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

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Gene: Sf3b6 (splicing factor 3B, subunit 6) Mus musculus
Analyze
Symbol: Sf3b6
Name: splicing factor 3B, subunit 6
RGD ID: 1615905
MGI Page MGI
Description: Predicted to enable mRNA binding activity. Acts upstream of or within blastocyst formation and mRNA splicing, via spliceosome. Located in nucleus. Is expressed in central nervous system; early conceptus; secondary oocyte; and sensory organ. Orthologous to human SF3B6 (splicing factor 3b subunit 6).
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: 0610009D07Rik; 6030419K15Rik; AV001342; pre-mRNA branch site protein p14; SF3B 14 kDa subunit; Sf3b1; Sf3b14; splicing factor 3B subunit 6; splicing factor 3B, 14 kDa subunit
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
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
cM Map122.09NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function
mRNA binding  (ISO,ISS)
protein binding  (ISO)

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. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
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
Additional References at PubMed
PMID:10349636   PMID:10922068   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12477932   PMID:14610273   PMID:15489334   PMID:16033648   PMID:16141072   PMID:16141073  
PMID:21267068   PMID:21677750   PMID:21873635   PMID:23211737   PMID:23937658   PMID:24457600   PMID:27869233   PMID:30196744   PMID:30457570   PMID:30550785   PMID:32325033  


Genomics

Comparative Map Data
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
cM Map122.09NCBI
SF3B6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38224,067,586 - 24,076,326 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 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
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8633,545,495 - 33,554,537 (+)NCBIGRCr8
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_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0628,434,194 - 28,443,236 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0627,908,751 - 27,917,793 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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
(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
NHGRI_mPanPan1-v212102,441,116 - 102,450,896 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12A102,445,602 - 102,454,858 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02A24,065,640 - 24,074,512 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12A24,162,976 - 24,172,111 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A24,162,976 - 24,172,040 (-)Ensemblpanpan1.1panPan2
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 Ensembl1718,719,198 - 18,730,393 (-)EnsemblROS_Cfam_1.0 Ensembl
ROS_Cfam_1.0 Ensembl1718,716,677 - 18,833,595 (-)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 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
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
358 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:151
Count of miRNA genes:128
Interacting mature miRNAs:140
Transcripts:ENSMUST00000046207
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
26884410Bzwq15_mbi-zygomatic width QTL 15, 16 week (mouse)12365000029749999Mouse
1301393Dyscalc3_mdystrophic cardiac calcinosis 3 (mouse)Not determined12122418579Mouse
12910983Pifs1_mpeptide-induced fatal syndrome 1 (mouse)12130433078Mouse
4141436Chldq7_mcholesterol and HDL QTL 7 (mouse)Not determined12127920733Mouse
4141660Nbwa1_mNZB and NZW autoimmunity 1 (mouse)Not determined1234013434340302Mouse
1301143Skull17_mskull morphology 17 (mouse)Not determined12122418579Mouse
1301655Bmd12_mbone mineral density 12 (mouse)Not determined12124662697Mouse
1301207Circp1_mcircadian photosensitivity 1 (mouse)Not determined12133430339Mouse
11039525Tbbr2_mTrypanosoma brucei brucei response 2 (mouse)12122418579Mouse
4141296Femwf9_mfemur work to failure 9 (mouse)Not determined127920733Mouse
1301925Ath6_matherosclerosis 6 (mouse)Not determined12132758756Mouse
1357519Vtbt12_mvertebral trabecular bone trait 12 (mouse)Not determined12124662697Mouse
10402496Lmr22_mleishmaniasis resistance 22 (mouse)Not determined12122418579Mouse

Markers in Region
0610009D07Rik  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map12A1.1UniSTS
cM Map12 UniSTS
AV001342  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38124,826,811 - 4,827,051UniSTSGRCm38
MGSCv37124,833,617 - 4,833,857UniSTSGRCm37
Celera124,758,354 - 4,758,594UniSTS
Cytogenetic Map12A1.1UniSTS
Whitehead/MRC_RH81261.73UniSTS


