SF3B6 (splicing factor 3b subunit 6) - Rat Genome Database

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Gene: SF3B6 (splicing factor 3b subunit 6) Canis lupus familiaris
Analyze
Symbol: SF3B6
Name: splicing factor 3b subunit 6
RGD ID: 12382306
Description: ENCODES a protein that exhibits mRNA binding (inferred); RNA binding (inferred); INVOLVED IN blastocyst formation (ortholog); mRNA splicing, via spliceosome (ortholog); PARTICIPATES IN spliceosome pathway; ASSOCIATED WITH genetic disease (ortholog); FOUND IN U2-type spliceosomal complex (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: SF3B14; splicing factor 3B, 14 kDa subunit
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease 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:30032202  


Genomics

Comparative Map Data
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
(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
(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
(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
(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
168 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 exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system reproductive system respiratory system adipose tissue
High
Medium 5 5 22 6 6 6 6 6 12 8 10 6
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSCAFT00000006355   ⟹   ENSCAFP00000005886
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl1718,548,638 - 18,704,161 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000068551   ⟹   ENSCAFP00000052364
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl1718,548,622 - 18,560,155 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845040100   ⟹   ENSCAFP00845031402
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl1718,716,677 - 18,833,595 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845040168   ⟹   ENSCAFP00845031461
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl1718,719,198 - 18,730,393 (-)Ensembl
RefSeq Acc Id: XM_038560910   ⟹   XP_038416838
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.01718,609,656 - 18,620,388 (-)NCBI
RefSeq Acc Id: XM_038624940   ⟹   XP_038480868
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.01718,568,742 - 18,579,681 (-)NCBI
RefSeq Acc Id: XM_038690848   ⟹   XP_038546776
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.01718,822,915 - 18,833,664 (-)NCBI
RefSeq Acc Id: XM_532889   ⟹   XP_532889
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.11718,548,633 - 18,559,694 (-)NCBI
Dog10K_Boxer_Tasha1718,447,236 - 18,457,834 (-)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: XP_532889   ⟸   XM_532889
- Peptide Label: isoform X2
- UniProtKB: A0A8C0LP02 (UniProtKB/TrEMBL),   A0A8C0QGX1 (UniProtKB/TrEMBL),   A0A8I3PC35 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCAFP00000005886   ⟸   ENSCAFT00000006355
RefSeq Acc Id: ENSCAFP00000052364   ⟸   ENSCAFT00000068551
RefSeq Acc Id: XP_038480868   ⟸   XM_038624940
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038546776   ⟸   XM_038690848
- Peptide Label: isoform X1
- UniProtKB: A0A8C0LP02 (UniProtKB/TrEMBL),   A0A8C0QGX1 (UniProtKB/TrEMBL),   A0A8I3PC35 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038416838   ⟸   XM_038560910
- Peptide Label: isoform X1
- UniProtKB: A0A8C0LP02 (UniProtKB/TrEMBL),   A0A8C0QGX1 (UniProtKB/TrEMBL),   A0A8I3PC35 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCAFP00845031402   ⟸   ENSCAFT00845040100
RefSeq Acc Id: ENSCAFP00845031461   ⟸   ENSCAFT00845040168
Protein Domains
RRM


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000003957 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030017011 UniProtKB/TrEMBL
  ENSCAFG00040005322 UniProtKB/TrEMBL
  ENSCAFG00845022727 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00845022757 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000006355.5 UniProtKB/TrEMBL
  ENSCAFT00000103885.1 UniProtKB/TrEMBL
  ENSCAFT00030031406.1 UniProtKB/TrEMBL
  ENSCAFT00040009977.1 UniProtKB/TrEMBL
  ENSCAFT00845040100.1 UniProtKB/TrEMBL
  ENSCAFT00845040168.1 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
KEGG Report cfa:475682 UniProtKB/TrEMBL
NCBI Gene SF3B6 ENTREZGENE
PANTHER FI21236P1 UniProtKB/TrEMBL
  RNA RECOGNITION MOTIF RRM DOMAIN CONTAINING PROTEIN UniProtKB/TrEMBL
Pfam RRM_1 UniProtKB/TrEMBL
PROSITE RRM UniProtKB/TrEMBL
SMART RRM UniProtKB/TrEMBL
Superfamily-SCOP SSF54928 UniProtKB/TrEMBL
UniProt A0A8C0LP02 ENTREZGENE
  A0A8C0QGX1 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3PC35 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3PJK5_CANLF UniProtKB/TrEMBL
  A0A8P0TRD0_CANLF UniProtKB/TrEMBL
VGNC ID VGNC:46074 ENTREZGENE