Sf3b3 (splicing factor 3b, subunit 3) - Rat Genome Database

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Gene: Sf3b3 (splicing factor 3b, subunit 3) Rattus norvegicus
Analyze
Symbol: Sf3b3
Name: splicing factor 3b, subunit 3
RGD ID: 1311636
Description: Predicted to enable U2 snRNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome and negative regulation of protein catabolic process. Predicted to be located in nucleolus and nucleoplasm. Predicted to be part of U2 snRNP and spliceosomal complex. Predicted to be active in nucleus. Orthologous to human SF3B3 (splicing factor 3b subunit 3); PARTICIPATES IN spliceosome pathway; INTERACTS WITH 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane; 17alpha-ethynylestradiol; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC292019; splicing factor 3B subunit 3
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81955,692,124 - 55,729,640 (-)NCBIGRCr8
mRatBN7.21938,782,749 - 38,820,271 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1938,783,040 - 38,820,245 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1945,587,776 - 45,625,282 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01946,241,144 - 46,278,650 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01948,551,807 - 48,589,416 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01943,392,071 - 43,429,582 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1943,392,085 - 43,429,580 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01954,224,944 - 54,262,545 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41940,730,284 - 40,765,321 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11940,735,269 - 40,770,202 (-)NCBI
Celera1938,176,297 - 38,213,784 (-)NCBICelera
Cytogenetic Map19q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

References - curated
# Reference Title Reference Citation
1. Proteomic analysis of in vivo-assembled pre-mRNA splicing complexes expands the catalog of participating factors. Chen YI, etal., Nucleic Acids Res. 2007;35(12):3928-44. Epub 2007 May 30.
2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
5. GOA pipeline RGD automated data pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:8889548   PMID:11564863   PMID:11991638   PMID:12477932   PMID:15146077   PMID:23951410   PMID:27720643   PMID:28541300   PMID:28781166   PMID:29360106   PMID:31505169  


Genomics

Comparative Map Data
Sf3b3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81955,692,124 - 55,729,640 (-)NCBIGRCr8
mRatBN7.21938,782,749 - 38,820,271 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1938,783,040 - 38,820,245 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1945,587,776 - 45,625,282 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01946,241,144 - 46,278,650 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01948,551,807 - 48,589,416 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01943,392,071 - 43,429,582 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1943,392,085 - 43,429,580 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01954,224,944 - 54,262,545 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41940,730,284 - 40,765,321 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11940,735,269 - 40,770,202 (-)NCBI
Celera1938,176,297 - 38,213,784 (-)NCBICelera
Cytogenetic Map19q12NCBI
SF3B3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381670,523,816 - 70,577,668 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1670,523,791 - 70,577,670 (+)EnsemblGRCh38hg38GRCh38
GRCh371670,557,719 - 70,611,571 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361669,115,202 - 69,163,702 (+)NCBINCBI36Build 36hg18NCBI36
Build 341669,115,201 - 69,163,701NCBI
Celera1654,916,621 - 54,970,452 (-)NCBICelera
Cytogenetic Map16q22.1NCBI
HuRef1656,388,754 - 56,442,561 (+)NCBIHuRef
CHM1_11671,965,025 - 72,018,903 (+)NCBICHM1_1
T2T-CHM13v2.01676,334,997 - 76,388,857 (+)NCBIT2T-CHM13v2.0
Sf3b3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398111,537,123 - 111,573,578 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8111,536,871 - 111,573,419 (-)EnsemblGRCm39 Ensembl
GRCm388110,810,491 - 110,846,806 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8110,810,239 - 110,846,787 (-)EnsemblGRCm38mm10GRCm38
MGSCv378113,334,392 - 113,370,703 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv368113,697,169 - 113,733,436 (-)NCBIMGSCv36mm8
Celera8115,034,001 - 115,070,341 (-)NCBICelera
Cytogenetic Map8E1NCBI
cM Map857.73NCBI
Sf3b3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554843,307,794 - 3,357,600 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554843,307,794 - 3,357,600 (+)NCBIChiLan1.0ChiLan1.0
SF3B3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21883,591,131 - 83,639,789 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11689,520,428 - 89,569,114 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01654,442,510 - 54,490,950 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11670,361,068 - 70,409,679 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1670,361,068 - 70,410,042 (+)Ensemblpanpan1.1panPan2
SF3B3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1576,490,622 - 76,543,877 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl576,490,682 - 76,543,877 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha576,451,911 - 76,505,135 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0576,927,032 - 76,980,307 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl576,927,088 - 76,980,301 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1576,748,978 - 76,802,232 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0576,572,045 - 76,625,098 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0577,064,314 - 77,117,437 (+)NCBIUU_Cfam_GSD_1.0
Sf3b3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934936,502,962 - 36,550,690 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647523,037,687 - 23,086,188 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647523,038,424 - 23,086,134 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SF3B3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl613,524,717 - 13,578,680 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1613,524,519 - 13,578,681 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2613,479,647 - 13,484,140 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SF3B3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1553,673,443 - 53,724,485 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl553,673,455 - 53,725,615 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604716,471,909 - 16,522,350 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sf3b3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474612,747,382 - 12,793,643 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474612,747,346 - 12,793,639 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Sf3b3
113 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:70
Count of miRNA genes:64
Interacting mature miRNAs:65
Transcripts:ENSRNOT00000023854
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192048357557337602Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19231612147316121Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)192932249057337602Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191545586057337602Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)193383821455283146Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19745724942983518Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)191715443357337602Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)1956937445569374Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191082797043544039Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191563020157337602Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)191560502346559041Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19320477748204777Rat
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)1956937445569374Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19218792746708701Rat
1549835Tcas7Tongue tumor susceptibility QTL 70.001tongue integrity trait (VT:0010553)squamous cell carcinoma of the head and neck tumor number (CMO:0001876)192481797839654489Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
724565Tcas5Tongue tumor susceptibility QTL 510.04tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)19997775339654489Rat

