Details for: SF3B4

Gene ID: 10262

Symbol: SF3B4

Ensembl ID: ENSG00000143368

Description: splicing factor 3b subunit 4

Associated with

Cells (max top 100)

(Marker Scores and respective Thresholds are uniquely calculated using our advanced thresholding algorithms to reveal cell-specific gene markers)

  • Cell Name: tracheobronchial smooth muscle cell (CL0019019)
    Fold Change: 3.41
    Marker Score: 1,000
  • Cell Name: skeletal muscle satellite cell (CL0000594)
    Fold Change: 3.19
    Marker Score: 2,133
  • Cell Name: extravillous trophoblast (CL0008036)
    Fold Change: 2.67
    Marker Score: 2,384
  • Cell Name: myeloid dendritic cell (CL0000782)
    Fold Change: 2.63
    Marker Score: 1,595
  • Cell Name: CD14-low, CD16-positive monocyte (CL0002396)
    Fold Change: 2.54
    Marker Score: 1,790
  • Cell Name: blood cell (CL0000081)
    Fold Change: 1.73
    Marker Score: 20,118
  • Cell Name: erythroid progenitor cell (CL0000038)
    Fold Change: 1.58
    Marker Score: 1,652
  • Cell Name: oogonial cell (CL0000024)
    Fold Change: 1.58
    Marker Score: 2,272
  • Cell Name: male germ cell (CL0000015)
    Fold Change: 1.57
    Marker Score: 452
  • Cell Name: Unknown (CL0002371)
    Fold Change: 1.56
    Marker Score: 1,659
  • Cell Name: neural cell (CL0002319)
    Fold Change: 1.56
    Marker Score: 753
  • Cell Name: ovarian surface epithelial cell (CL2000064)
    Fold Change: 1.53
    Marker Score: 4,163
  • Cell Name: primordial germ cell (CL0000670)
    Fold Change: 1.53
    Marker Score: 1,915
  • Cell Name: placental villous trophoblast (CL2000060)
    Fold Change: 1.53
    Marker Score: 5,999
  • Cell Name: thymocyte (CL0000893)
    Fold Change: 1.52
    Marker Score: 1,588
  • Cell Name: fraction A pre-pro B cell (CL0002045)
    Fold Change: 1.45
    Marker Score: 1,462
  • Cell Name: medullary thymic epithelial cell (CL0002365)
    Fold Change: 1.44
    Marker Score: 2,356
  • Cell Name: erythroid progenitor cell, mammalian (CL0001066)
    Fold Change: 1.43
    Marker Score: 459
  • Cell Name: basal cell of epithelium of trachea (CL1000348)
    Fold Change: 1.43
    Marker Score: 10,645
  • Cell Name: interstitial cell of ovary (CL0002094)
    Fold Change: 1.43
    Marker Score: 9,272
  • Cell Name: tonsil germinal center B cell (CL2000006)
    Fold Change: 1.41
    Marker Score: 4,186
  • Cell Name: CD4-positive, alpha-beta memory T cell, CD45RO-positive (CL0001204)
    Fold Change: 1.41
    Marker Score: 9,014
  • Cell Name: CD8-alpha-alpha-positive, alpha-beta intraepithelial T cell (CL0000915)
    Fold Change: 1.4
    Marker Score: 1,975
  • Cell Name: Unknown (CL0000548)
    Fold Change: 1.37
    Marker Score: 999
  • Cell Name: respiratory epithelial cell (CL0002368)
    Fold Change: 1.37
    Marker Score: 753
  • Cell Name: large pre-B-II cell (CL0000957)
    Fold Change: 1.36
    Marker Score: 3,687
  • Cell Name: plasmablast (CL0000980)
    Fold Change: 1.35
    Marker Score: 1,800
  • Cell Name: double negative T regulatory cell (CL0011024)
    Fold Change: 1.35
    Marker Score: 1,307
  • Cell Name: bladder urothelial cell (CL1001428)
    Fold Change: 1.33
    Marker Score: 1,960
  • Cell Name: retinal ganglion cell (CL0000740)
    Fold Change: 1.32
    Marker Score: 1,652
  • Cell Name: epithelial cell of nephron (CL1000449)
    Fold Change: 1.32
    Marker Score: 2,759
