Sf3b6 (splicing factor 3B, subunit 6) - Rat Genome Database

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Gene: Sf3b6 (splicing factor 3B, subunit 6) Rattus norvegicus
Analyze
Symbol: Sf3b6
Name: splicing factor 3B, subunit 6
RGD ID: 2318878
Description: Predicted to enable mRNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to act upstream of or within blastocyst formation. Predicted to be located in nucleoplasm. Predicted to be part of U2 snRNP and spliceosomal complex. Orthologous to human SF3B6 (splicing factor 3b subunit 6); PARTICIPATES IN spliceosome pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; paracetamol; tetrachloromethane.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC100365504; splicing factor 3B subunit 6; splicing factor 3B, 14 kDa subunit-like; uncharacterized protein LOC100365504
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2627,826,044 - 27,835,086 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl627,826,029 - 27,835,156 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx628,118,290 - 28,127,332 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0628,434,194 - 28,443,236 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0627,908,751 - 27,917,793 (+)NCBIRnor_WKY
Rnor_6.0629,991,232 - 29,999,668 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl629,991,307 - 29,999,410 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0639,886,845 - 39,895,262 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera627,295,792 - 27,304,777 (+)NCBICelera
Cytogenetic Map6q14NCBI
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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
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:16432215   PMID:22658674   PMID:22681889   PMID:23211737   PMID:27720643   PMID:27869233   PMID:28541300  


Genomics

Comparative Map Data
Sf3b6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2627,826,044 - 27,835,086 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl627,826,029 - 27,835,156 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx628,118,290 - 28,127,332 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0628,434,194 - 28,443,236 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0627,908,751 - 27,917,793 (+)NCBIRnor_WKY
Rnor_6.0629,991,232 - 29,999,668 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl629,991,307 - 29,999,410 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0639,886,845 - 39,895,262 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera627,295,792 - 27,304,777 (+)NCBICelera
Cytogenetic Map6q14NCBI
SF3B6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38224,067,586 - 24,076,326 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl224,067,586 - 24,076,373 (-)EnsemblGRCh38hg38GRCh38
GRCh37224,290,456 - 24,299,196 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36224,143,958 - 24,152,818 (-)NCBINCBI36Build 36hg18NCBI36
Celera224,130,785 - 24,139,642 (-)NCBICelera
Cytogenetic Map2p23.3NCBI
HuRef224,029,317 - 24,038,126 (-)NCBIHuRef
CHM1_1224,219,844 - 24,228,700 (-)NCBICHM1_1
T2T-CHM13v2.0224,102,271 - 24,111,005 (-)NCBIT2T-CHM13v2.0
Sf3b6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39124,867,608 - 4,877,659 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl124,867,544 - 4,877,659 (+)EnsemblGRCm39 Ensembl
GRCm38124,817,608 - 4,827,659 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl124,817,544 - 4,827,659 (+)EnsemblGRCm38mm10GRCm38
MGSCv37124,824,414 - 4,834,465 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36124,832,269 - 4,849,746 (+)NCBIMGSCv36mm8
Celera124,749,151 - 4,759,202 (+)NCBICelera
Cytogenetic Map12A1.1NCBI
Sf3b6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554696,275,900 - 6,286,908 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554696,275,894 - 6,286,908 (-)NCBIChiLan1.0ChiLan1.0
SF3B6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A24,162,976 - 24,172,111 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A24,162,976 - 24,172,040 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A24,065,640 - 24,074,512 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
SF3B6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11718,548,633 - 18,559,694 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1718,548,622 - 18,704,161 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1718,447,236 - 18,457,834 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01718,822,915 - 18,833,664 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1718,716,677 - 18,833,595 (-)EnsemblROS_Cfam_1.0 Ensembl
ROS_Cfam_1.0 Ensembl1718,719,198 - 18,730,393 (-)EnsemblROS_Cfam_1.0 Ensembl
UNSW_CanFamBas_1.01718,568,742 - 18,579,681 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01718,609,656 - 18,620,388 (-)NCBIUU_Cfam_GSD_1.0
Sf3b6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629262,926,788 - 62,932,864 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364937,906,701 - 7,912,438 (+)EnsemblSpeTri2.0
SpeTri2.0NW_0049364937,906,701 - 7,912,777 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SF3B6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl3114,605,971 - 114,620,563 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.13114,605,863 - 114,618,123 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.23121,870,648 - 121,882,905 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SF3B6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11483,593,429 - 83,602,309 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1483,593,025 - 83,604,002 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604528,563,396 - 28,573,269 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sf3b6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247386,395,616 - 6,404,855 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247386,395,610 - 6,404,794 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Sf3b6
51 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:15
Count of miRNA genes:11
Interacting mature miRNAs:15
Transcripts:ENSRNOT00000075790
Prediction methods:Miranda, Rnahybrid, Targetscan
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
1331743Uae28Urinary albumin excretion QTL 284.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)6134235784Rat
1578758Tcas9Tongue tumor susceptibility QTL 93.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)6137618905Rat
1598843Cm63Cardiac mass QTL 632.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)6139036266Rat
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6141223769Rat
8552962Pigfal16Plasma insulin-like growth factor 1 level QTL 169.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)6141223769Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6141223769Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6141223769Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6141223769Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6142487980Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6142487980Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6142487980Rat
7411584Foco4Food consumption QTL 44.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6142838846Rat
738024Sach5Saccharine consumption QTL 53.90.00039consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)6143394190Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6172227641Rat
1300128Rf16Renal function QTL 163.89renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449734434305Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449754641141Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)610894415110548006Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)61173566972593685Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)61173566972593685Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)615107216107351382Rat
2292589Emca10Estrogen-induced mammary cancer QTL 100.048mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)61653614061536140Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)61653614071636405Rat
1641898Colcr4Colorectal carcinoma resistance QTL43.710.0007intestine integrity trait (VT:0010554)well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)62033877762613667Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat

