3)
  • Lung(2.6)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SF3B4 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • cerebellum
  • cerebrospinal fluid
  • cheek
  • chin
  • ear
  • epiglottis
  • eye
  • eyelid
  • face
  • forehead
  • head
  • inner ear
  • jaw
  • larynx
  • lip
  • mandible
  • maxilla
  • meninges
  • middle ear
  • mouth
  • neck
  • nose
  • outer ear
  • pharynx
  • skull
  • vocal cord
Thorax:
  • chest wall
  • heart
  • heart valve
  • lung
  • rib
  • rib cage
  • trachea
Abdomen:
  • abdominal wall
  • duodenum
  • intestine
  • kidney
  • large intestine
  • small intestine
  • stomach
Pelvis:
  • pelvis
  • uterus
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • finger
  • foot
  • forearm
  • hand
  • hip
  • knee
  • lower limb
  • radius
  • shoulder
  • thigh
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • hair
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with SF3B4: view

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for SF3B4 Gene

Orthologs for SF3B4 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SF3B4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SF3B4 33 34
  • 99.53 (n)
oppossum
(Monodelphis domestica)
Mammalia SF3B4 34
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SF3B4 33 34
  • 94.42 (n)
dog
(Canis familiaris)
Mammalia SF3B4 33 34
  • 91.59 (n)
rat
(Rattus norvegicus)
Mammalia Sf3b4 33
  • 91.04 (n)
mouse
(Mus musculus)
Mammalia Sf3b4 33 16 34
  • 90.17 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SF3B4 34
  • 56 (a)
OneToOne
chicken
(Gallus gallus)
Aves SF3B4 33 34
  • 78.22 (n)
lizard
(Anolis carolinensis)
Reptilia SF3B4 34
  • 88 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Spx-prov 33
African clawed frog
(Xenopus laevis)
Amphibia spx-prov 33
zebrafish
(Danio rerio)
Actinopterygii sf3b4 33 34
  • 70.25 (n)
fruit fly
(Drosophila melanogaster)
Insecta Spx 35 34
  • 81 (a)
worm
(Caenorhabditis elegans)
Secernentea sap-49 35 34
  • 73 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes HSH49 34 36
  • 33 (a)
OneToMany
rice
(Oryza sativa)
Liliopsida Os.5866 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 60 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4595 33
Species where no ortholog for SF3B4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SF3B4 Gene

ENSEMBL:
Gene Tree for SF3B4 (if available)
TreeFam:
Gene Tree for SF3B4 (if available)

Paralogs for SF3B4 Gene

(11) SIMAP similar genes for SF3B4 Gene using alignment to 2 proteins:

Pseudogenes.org Pseudogenes for SF3B4 Gene

genes like me logo Genes that share paralogs with SF3B4: view

No data available for Paralogs for SF3B4 Gene

Variants for SF3B4 Gene

Sequence variations from dbSNP and Humsavar for SF3B4 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs113949235 likely-benign, Nager syndrome 149,926,014(-) G/A coding_sequence_variant, synonymous_variant
rs115070660 conflicting-interpretations-of-pathogenicity, likely-benign, not specified, Nager syndrome 149,926,400(-) A/G coding_sequence_variant, synonymous_variant
rs143105666 likely-benign, Nager syndrome 149,926,563(-) G/A/C coding_sequence_variant, synonymous_variant
rs148753561 uncertain-significance, Nager syndrome 149,926,482(-) C/T coding_sequence_variant, synonymous_variant
rs17643644 benign, Nager syndrome 149,928,056(-) G/A 5_prime_UTR_variant

Structural Variations from Database of Genomic Variants (DGV) for SF3B4 Gene

Variant ID Type Subtype PubMed ID
nsv831537 CNV loss 17160897

Variation tolerance for SF3B4 Gene

Residual Variation Intolerance Score: 28.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.08; 1.86% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SF3B4 Gene

Human Gene Mutation Database (HGMD)
SF3B4
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SF3B4

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SF3B4 Gene

Disorders for SF3B4 Gene

MalaCards: The human disease database

(8) MalaCards diseases for SF3B4 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
acrofacial dysostosis 1, nager type
  • afd1
hereditary hearing loss and deafness
acrofacial dysostosis syndrome of rodriguez
  • rodriguez lethal acrofacial dysostosis syndrome
acrofacial dysostosis
radioulnar synostosis
  • congenital radioulnar synostosis
- elite association - COSMIC cancer census association via MalaCards
Search SF3B4 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SF3B4_HUMAN
  • Acrofacial dysostosis 1, Nager type (AFD1) [MIM:154400]: A form of acrofacial dysostosis, a group of disorders which are characterized by malformation of the craniofacial skeleton and the limbs. The major facial features of AFD1 include downslanted palpebral fissures, midface retrusion, and micrognathia, the latter of which often requires the placement of a tracheostomy in early childhood. Limb defects typically involve the anterior (radial) elements of the upper limbs and manifest as small or absent thumbs, triphalangeal thumbs, radial hyoplasia or aplasia, and radioulnar synostosis. Phocomelia of the upper limbs and, occasionally, lower-limb defects have also been reported. {ECO:0000269 PubMed:22541558}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for SF3B4

genes like me logo Genes that share disorders with SF3B4: view

No data available for Genatlas for SF3B4 Gene

Publications for SF3B4 Gene

  1. The prespliceosome components SAP 49 and SAP 145 interact in a complex implicated in tethering U2 snRNP to the branch site. (PMID: 7958871) Champion-Arnaud P … Reed R (Genes & development 1994) 2 3 4 22 58
  2. Haploinsufficiency of SF3B4, a component of the pre-mRNA spliceosomal complex, causes Nager syndrome. (PMID: 22541558) Bernier FP … Parboosingh JS (American journal of human genetics 2012) 3 4 58
  3. Many sequence variants affecting diversity of adult human height. (PMID: 18391951) Gudbjartsson DF … Stefansson K (Nature genetics 2008) 3 44 58
  4. Splicing factor 3b subunit 4 binds BMPR-IA and inhibits osteochondral cell differentiation. (PMID: 17513295) Watanabe H … Watanabe H (The Journal of biological chemistry 2007) 3 22 58
  5. Human immunodeficiency virus type 1 Vpr induces G2 checkpoint activation by interacting with the splicing factor SAP145. (PMID: 16923959) Terada Y … Yasuda Y (Molecular and cellular biology 2006) 3 22 58

Products for SF3B4 Gene

Sources for SF3B4 Gene

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