  • Cell Name: CD34-positive, CD38-negative hematopoietic stem cell (CL0001024)
    Fold Change: 1.31
    Marker Score: 951
  • Cell Name: double-positive, alpha-beta thymocyte (CL0000809)
    Fold Change: 1.31
    Marker Score: 2,568
  • Cell Name: progenitor cell of mammary luminal epithelium (CL0009116)
    Fold Change: 1.3
    Marker Score: 5,020
  • Cell Name: kidney epithelial cell (CL0002518)
    Fold Change: 1.27
    Marker Score: 1,347
  • Cell Name: hematopoietic cell (CL0000988)
    Fold Change: 1.27
    Marker Score: 842
  • Cell Name: hematopoietic stem cell (CL0000037)
    Fold Change: 1.25
    Marker Score: 658
  • Cell Name: Leydig cell (CL0000178)
    Fold Change: 1.25
    Marker Score: 1,344
  • Cell Name: mesodermal cell (CL0000222)
    Fold Change: 1.25
    Marker Score: 16,436
  • Cell Name: hematopoietic precursor cell (CL0008001)
    Fold Change: 1.24
    Marker Score: 434
  • Cell Name: primitive red blood cell (CL0002355)
    Fold Change: 1.24
    Marker Score: 927
  • Cell Name: proerythroblast (CL0000547)
    Fold Change: 1.24
    Marker Score: 838
  • Cell Name: granulosa cell (CL0000501)
    Fold Change: 1.23
    Marker Score: 12,370
  • Cell Name: mesenchymal cell (CL0008019)
    Fold Change: 1.23
    Marker Score: 2,083
  • Cell Name: keratinocyte (CL0000312)
    Fold Change: 1.21
    Marker Score: 1,008
  • Cell Name: type A enteroendocrine cell (CL0002067)
    Fold Change: 1.2
    Marker Score: 484
  • Cell Name: mature T cell (CL0002419)
    Fold Change: 1.19
    Marker Score: 11,779
  • Cell Name: mature gamma-delta T cell (CL0000800)
    Fold Change: 1.19
    Marker Score: 3,752
  • Cell Name: oocyte (CL0000023)
    Fold Change: 1.18
    Marker Score: 292
  • Cell Name: CD8-positive, alpha-beta memory T cell (CL0000909)
    Fold Change: 1.18
    Marker Score: 1,000
  • Cell Name: decidual cell (CL2000002)
    Fold Change: 1.17
    Marker Score: 5,028
  • Cell Name: CD14-positive, CD16-positive monocyte (CL0002397)
    Fold Change: 1.17
    Marker Score: 2,270
  • Cell Name: kidney cell (CL1000497)
    Fold Change: 1.15
    Marker Score: 769
  • Cell Name: cortical thymic epithelial cell (CL0002364)
    Fold Change: 1.15
    Marker Score: 4,259
  • Cell Name: neuroblast (sensu Vertebrata) (CL0000031)
    Fold Change: 1.13
    Marker Score: 710
  • Cell Name: class switched memory B cell (CL0000972)
    Fold Change: 1.13
    Marker Score: 1,061
  • Cell Name: pro-T cell (CL0000827)
    Fold Change: 1.13
    Marker Score: 4,612
  • Cell Name: migratory enteric neural crest cell (CL0002607)
    Fold Change: 1.12
    Marker Score: 1,058
  • Cell Name: effector memory CD8-positive, alpha-beta T cell, terminally differentiated (CL0001062)
    Fold Change: 1.11
    Marker Score: 1,633
  • Cell Name: pancreatic ductal cell (CL0002079)
    Fold Change: 1.11
    Marker Score: 1,151
  • Cell Name: CD4-positive, alpha-beta thymocyte (CL0000810)
    Fold Change: 1.11
    Marker Score: 618
  • Cell Name: ciliated columnar cell of tracheobronchial tree (CL0002145)
    Fold Change: 1.09
    Marker Score: 9,474
  • Cell Name: B-1 B cell (CL0000819)
    Fold Change: 1.09
    Marker Score: 1,901
  • Cell Name: megakaryocyte (CL0000556)
    Fold Change: 1.09
    Marker Score: 617
  • Cell Name: early lymphoid progenitor (CL0000936)
    Fold Change: 1.09
    Marker Score: 532
  • Cell Name: T-helper 22 cell (CL0001042)
