SF3B4 (splicing factor 3b subunit 4) - Rat Genome Database

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Gene: SF3B4 (splicing factor 3b subunit 4) Sus scrofa
Analyze
Symbol: SF3B4
Name: splicing factor 3b subunit 4
RGD ID: 14116599
Description: ENCODES a protein that exhibits RNA binding (inferred); splicing factor binding (inferred); INVOLVED IN positive regulation of mRNA splicing, via spliceosome (ortholog); PARTICIPATES IN spliceosome pathway; ASSOCIATED WITH cervical cancer (ortholog); gastrointestinal stromal tumor (ortholog); genetic disease (ortholog); FOUND IN U2-type spliceosomal complex (ortholog); INTERACTS WITH deoxynivalenol
Type: protein-coding
RefSeq Status: MODEL
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl499,123,585 - 99,129,218 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1499,123,564 - 99,129,218 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24108,590,400 - 108,596,048 (-)NCBISscrofa10.2Sscrofa10.2susScr3
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:14681463   PMID:17145712   PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
SF3B4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl499,123,585 - 99,129,218 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1499,123,564 - 99,129,218 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24108,590,400 - 108,596,048 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SF3B4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381149,923,317 - 149,927,803 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1149,923,317 - 149,927,803 (-)EnsemblGRCh38hg38GRCh38
GRCh371149,895,209 - 149,899,695 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361148,161,835 - 148,166,326 (-)NCBINCBI36Build 36hg18NCBI36
Build 341146,708,283 - 146,712,775NCBI
Celera1123,011,181 - 123,015,672 (-)NCBICelera
Cytogenetic Map1q21.2NCBI
HuRef1121,275,693 - 121,280,628 (-)NCBIHuRef
CHM1_11151,291,443 - 151,296,378 (-)NCBICHM1_1
T2T-CHM13v2.01149,047,800 - 149,055,723 (-)NCBIT2T-CHM13v2.0
Sf3b4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39396,079,822 - 96,084,880 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl396,079,648 - 96,084,880 (+)EnsemblGRCm39 Ensembl
GRCm38396,172,506 - 96,177,564 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl396,172,332 - 96,177,564 (+)EnsemblGRCm38mm10GRCm38
MGSCv37395,976,473 - 95,981,487 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36396,257,955 - 96,262,969 (+)NCBIMGSCv36mm8
Celera397,608,698 - 97,613,377 (+)NCBICelera
Cytogenetic Map3F2.1NCBI
cM Map341.65NCBI
Sf3b4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82186,421,667 - 186,426,419 (+)NCBIGRCr8
mRatBN7.22183,732,791 - 183,737,545 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2183,732,754 - 183,737,959 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2191,396,404 - 191,401,180 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02189,200,725 - 189,205,496 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02184,028,938 - 184,033,714 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02198,312,428 - 198,317,180 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2198,312,428 - 198,317,180 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02217,799,411 - 217,804,163 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42190,976,681 - 190,981,433 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12190,939,434 - 190,944,187 (+)NCBI
Celera2176,260,078 - 176,264,830 (+)NCBICelera
Cytogenetic Map2q34NCBI
Sf3b4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955413826,190 - 832,496 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955413826,190 - 830,502 (+)NCBIChiLan1.0ChiLan1.0
SF3B4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2199,909,044 - 99,915,823 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1199,665,027 - 99,670,781 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01125,268,113 - 125,273,405 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11128,924,317 - 128,929,610 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1128,924,317 - 128,929,610 (-)Ensemblpanpan1.1panPan2
SF3B4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11759,208,989 - 59,214,643 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1759,208,990 - 59,213,991 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1758,656,507 - 58,661,447 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01760,205,440 - 60,210,382 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1760,205,444 - 60,210,309 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11759,054,911 - 59,059,850 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01759,138,641 - 59,143,584 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01759,865,732 - 59,870,673 (-)NCBIUU_Cfam_GSD_1.0
Sf3b4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505821,230,367 - 21,234,846 (-)NCBIHiC_Itri_2
SpeTri2.0NW_004936580260,013 - 265,057 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SF3B4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Vero_WHO_p1.0NW_02366603813,378,934 - 13,383,927 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sf3b4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462477217,701,341 - 17,706,550 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462477217,701,930 - 17,706,613 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in SF3B4
157 total Variants

Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system hemolymphoid system musculoskeletal system nervous system renal system reproductive system respiratory system
High
Medium 1 1 2 3
Low 10 3 2 3 2 20 2 3 3
Below cutoff

Sequence


RefSeq Acc Id: ENSSSCT00000007303   ⟹   ENSSSCP00000007108
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl499,123,585 - 99,129,218 (+)Ensembl
RefSeq Acc Id: XM_001926489   ⟹   XP_001926524
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1499,123,564 - 99,129,218 (+)NCBI
Sequence:
RefSeq Acc Id: XP_001926524   ⟸   XM_001926489
- UniProtKB: F1SDG0 (UniProtKB/TrEMBL),   A0A8D1J3P2 (UniProtKB/TrEMBL),   A0A8D1SB76 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSSSCP00000007108   ⟸   ENSSSCT00000007303
Protein Domains
RRM


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000006665 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCG00005017918 UniProtKB/TrEMBL
  ENSSSCG00015003392 UniProtKB/TrEMBL
  ENSSSCG00025066588 UniProtKB/TrEMBL
  ENSSSCG00030052051 UniProtKB/TrEMBL
  ENSSSCG00035050269 UniProtKB/TrEMBL
  ENSSSCG00040027292 UniProtKB/TrEMBL
  ENSSSCG00045034871 UniProtKB/TrEMBL
  ENSSSCG00050078287 UniProtKB/TrEMBL
  ENSSSCG00055029189 UniProtKB/TrEMBL
  ENSSSCG00060024518 UniProtKB/TrEMBL
  ENSSSCG00065073432 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000007303 ENTREZGENE
  ENSSSCT00000007303.4 UniProtKB/TrEMBL
  ENSSSCT00005028388.1 UniProtKB/TrEMBL
  ENSSSCT00005028406.1 UniProtKB/TrEMBL
  ENSSSCT00015004348.1 UniProtKB/TrEMBL
  ENSSSCT00025091441.1 UniProtKB/TrEMBL
  ENSSSCT00030072534.1 UniProtKB/TrEMBL
  ENSSSCT00035066982.1 UniProtKB/TrEMBL
  ENSSSCT00040036515.1 UniProtKB/TrEMBL
  ENSSSCT00045059819.1 UniProtKB/TrEMBL
  ENSSSCT00050107845.1 UniProtKB/TrEMBL
  ENSSSCT00055057952.1 UniProtKB/TrEMBL
  ENSSSCT00060033239.1 UniProtKB/TrEMBL
  ENSSSCT00065101082.1 UniProtKB/TrEMBL
Gene3D-CATH 3.30.70.330 UniProtKB/TrEMBL
InterPro Nucleotide-bd_a/b_plait_sf UniProtKB/TrEMBL
  RBD_domain_sf UniProtKB/TrEMBL
  RRM_dom UniProtKB/TrEMBL
  SF3B4_RRM1 UniProtKB/TrEMBL
  SF3B4_RRM2 UniProtKB/TrEMBL
KEGG Report ssc:100157814 UniProtKB/TrEMBL
NCBI Gene SF3B4 ENTREZGENE
PANTHER SPLICING FACTOR 3B SUBUNIT 4 UniProtKB/TrEMBL
  SPLICING FACTOR 3B SUBUNIT 4 UniProtKB/TrEMBL
  SPLICING FACTOR 3B SUBUNIT 4 UniProtKB/TrEMBL
Pfam RRM_1 UniProtKB/TrEMBL
PRINTS PRICHEXTENSN UniProtKB/TrEMBL
PROSITE RRM UniProtKB/TrEMBL
SMART RRM UniProtKB/TrEMBL
Superfamily-SCOP SSF54928 UniProtKB/TrEMBL
UniProt A0A8D0IXW9_PIG UniProtKB/TrEMBL
  A0A8D0J2B6_PIG UniProtKB/TrEMBL
  A0A8D1J3P2 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1SB76 ENTREZGENE, UniProtKB/TrEMBL
  F1SDG0 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:98855 ENTREZGENE