Sf3b5 (splicing factor 3b, subunit 5) - Rat Genome Database

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Gene: Sf3b5 (splicing factor 3b, subunit 5) Rattus norvegicus
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Symbol: Sf3b5
Name: splicing factor 3b, subunit 5
RGD ID: 1586993
Description: Predicted to enable RNA binding activity and splicing factor binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to be located in nucleus. Predicted to be part of U12-type spliceosomal complex; U2 snRNP; and U2-type precatalytic spliceosome. Orthologous to human SF3B5 (splicing factor 3b subunit 5); PARTICIPATES IN spliceosome pathway; INTERACTS WITH 4,4'-sulfonyldiphenol; bisphenol A; bisphenol F.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC680891; similar to Splicing factor 3B subunit 5 (SF3b5) (Pre-mRNA splicing factor SF3b 10 kDa subunit); splicing factor 3B subunit 5
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr819,177,189 - 9,177,901 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl19,177,098 - 9,177,900 (+)EnsemblGRCr8
mRatBN7.217,357,040 - 7,357,752 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl17,350,731 - 7,357,839 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx17,058,302 - 7,059,016 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0113,057,380 - 13,058,094 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.017,340,548 - 7,341,262 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.017,101,715 - 7,102,427 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl17,101,715 - 7,102,426 (+)Ensemblrn6Rnor6.0
Rnor_5.018,739,573 - 8,740,285 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.417,746,652 - 7,747,354 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera15,856,835 - 5,857,547 (+)NCBICelera
Cytogenetic Map1p13NCBI
JBrowse:




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. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:15146077   PMID:27720643   PMID:28541300   PMID:28781166   PMID:29360106  


Genomics

Comparative Map Data
Sf3b5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr819,177,189 - 9,177,901 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl19,177,098 - 9,177,900 (+)EnsemblGRCr8
mRatBN7.217,357,040 - 7,357,752 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl17,350,731 - 7,357,839 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx17,058,302 - 7,059,016 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0113,057,380 - 13,058,094 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.017,340,548 - 7,341,262 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.017,101,715 - 7,102,427 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl17,101,715 - 7,102,426 (+)Ensemblrn6Rnor6.0
Rnor_5.018,739,573 - 8,740,285 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.417,746,652 - 7,747,354 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera15,856,835 - 5,857,547 (+)NCBICelera
Cytogenetic Map1p13NCBI
SF3B5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386144,094,884 - 144,095,573 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6144,094,884 - 144,095,573 (-)Ensemblhg38GRCh38
GRCh376144,416,021 - 144,416,710 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 366144,457,711 - 144,458,447 (-)NCBIBuild 36Build 36hg18NCBI36
Build 346144,457,710 - 144,458,447NCBI
Celera6145,156,476 - 145,157,212 (-)NCBICelera
Cytogenetic Map6q24.2NCBI
HuRef6141,979,710 - 141,980,446 (-)NCBIHuRef
CHM1_16144,678,914 - 144,679,650 (-)NCBICHM1_1
T2T-CHM13v2.06145,287,613 - 145,288,302 (-)NCBIT2T-CHM13v2.0
Sf3b5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391012,884,194 - 12,884,927 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1012,881,087 - 12,884,927 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381013,008,450 - 13,009,183 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1013,005,343 - 13,009,183 (+)Ensemblmm10GRCm38
MGSCv371012,728,256 - 12,728,989 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361012,698,652 - 12,699,364 (+)NCBIMGSCv36mm8
Celera1012,903,178 - 12,903,914 (+)NCBICelera
Cytogenetic Map10A2NCBI
cM Map104.72NCBI
Sf3b5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543616,380,549 - 16,380,809 (+)Ensembl
ChiLan1.0NW_00495543616,380,412 - 16,381,373 (+)NCBIChiLan1.0ChiLan1.0
SF3B5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v25164,080,318 - 164,081,059 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan16161,974,738 - 161,975,476 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v06141,873,848 - 141,874,584 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.16146,593,845 - 146,594,592 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6146,594,201 - 146,594,461 (-)EnsemblpanPan2panpan1.1
SF3B5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1135,558,249 - 35,558,998 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl135,558,599 - 35,558,859 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha136,454,018 - 36,454,762 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0135,739,290 - 35,740,034 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl135,739,640 - 35,739,900 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1135,599,415 - 35,600,159 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0135,484,762 - 35,485,506 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0135,795,467 - 35,796,211 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Sf3b5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946130,483,813 - 130,484,538 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366252,151,153 - 2,151,413 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366252,151,018 - 2,151,743 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SF3B5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl121,231,408 - 21,231,668 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1121,231,264 - 21,232,014 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2123,568,334 - 23,569,083 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SF3B5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11329,144,964 - 29,145,699 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1329,145,071 - 29,145,694 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660401,279,259 - 1,280,005 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sf3b5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475310,227,560 - 10,227,820 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462475310,227,419 - 10,228,106 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Sf3b5
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v12224,204,148 - 224,204,852 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Sf3b5
1 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:24
Count of miRNA genes:23
Interacting mature miRNAs:23
Transcripts:ENSRNOT00000019994
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2313090Bmd69Bone mineral density QTL 694.40.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)1529322934184556Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1774611852746118Rat
4889451Eae29Experimental allergic encephalomyelitis QTL 295.51nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1774612152746121Rat
70179Xhs2X-ray hypersensitivity QTL 23.2intestine integrity trait (VT:0010554)post-insult time to onset of moribundity (CMO:0001896)1143965634Rat
1354647Despr8Despair related QTL 80.0000341locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)1126564886Rat
7421626Bp360Blood pressure QTL 3600.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1694102251941022Rat
2313070Bss52Bone structure and strength QTL 524.40.0001body length (VT:0001256)body length (CMO:0000013)1529322934184556Rat
1357401Bw43Body weight QTL 433.75body mass (VT:0001259)body weight (CMO:0000012)1690935351909353Rat
1600360Mcs16Mammary carcinoma susceptibility QTL 162.4mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1126564886Rat
5684998Bss101Bone structure and strength QTL 1013.6tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)1690935351909353Rat
5684999Bss102Bone structure and strength QTL 1025.57e-07tibia strength trait (VT:1000284)tibia stiffness (CMO:0001735)1690935351909353Rat
2317755Glom22Glomerulus QTL 223.8urine protein amount (VT:0005160)urine protein level (CMO:0000591)1134184556Rat
1300170Rf6Renal function QTL 63.14renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)1128483164Rat
2313053Bss51Bone structure and strength QTL 513.80.0001tibia length (VT:0004357)tibia length (CMO:0000450)1529322934184556Rat