    Fold Change: 1.08
    Marker Score: 4,632
  • Cell Name: CD14-positive, CD16-negative classical monocyte (CL0002057)
    Fold Change: 1.08
    Marker Score: 60,169
  • Cell Name: colon epithelial cell (CL0011108)
    Fold Change: 1.07
    Marker Score: 3,366
  • Cell Name: classical monocyte (CL0000860)
    Fold Change: 1.07
    Marker Score: 4,447
  • Cell Name: pancreatic stellate cell (CL0002410)
    Fold Change: 1.07
    Marker Score: 675
  • Cell Name: late promyelocyte (CL0002151)
    Fold Change: 1.07
    Marker Score: 268
  • Cell Name: conjunctival epithelial cell (CL1000432)
    Fold Change: 1.06
    Marker Score: 1,112
  • Cell Name: mature alpha-beta T cell (CL0000791)
    Fold Change: 1.05
    Marker Score: 55,507
  • Cell Name: Sertoli cell (CL0000216)
    Fold Change: 1.04
    Marker Score: 6,195
  • Cell Name: elicited macrophage (CL0000861)
    Fold Change: 1.04
    Marker Score: 6,341
  • Cell Name: malignant cell (CL0001064)
    Fold Change: 1.04
    Marker Score: 13,986
  • Cell Name: CD4-positive, alpha-beta cytotoxic T cell (CL0000934)
    Fold Change: 1.04
    Marker Score: 910
  • Cell Name: central memory CD8-positive, alpha-beta T cell (CL0000907)
    Fold Change: 1.04
    Marker Score: 2,527
  • Cell Name: enteric smooth muscle cell (CL0002504)
    Fold Change: 1.03
    Marker Score: 2,430
  • Cell Name: neural crest cell (CL0011012)
    Fold Change: 1.03
    Marker Score: 1,102
  • Cell Name: mucosal invariant T cell (CL0000940)
    Fold Change: 1.03
    Marker Score: 912
  • Cell Name: eurydendroid cell (CL0000253)
    Fold Change: 1.02
    Marker Score: 418
  • Cell Name: small pre-B-II cell (CL0000954)
    Fold Change: 1.02
    Marker Score: 1,225
  • Cell Name: dendritic cell, human (CL0001056)
    Fold Change: 1.02
    Marker Score: 1,037
  • Cell Name: myeloid leukocyte (CL0000766)
    Fold Change: 1.02
    Marker Score: 1,226
  • Cell Name: CD16-negative, CD56-bright natural killer cell, human (CL0000938)
    Fold Change: 1.01
    Marker Score: 826
  • Cell Name: enteric neuron (CL0007011)
    Fold Change: 1
    Marker Score: 532
  • Cell Name: cerebral cortex GABAergic interneuron (CL0010011)
    Fold Change: 1
    Marker Score: 71,632
  • Cell Name: forebrain radial glial cell (CL0013000)
    Fold Change: 0.99
    Marker Score: 47,856
  • Cell Name: centrocyte (CL0009111)
    Fold Change: 0.99
    Marker Score: 236
  • Cell Name: late pro-B cell (CL0002048)
    Fold Change: 0.99
    Marker Score: 1,163
  • Cell Name: nephron tubule epithelial cell (CL1000494)
    Fold Change: 0.99
    Marker Score: 231
  • Cell Name: effector memory CD4-positive, alpha-beta T cell (CL0000905)
    Fold Change: 0.98
    Marker Score: 720
  • Cell Name: centroblast (CL0009112)
    Fold Change: 0.98
    Marker Score: 484
  • Cell Name: absorptive cell (CL0000212)
    Fold Change: 0.98
    Marker Score: 30,379
  • Cell Name: Hofbauer cell (CL3000001)
    Fold Change: 0.98
    Marker Score: 537
  • Cell Name: lung ciliated cell (CL1000271)
    Fold Change: 0.96
    Marker Score: 457
  • Cell Name: CD4-positive helper T cell (CL0000492)
    Fold Change: 0.96
    Marker Score: 1,046
  • Cell Name: smooth muscle cell (CL0000192)
    Fold Change: 0.96
    Marker Score: 631
  • Cell Name: naive thymus-derived CD8-positive, alpha-beta T cell (CL0000900)
    Fold Change: 0.96
    Marker Score: 1,713