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSMUST00000046207   ⟹   ENSMUSP00000043662
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl124,867,544 - 4,877,659 (+)Ensembl
GRCm38.p6 Ensembl124,817,544 - 4,827,659 (+)Ensembl
Ensembl Acc Id: ENSMUST00000218650
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl124,876,695 - 4,877,266 (+)Ensembl
GRCm38.p6 Ensembl124,826,695 - 4,827,266 (+)Ensembl
Ensembl Acc Id: ENSMUST00000218705
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl124,867,575 - 4,869,050 (+)Ensembl
GRCm38.p6 Ensembl124,817,575 - 4,819,050 (+)Ensembl
Ensembl Acc Id: ENSMUST00000219128   ⟹   ENSMUSP00000151723
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl124,870,594 - 4,877,098 (+)Ensembl
GRCm38.p6 Ensembl124,820,594 - 4,827,098 (+)Ensembl
Ensembl Acc Id: ENSMUST00000219359
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl124,867,561 - 4,872,108 (+)Ensembl
GRCm38.p6 Ensembl124,817,561 - 4,822,108 (+)Ensembl
RefSeq Acc Id: NM_025323   ⟹   NP_079599
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39124,867,608 - 4,877,659 (+)NCBI
GRCm38124,817,608 - 4,827,659 (+)ENTREZGENE
MGSCv37124,824,414 - 4,834,465 (+)RGD
Celera124,749,151 - 4,759,202 (+)RGD
cM Map12 ENTREZGENE
Sequence:
RefSeq Acc Id: NP_079599   ⟸   NM_025323
- UniProtKB: Q3U9T9 (UniProtKB/Swiss-Prot),   P59708 (UniProtKB/Swiss-Prot),   A0A1W2P7L7 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSMUSP00000043662   ⟸   ENSMUST00000046207
Ensembl Acc Id: ENSMUSP00000151723   ⟸   ENSMUST00000219128
Protein Domains
RRM

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P59708-F1-model_v2 AlphaFold P59708 1-125 view protein structure

Promoters
RGD ID:8677858
Promoter ID:EPDNEW_M16959
Type:initiation region
Name:Sf3b6_1
Description:Mus musculus splicing factor 3B, subunit 6 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38124,817,561 - 4,817,621EPDNEW
RGD ID:6822524
Promoter ID:MM_KWN:11097
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day4,   3T3L1_Day6,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Liver,   Lung,   MEF_B4,   MEF_B6,   Spleen
Transcripts:NM_025323
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36124,824,069 - 4,824,569 (+)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1913305 AgrOrtholog
Ensembl Genes ENSMUSG00000037361 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000046207 ENTREZGENE
  ENSMUST00000046207.9 UniProtKB/Swiss-Prot
  ENSMUST00000219128.2 UniProtKB/TrEMBL
Gene3D-CATH 3.30.70.330 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Nucleotide-bd_a/b_plait_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RBD_domain_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RRM_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RRT5_SRSF_SR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SF3B6_RRM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:66055 UniProtKB/Swiss-Prot
MGD MGI:1913305 ENTREZGENE
NCBI Gene 66055 ENTREZGENE
PANTHER RNA RECOGNITION MOTIF RRM DOMAIN CONTAINING PROTEIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam RRM_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Sf3b6 PhenoGen
PROSITE RRM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART RRM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF54928 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A1W2P7L7 ENTREZGENE, UniProtKB/TrEMBL
  P59708 ENTREZGENE
  Q3U9T9 ENTREZGENE
  SF3B6_MOUSE UniProtKB/Swiss-Prot
UniProt Secondary Q3U9T9 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-04-22 Sf3b6  splicing factor 3B, subunit 6  Sf3b14  splicing factor 3B, 14 kDa subunit  Symbol and/or name change 5135510 APPROVED
2014-03-26 Sf3b14  splicing factor 3B, 14 kDa subunit  0610009D07Rik  RIKEN cDNA 0610009D07 gene  Symbol and/or name change 5135510 APPROVED