Human Gene SF3B4 (uc009wll.1)
  Description: Homo sapiens splicing factor 3b, subunit 4, 49kDa (SF3B4), mRNA.
RefSeq Summary (NM_005850): 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].
Transcript (Including UTRs)
   Position: hg19 chr1:149,897,438-149,899,962 Size: 2,525 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg19 chr1:149,897,546-149,899,651 Size: 2,106 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:149,897,438-149,899,962)mRNA (may differ from genome)Protein (364 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
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MGIneXtProtOMIMPubMedReactomeTreefam
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SF3B4_HUMAN
DESCRIPTION: RecName: Full=Splicing factor 3B subunit 4; AltName: Full=Pre-mRNA-splicing factor SF3b 49 kDa subunit; AltName: Full=SF3b50; AltName: Full=Spliceosome-associated protein 49; Short=SAP 49;
FUNCTION: Subunit of the splicing factor SF3B 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. May also be involved in the assembly of the 'E' complex. SF3B4 has been found in complex 'B' and 'C' as well. Belongs also to the minor U12- dependent spliceosome, which is involved in the splicing of rare class of nuclear pre-mRNA intron.
SUBUNIT: Component of splicing factor SF3B which is composed of at least eight subunits; SF3B1/SAP155/SF3B155, SF3B2/SAP145/SF3B145, SF3B3/SAP130/SF3B130, SF3B4/SAP49/SF3B49, SF3B14A, PHF5A/SF3B14B, SF3B10 and SF3B125. SF3B associates with the splicing factor SF3A and a 12S RNA unit to form the U2 small nuclear ribonucleoproteins complex (U2 snRNP). Component of the U11/U12 snRNPs that are part of the U12-type spliceosome. SF3B4 interacts directly with SF3B2.
INTERACTION: P62993:GRB2; NbExp=2; IntAct=EBI-348469, EBI-401755;
SUBCELLULAR LOCATION: Nucleus (By similarity).
DISEASE: Defects in SF3B4 are the cause of acrofacial dysostosis type 1 (AFD1) [MIM:154400]. AFD1 is 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.
SIMILARITY: Belongs to the SF3B4 family.
SIMILARITY: Contains 2 RRM (RNA recognition motif) domains.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SF3B4
CDC HuGE Published Literature: SF3B4
Positive Disease Associations: height
Related Studies:
  1. height
    Gudbjartsson ,et al. 2008, Many sequence variants affecting diversity of adult human height, Nature genetics 2008 40- 5 : 609-15. [PubMed 18391951]

-  MalaCards Disease Associations
  MalaCards Gene Search: SF3B4
Diseases sorted by gene-association score: acrofacial dysostosis 1, nager type* (1378), acrofacial dysostosis syndrome of rodriguez* (368), acrofacial dysostosis (19), radioulnar synostosis (12), phocomelia (11), dysostosis (10), treacher collins syndrome 1 (6)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 48.41 RPKM in Testis
Total median expression: 1159.53 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -121.00311-0.389 Picture PostScript Text
3' UTR -14.60108-0.135 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR012677 - Nucleotide-bd_a/b_plait
IPR000504 - RRM_dom

Pfam Domains:
PF00076 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
PF13893 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)

SCOP Domains:
54928 - RNA-binding domain, RBD

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1X5T - NMR MuPIT 1X5U - NMR


ModBase Predicted Comparative 3D Structure on Q15427
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsemblFlyBaseWormBaseSGD
 Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence
 AlignmentAlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0005515 protein binding

Biological Process:
GO:0000375 RNA splicing, via transesterification reactions
GO:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0008380 RNA splicing
GO:0048026 positive regulation of mRNA splicing, via spliceosome

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0005689 U12-type spliceosomal complex


-  Descriptions from all associated GenBank mRNAs
  AK223322 - Homo sapiens mRNA for splicing factor 3b, subunit 4 variant, clone: TMS07207.
AK097315 - Homo sapiens cDNA FLJ39996 fis, clone STOMA2002166, highly similar to Splicing factor 3B subunit 4.
BC004273 - Homo sapiens splicing factor 3b, subunit 4, 49kDa, mRNA (cDNA clone MGC:10828 IMAGE:3615080), complete cds.
BC013886 - Homo sapiens splicing factor 3b, subunit 4, 49kDa, mRNA (cDNA clone MGC:11086 IMAGE:3829990), complete cds.
BC090883 - Homo sapiens splicing factor 3b, subunit 4, 49kDa, mRNA (cDNA clone MGC:102968 IMAGE:30386953), complete cds.
KJ892980 - Synthetic construct Homo sapiens clone ccsbBroadEn_02374 SF3B4 gene, encodes complete protein.
DQ892971 - Synthetic construct clone IMAGE:100005601; FLH191283.01X; RZPDo839B0777D splicing factor 3b, subunit 4, 49kDa (SF3B4) gene, encodes complete protein.
DQ896220 - Synthetic construct Homo sapiens clone IMAGE:100010680; FLH263613.01L; RZPDo839B0967D splicing factor 3b, subunit 4, 49kDa (SF3B4) gene, encodes complete protein.
EU176749 - Synthetic construct Homo sapiens clone IMAGE:100011580; FLH263614.01L; RZPDo839H11255D splicing factor 3b, subunit 4, 49kDa (SF3B4) gene, encodes complete protein.
AB528332 - Synthetic construct DNA, clone: pF1KB6663, Homo sapiens SF3B4 gene for splicing factor 3b, subunit 4, 49kDa, without stop codon, in Flexi system.
AK310495 - Homo sapiens cDNA, FLJ17537.
CU680692 - Synthetic construct Homo sapiens gateway clone IMAGE:100017240 5' read SF3B4 mRNA.
DQ584562 - Homo sapiens piRNA piR-51674, complete sequence.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa03040 - Spliceosome

Reactome (by CSHL, EBI, and GO)

Protein Q15427 (Reactome details) participates in the following event(s):

R-HSA-72124 Formation of the Spliceosomal A Complex
R-HSA-75080 Formation of AT-AC A complex
R-HSA-75083 ATAC spliceosome mediated 3' splice site cleavage, exon ligation
R-HSA-72143 Lariat Formation and 5'-Splice Site Cleavage
R-HSA-72139 Formation of the active Spliceosomal C (B*) complex
R-HSA-72127 Formation of the Spliceosomal B Complex
R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex
R-HSA-156661 Formation of Exon Junction Complex
R-HSA-75081 Formation of AT-AC B Complex
R-HSA-75082 ATAC spliceosome mediated Lariat formation,5' splice site cleavage
R-HSA-75079 Formation of AT-AC C complex
R-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-72165 mRNA Splicing - Minor Pathway
R-HSA-72172 mRNA Splicing
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: AK310495, NM_005850, NP_005841, Q15427, Q5SZ63, SAP49, SF3B4_HUMAN
UCSC ID: uc009wll.1
RefSeq Accession: NM_005850
Protein: Q15427 (aka SF3B4_HUMAN or S3B4_HUMAN)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK310495.1
exon count: 4CDS single in 3' UTR: no RNA size: 1212
ORF size: 1095CDS single in intron: no Alignment % ID: 99.92
txCdsPredict score: 2196.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 290# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.