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Marker Score to the Marker Score Threshold, indicating how much the gene expression has changed compared to a baseline.
Marker Score: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Marker Score to the Marker Score Threshold, indicating how much the gene expression has changed compared to a baseline.
Marker Score: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Marker Score to the Marker Score Threshold, indicating how much the gene expression has changed compared to a baseline.
Marker Score: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Other Information

**Key Characteristics:** SF3B4 is a critical subunit of the spliceosome complex, which is composed of several proteins and RNAs. This complex is responsible for recognizing and removing introns from pre-mRNA, a process known as splicing. SF3B4, along with other spliceosomal components, forms a dynamic assembly that undergoes conformational changes to facilitate the splicing reaction. The gene is significantly expressed in various cell types, including tracheobronchial smooth muscle cells, skeletal muscle satellite cells, and myeloid dendritic cells, highlighting its importance in different tissues. **Pathways and Functions:** The SF3B4 gene is involved in several key pathways, including: 1. **Metabolism of RNA**: SF3B4 plays a crucial role in the metabolism of RNA, ensuring the proper processing and maturation of pre-mRNA. 2. **mRNA Processing**: SF3B4 is essential for the removal of introns and the joining of exons to produce mature mRNA. 3. **mRNA Splicing**: SF3B4 is a key component of the spliceosome complex, facilitating the splicing reaction and the production of mature mRNA. 4. **Protein Binding**: SF3B4 interacts with other proteins to facilitate the assembly and function of the spliceosome complex. 5. **RNA Binding**: SF3B4 binds to RNA molecules, including pre-mRNA, to facilitate the splicing reaction. **Clinical Significance:** Dysregulation of SF3B4 has been implicated in various diseases, including: 1. **Spinal Muscular Atrophy**: SF3B4 mutations have been linked to spinal muscular atrophy, a genetic disorder characterized by muscle weakness and wasting. 2. **Immune System Disorders**: SF3B4 has been implicated in immune system disorders, including autoimmune diseases and cancer. 3. **Neurological Disorders**: SF3B4 has been linked to neurological disorders, including Alzheimer's disease and Parkinson's disease. In conclusion, SF3B4 is a critical gene that plays a vital role in RNA splicing, ensuring the accurate translation of genetic information into proteins. Its dysregulation has been implicated in various diseases, highlighting the importance of further research into the functions and clinical significance of this gene.

Genular Protein ID: 2906649069

Symbol: SF3B4_HUMAN

Name: Splicing factor 3B subunit 4

UniProtKB Accession Codes:

Q15427 Q5SZ63

Database IDs:

AGR 1 AlphaFoldDB 1 Antibodypedia 1 Bgee 1 BioGRID 1 BioGRID-ORCS 1 BioMuta 1 CCDS 1 CDD 2 CORUM 1 CTD 1 ChiTaRS 1 ComplexPortal 2 DMDM 1 DNASU 1 DisGeNET 1 EMBL 9 EMDB 17 EPD 1 Ensembl 1 EvolutionaryTrace 1 ExpressionAtlas 1 GO 15 Gene3D 1 GeneCards 1 GeneTree 1 GeneWiki 1 Genevisible 1 GenomeRNAi 1 GlyGen 1 HGNC 1 HOGENOM 1 HPA 1 InParanoid 1 IntAct 1 InterPro 5 KEGG 1 MANE-Select 1 MIM 3 MINT 1 MalaCards 1 MassIVE 1 MaxQB 1 NCBI Taxonomy 1 OMA 1 OpenTargets 1 Orphanet 2 OrthoDB 1 PANTHER 2 PDB 27 PDBsum 20 PIR 1 PRINTS 1 PRO 1 PROSITE 1 PROSITE-ProRule 1 PathwayCommons 1 PaxDb 1 PeptideAtlas 1 Pfam 1 PharmGKB 1 Pharos 1 PhosphoSitePlus 1 PhylomeDB 1 Proteomes 1 ProteomicsDB 1 Pumba 1 RNAct 1 Reactome 2 RefSeq 1 SAM 1 SIGNOR 1 SMART 1 SMR 1 STRING 1 SUPFAM 1 SignaLink 1 SwissPalm 1 TreeFam 1 UCSC 1 UniProtKB 1 VEuPathDB 1 eggNOG 1 iPTMnet 1 jPOST 1 neXtProt 1

Citations:

PubMed ID: 7958871

Title: The prespliceosome components SAP 49 and SAP 145 interact in a complex implicated in tethering U2 snRNP to the branch site.

PubMed ID: 7958871

DOI: 10.1101/gad.8.16.1974

PubMed ID: 16710414

Title: The DNA sequence and biological annotation of human chromosome 1.

PubMed ID: 16710414

DOI: 10.1038/nature04727

PubMed ID: 15489334

Title: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

PubMed ID: 15489334

DOI: 10.1101/gr.2596504

PubMed ID: 10882114

Title: Functional association of U2 snRNP with the ATP-independent spliceosomal complex E.

PubMed ID: 10882114

DOI: 10.1016/s1097-2765(00)80318-4

PubMed ID: 12234937

Title: Characterization of novel SF3b and 17S U2 snRNP proteins, including a human Prp5p homologue and an SF3b DEAD-box protein.

PubMed ID: 12234937

DOI: 10.1093/emboj/cdf480

PubMed ID: 12738865

Title: Molecular architecture of the multiprotein splicing factor SF3b.

PubMed ID: 12738865

DOI: 10.1126/science.1084155

PubMed ID: 15146077

Title: The human 18S U11/U12 snRNP contains a set of novel proteins not found in the U2-dependent spliceosome.

PubMed ID: 15146077

DOI: 10.1261/rna.7320604

PubMed ID: 15592455

Title: Immunoaffinity profiling of tyrosine phosphorylation in cancer cells.

PubMed ID: 15592455

DOI: 10.1038/nbt1046

PubMed ID: 19413330

Title: Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.

PubMed ID: 19413330

DOI: 10.1021/ac9004309

PubMed ID: 21269460

Title: Initial characterization of the human central proteome.

PubMed ID: 21269460

DOI: 10.1186/1752-0509-5-17

PubMed ID: 22541558

Title: Haploinsufficiency of SF3B4, a component of the pre-mRNA spliceosomal complex, causes Nager syndrome.

PubMed ID: 22541558

DOI: 10.1016/j.ajhg.2012.04.004

PubMed ID: 22223895

Title: Comparative large-scale characterisation of plant vs. mammal proteins reveals similar and idiosyncratic N-alpha acetylation features.

PubMed ID: 22223895

DOI: 10.1074/mcp.m111.015131

PubMed ID: 22814378

Title: N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB.

PubMed ID: 22814378

DOI: 10.1073/pnas.1210303109

PubMed ID: 25737013

Title: PRMT9 is a type II methyltransferase that methylates the splicing factor SAP145.

PubMed ID: 25737013

DOI: 10.1038/ncomms7428

PubMed ID: 27720643

Title: Molecular architecture of SF3b and structural consequences of its cancer-related mutations.

PubMed ID: 27720643

DOI: 10.1016/j.molcel.2016.08.036

PubMed ID: 28541300

Title: Splicing modulators act at the branch point adenosine binding pocket defined by the PHF5A-SF3b complex.

PubMed ID: 28541300

DOI: 10.1038/ncomms15522

PubMed ID: 32494006

Title: Molecular architecture of the human 17S U2 snRNP.