Markers in Region
RH142392  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.217,357,154 - 7,357,322 (+)MAPPERmRatBN7.2
Rnor_6.017,101,830 - 7,101,997NCBIRnor6.0
Rnor_5.018,739,688 - 8,739,855UniSTSRnor5.0
RGSC_v3.417,746,764 - 7,746,931UniSTSRGSC3.4
Celera15,856,950 - 5,857,117UniSTS
RH 3.4 Map1115.1UniSTS
Cytogenetic Map1p13UniSTS


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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000019994   ⟹   ENSRNOP00000019994
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl19,177,098 - 9,177,900 (+)Ensembl
mRatBN7.2 Ensembl17,350,731 - 7,357,839 (+)Ensembl
Rnor_6.0 Ensembl17,101,715 - 7,102,426 (+)Ensembl
RefSeq Acc Id: NM_001126092   ⟹   NP_001119564
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr819,177,189 - 9,177,901 (+)NCBI
mRatBN7.217,357,040 - 7,357,752 (+)NCBI
Rnor_6.017,101,715 - 7,102,427 (+)NCBI
Rnor_5.018,739,573 - 8,740,285 (+)NCBI
RGSC_v3.417,746,652 - 7,747,354 (+)RGD
Celera15,856,835 - 5,857,547 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001119564 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL93724 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000019994
  ENSRNOP00000019994.2
RefSeq Acc Id: NP_001119564   ⟸   NM_001126092
- UniProtKB: D4A5T1 (UniProtKB/TrEMBL),   A6JP52 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000019994   ⟸   ENSRNOT00000019994

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A5T1-F1-model_v2 AlphaFold D4A5T1 1-86 view protein structure

Transcriptome

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

Promoters
RGD ID:13689492
Promoter ID:EPDNEW_R17
Type:initiation region
Name:Sf3b5_1
Description:splicing factor 3b, subunit 5
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_6.017,101,741 - 7,101,801EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1586993 AgrOrtholog
BioCyc Gene G2FUF-62369 BioCyc
Ensembl Genes ENSRNOG00000014908 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000019994 ENTREZGENE
  ENSRNOT00000019994.7 UniProtKB/TrEMBL
InterPro SF3b5/RDS3-10 UniProtKB/TrEMBL
  Splicing_factor_3B_subunit_5 UniProtKB/TrEMBL
KEGG Report rno:680891 UniProtKB/TrEMBL
NCBI Gene 680891 ENTREZGENE
PANTHER SF3b10 UniProtKB/TrEMBL
  SPLICING FACTOR 3B SUBUNIT 5 UniProtKB/TrEMBL
Pfam SF3b10 UniProtKB/TrEMBL
PhenoGen Sf3b5 PhenoGen
PIRSF Splicing_factor_3B_subunit_5 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000014908 RatGTEx
UniProt A6JP52 ENTREZGENE, UniProtKB/TrEMBL
  D4A5T1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-07-08 Sf3b5  splicing factor 3b, subunit 5  LOC684491  similar to Splicing factor 3B subunit 5 (SF3b5) (Pre-mRNA splicing factor SF3b 10 kDa subunit)  Data merged from RGD:1590276 1643240 APPROVED
2008-03-05 Sf3b5  splicing factor 3b, subunit 5  LOC680891  similar to Splicing factor 3B subunit 5 (SF3b5) (Pre-mRNA splicing factor SF3b 10 kDa subunit)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC684491  similar to Splicing factor 3B subunit 5 (SF3b5) (Pre-mRNA splicing factor SF3b 10 kDa subunit)      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC680891  similar to Splicing factor 3B subunit 5 (SF3b5) (Pre-mRNA splicing factor SF3b 10 kDa subunit)      Symbol and Name status set to provisional 70820 PROVISIONAL