Markers in Region
AV001342  
Rat AssemblyChrPosition (strand)SourceJBrowse
Celera627,304,422 - 27,304,650UniSTS
AA848523  
Rat AssemblyChrPosition (strand)SourceJBrowse
Celera627,304,374 - 27,304,738UniSTS
RH 3.4 Map6118.6UniSTS


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 exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000075790   ⟹   ENSRNOP00000065625
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl627,828,246 - 27,835,011 (+)Ensembl
Rnor_6.0 Ensembl629,991,307 - 29,999,410 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000110429   ⟹   ENSRNOP00000091764
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl627,826,029 - 27,835,156 (+)Ensembl
RefSeq Acc Id: NM_001271222   ⟹   NP_001258151
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2627,826,044 - 27,835,086 (+)NCBI
Rnor_6.0629,991,232 - 29,999,668 (-)NCBI
Rnor_5.0639,886,845 - 39,895,262 (+)NCBI
Celera627,295,792 - 27,304,777 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001258151 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM03048 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001258151   ⟸   NM_001271222
- UniProtKB: A0A8I6AFT8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000065625   ⟸   ENSRNOT00000075790
RefSeq Acc Id: ENSRNOP00000091764   ⟸   ENSRNOT00000110429
Protein Domains
RRM

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0R835-F1-model_v2 AlphaFold M0R835 1-123 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2318878 AgrOrtholog
BioCyc Gene G2FUF-38264 BioCyc
Ensembl Genes ENSRNOG00000046172 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000065625.3 UniProtKB/TrEMBL
  ENSRNOP00000091764 ENTREZGENE
  ENSRNOP00000091764.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000075790.3 UniProtKB/TrEMBL
  ENSRNOT00000110429 ENTREZGENE
  ENSRNOT00000110429.1 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
  SF3B6_RRM UniProtKB/TrEMBL
NCBI Gene 100365504 ENTREZGENE
Pfam RRM_1 UniProtKB/TrEMBL
PhenoGen Sf3b6 PhenoGen
PROSITE RRM UniProtKB/TrEMBL
SMART RRM UniProtKB/TrEMBL
Superfamily-SCOP SSF54928 UniProtKB/TrEMBL
UniProt A0A8I6AFT8 ENTREZGENE, UniProtKB/TrEMBL
  M0R835_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-07-24 Sf3b6  splicing factor 3B, subunit 6  LOC100365504  splicing factor 3B, 14 kDa subunit-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-05 LOC100365504  splicing factor 3B, 14 kDa subunit-like      Symbol and Name status set to provisional 70820 PROVISIONAL