PubMed ID: 32494006

DOI: 10.1038/s41586-020-2344-3

PubMed ID: 33509932

Title: Structure of the activated human minor spliceosome.

PubMed ID: 33509932

DOI: 10.1126/science.abg0879

PubMed ID: 36797247

Title: Mechanisms of the RNA helicases DDX42 and DDX46 in human U2 snRNP assembly.

PubMed ID: 36797247

DOI: 10.1038/s41467-023-36489-x

Sequence Information:

  • Length: 424
  • Mass: 44386
  • Checksum: 212472A25D3FF002
  • Sequence:
    • MAAGPISERN QDATVYVGGL DEKVSEPLLW ELFLQAGPVV NTHMPKDRVT GQHQGYGFVE 
FLSEEDADYA IKIMNMIKLY GKPIRVNKAS AHNKNLDVGA NIFIGNLDPE IDEKLLYDTF 
SAFGVILQTP KIMRDPDTGN SKGYAFINFA SFDASDAAIE AMNGQYLCNR PITVSYAFKK 
DSKGERHGSA AERLLAAQNP LSQADRPHQL FADAPPPPSA PNPVVSSLGS GLPPPGMPPP 
GSFPPPVPPP GALPPGIPPA MPPPPMPPGA AGHGPPSAGT PGAGHPGHGH SHPHPFPPGG 
MPHPGMSQMQ LAHHGPHGLG HPHAGPPGSG GQPPPRPPPG MPHPGPPPMG MPPRGPPFGS 
PMGHPGPMPP HGMRGPPPLM PPHGYTGPPR PPPYGYQRGP LPPPRPTPRP PVPPRGPLRG 
PLPQ

Genular Protein ID: 833954717

Symbol: B3KUJ0_HUMAN

Name: N/A

UniProtKB Accession Codes:

B3KUJ0

Database IDs:

ARBA 5 AlphaFoldDB 1 BioGRID-ORCS 1 CDD 2 CTD 1 DNASU 1 EMBL 2 GO 2 Gene3D 1 Genevisible 1 GenomeRNAi 1 IntAct 1 InterPro 5 KEGG 1 NCBI Taxonomy 1 OrthoDB 1 PANTHER 2 PRINTS 1 PROSITE 2 PROSITE-ProRule 1 PeptideAtlas 1 Pfam 1 RefSeq 1 SAM 1 SMART 1 SUPFAM 1

Citations:

PubMed ID: 14702039

Title: Complete sequencing and characterization of 21,243 full-length human cDNAs.

PubMed ID: 14702039

DOI: 10.1038/ng1285

Sequence Information:

  • Length: 424
  • Mass: 44484
  • Checksum: A01CDBDF5992621F
  • Sequence:
    • MAAGPISERN QDATVYVGGL DEKVSEPLLW ELFLQAGPVV NTHMPKDRVT GQHQGYGFVE 
FLSEEDADYA IKIMNMIKLY GKPIRVNKAL AHNKNLDVGA NIFIENLDPE IDEKLLYDTF 
SAFGVILQTP KIMRDPDTGN SKGYAFINFA SFDASDAAIE AMNGQYLCNR PITVSYAFKK 
DSKGERHGSA AERLLAAQNP LSQADRPHQL FADAPPPPSA PNPVVSSLGS GLPPPGMPPP 
GSFPPPVPPP GALPPGIPPA MPPPPMPPGA AGHGPPSAGT PGAGHPGHGH SHPHPFPPGG 
MPHPGMSQMQ LAHHGPHGLG HPHAGPPGSG GQPPPRPPPG MPHPGPPPMG MPPRGPPFGS 
PMGHPGPMPP HGMRGPPPLM PPHGYTGPPR PPPYGYQRGP LPPPRPTPRP PVPPRGPLRG 
PLPQ

Database document:

This is a preview of the gene's schema. Only a few entries are kept for 'singleCellExpressions,' 'mRNAExpressions,' and other large data arrays for visualization purposes. You can zoom in with the mouse wheel for a closer view, and the text will adjust automatically if necessary. For the full schema, download it here.