Markers in Region
RH141009  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21938,783,093 - 38,783,289 (-)MAPPERmRatBN7.2
Rnor_6.01943,429,042 - 43,429,237NCBIRnor6.0
Rnor_5.01954,262,005 - 54,262,200UniSTSRnor5.0
RGSC_v3.41940,730,629 - 40,730,824UniSTSRGSC3.4
Celera1938,176,642 - 38,176,837UniSTS
RH 3.4 Map19475.3UniSTS
Cytogenetic Map19q12UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000023854   ⟹   ENSRNOP00000023854
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1938,783,040 - 38,820,245 (-)Ensembl
Rnor_6.0 Ensembl1943,392,085 - 43,429,580 (+)Ensembl
RefSeq Acc Id: NM_001106187   ⟹   NP_001099657
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81955,692,124 - 55,729,621 (-)NCBI
mRatBN7.21938,782,749 - 38,820,248 (-)NCBI
Rnor_6.01943,392,085 - 43,429,582 (+)NCBI
Rnor_5.01954,224,944 - 54,262,545 (+)NCBI
Celera1938,176,297 - 38,213,784 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006255620   ⟹   XP_006255682
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81955,692,401 - 55,729,640 (-)NCBI
mRatBN7.21938,783,026 - 38,820,271 (-)NCBI
Rnor_6.01943,392,071 - 43,429,305 (+)NCBI
Rnor_5.01954,224,944 - 54,262,545 (+)NCBI
Sequence:
RefSeq Acc Id: XM_063277936   ⟹   XP_063134006
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81955,692,401 - 55,729,637 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001099657 (Get FASTA)   NCBI Sequence Viewer  
  XP_006255682 (Get FASTA)   NCBI Sequence Viewer  
  XP_063134006 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI68883 (Get FASTA)   NCBI Sequence Viewer  
  EDL92549 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000023854.6
RefSeq Acc Id: NP_001099657   ⟸   NM_001106187
- UniProtKB: E9PT66 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006255682   ⟸   XM_006255620
- Peptide Label: isoform X1
- UniProtKB: E9PT66 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000023854   ⟸   ENSRNOT00000023854
RefSeq Acc Id: XP_063134006   ⟸   XM_063277936
- Peptide Label: isoform X1
- UniProtKB: E9PT66 (UniProtKB/TrEMBL)
Protein Domains
Cleavage/polyadenylation specificity factor A

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-E9PT66-F1-model_v2 AlphaFold E9PT66 1-1217 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13701146
Promoter ID:EPDNEW_R11670
Type:multiple initiation site
Name:Sf3b3_1
Description:splicing factor 3b, subunit 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01943,392,080 - 43,392,140EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311636 AgrOrtholog
BioCyc Gene G2FUF-5684 BioCyc
Ensembl Genes ENSRNOG00000017724 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000023854.7 UniProtKB/TrEMBL
Gene3D-CATH 1.10.150.910 UniProtKB/TrEMBL
  2.130.10.10 UniProtKB/TrEMBL
InterPro Cleavage/polyA-sp_fac_asu_C UniProtKB/TrEMBL
  Cleavage/polyA-sp_fac_asu_N UniProtKB/TrEMBL
  RSE1/DDB1/CFT1/CPSF1 UniProtKB/TrEMBL
  WD40/YVTN_repeat-like_dom UniProtKB/TrEMBL
  WD40_repeat_dom_sf UniProtKB/TrEMBL
KEGG Report rno:292019 UniProtKB/TrEMBL
NCBI Gene 292019 ENTREZGENE
PANTHER DNA REPAIR/RNA PROCESSING CPSF FAMILY UniProtKB/TrEMBL
  SPLICING FACTOR 3B SUBUNIT 3 UniProtKB/TrEMBL
Pfam CPSF_A UniProtKB/TrEMBL
  MMS1_N UniProtKB/TrEMBL
PhenoGen Sf3b3 PhenoGen
RatGTEx ENSRNOG00000017724 RatGTEx
Superfamily-SCOP SSF50978 UniProtKB/TrEMBL
UniProt B5DF12_RAT UniProtKB/TrEMBL
  E9PT66 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Sf3b3  splicing factor 3b, subunit 3   Sf3b3_predicted  splicing factor 3b, subunit 3 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Sf3b3_predicted  splicing factor 3b, subunit 3 (predicted)      Symbol and Name status set to approved 70820 APPROVED