U2af1 (U2 small nuclear RNA auxiliary factor 1) - Rat Genome Database

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Gene: U2af1 (U2 small nuclear RNA auxiliary factor 1) Rattus norvegicus
Analyze
Symbol: U2af1
Name: U2 small nuclear RNA auxiliary factor 1
RGD ID: 1584190
Description: Predicted to enable RS domain binding activity and pre-mRNA 3'-splice site binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to be located in nuclear speck. Predicted to be part of U2AF complex and catalytic step 2 spliceosome. Orthologous to human U2AF1 (U2 small nuclear RNA auxiliary factor 1); PARTICIPATES IN spliceosome pathway; INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 4,4'-sulfonyldiphenol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: hypothetical protein LOC687575; LOC687575; similar to Splicing factor U2AF 35 kDa subunit (U2 auxiliary factor 35 kDa subunit) (U2 snRNP auxiliary factor small subunit); splicing factor U2AF 35 kDa subunit; uncharacterized protein LOC687575
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
GRCr8209,744,206 - 9,755,146 (-)NCBIGRCr8
mRatBN7.2209,742,904 - 9,753,840 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl209,742,905 - 9,753,832 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2010,444,482 - 10,455,368 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0209,805,670 - 9,816,556 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02010,274,178 - 10,285,068 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02010,396,652 - 10,407,564 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2010,396,621 - 10,407,554 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02012,582,585 - 12,593,487 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera2011,256,755 - 11,267,643 (-)NCBICelera
Cytogenetic Map20p12NCBI
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. 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.
2. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. Comprehensive gene review and curation RGD comprehensive gene curation
5. The spliceosome: design principles of a dynamic RNP machine. Wahl MC, etal., Cell. 2009 Feb 20;136(4):701-18. doi: 10.1016/j.cell.2009.02.009.
Additional References at PubMed
PMID:1824937   PMID:2531895   PMID:9731529   PMID:11991638   PMID:12477932   PMID:15798186   PMID:18758164   PMID:22658674   PMID:22681889   PMID:24912190  


Genomics

Comparative Map Data
U2af1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8209,744,206 - 9,755,146 (-)NCBIGRCr8
mRatBN7.2209,742,904 - 9,753,840 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl209,742,905 - 9,753,832 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2010,444,482 - 10,455,368 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0209,805,670 - 9,816,556 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02010,274,178 - 10,285,068 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02010,396,652 - 10,407,564 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2010,396,621 - 10,407,554 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02012,582,585 - 12,593,487 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera2011,256,755 - 11,267,643 (-)NCBICelera
Cytogenetic Map20p12NCBI
U2AF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382143,092,956 - 43,107,578 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2143,092,956 - 43,107,570 (-)EnsemblGRCh38hg38GRCh38
GRCh372144,513,066 - 44,527,688 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362143,386,135 - 43,400,757 (-)NCBINCBI36Build 36hg18NCBI36
Build 342143,386,135 - 43,400,703NCBI
Celera2129,665,729 - 29,680,351 (-)NCBICelera
Cytogenetic Map21q22.3NCBI
HuRef2129,931,179 - 29,945,801 (-)NCBIHuRef
CHM1_12144,073,930 - 44,088,542 (-)NCBICHM1_1
T2T-CHM13v2.02141,484,016 - 41,498,649 (-)NCBIT2T-CHM13v2.0
U2af1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391731,866,055 - 31,878,122 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1731,866,055 - 31,877,866 (-)EnsemblGRCm39 Ensembl
GRCm381731,647,081 - 31,659,148 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1731,647,081 - 31,658,892 (-)EnsemblGRCm38mm10GRCm38
MGSCv371731,784,027 - 31,795,699 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361731,375,793 - 31,387,425 (-)NCBIMGSCv36mm8
Celera1732,564,314 - 32,575,985 (-)NCBICelera
Cytogenetic Map17B1NCBI
cM Map1717.02NCBI
U2af1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540738,895,711 - 38,909,820 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540738,895,741 - 38,909,820 (+)NCBIChiLan1.0ChiLan1.0
U2AF1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22239,148,192 - 39,162,728 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12134,001,084 - 34,015,646 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02129,399,601 - 29,414,156 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12142,707,738 - 42,719,086 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2142,707,738 - 42,719,086 (-)Ensemblpanpan1.1panPan2
U2AF1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13137,263,265 - 37,276,710 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3136,412,908 - 36,426,355 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03136,805,348 - 36,818,994 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3136,805,359 - 36,818,952 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13136,672,392 - 36,686,045 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03136,651,910 - 36,665,348 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03137,149,648 - 37,163,284 (-)NCBIUU_Cfam_GSD_1.0
U2af1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440497136,500,032 - 36,511,642 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936500958,256 - 967,829 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936500937,537 - 967,791 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
U2AF1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13206,244,773 - 206,257,702 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113206,244,772 - 206,257,697 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
LOC103219520
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1286,949,910 - 86,964,655 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl286,950,056 - 86,964,579 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605414,950,099 - 14,964,875 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
U2af1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474527,647,597 - 27,660,809 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474527,647,672 - 27,660,599 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in U2af1
56 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:162
Count of miRNA genes:128
Interacting mature miRNAs:147
Transcripts:ENSRNOT00000074081
Prediction methods:Microtar, 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
4889870Pur30Proteinuria QTL 30190.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20804241029322208Rat
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124159021Rat
4889857Pur27Proteinuria QTL 2712.20.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20460660717617956Rat
70154Insul2Insulin level QTL 23.75blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20669170617489458Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
1581577Pur15Proteinuria QTL 154.380.0002urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)20804241017617956Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20289259726381954Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20126123605Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125159026Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20460660717617956Rat
1331772Cdexp2CD45RC expression in CD8 T cells QTL 25.7CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)20362164910078919Rat
631265Iresp1Immunoglobin response QTL18.3blood anti-double stranded DNA antibody amount (VT:0004762)serum anti-DNA antibody level (CMO:0001533)20903971913461775Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20362165614101050Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat


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: ENSRNOT00000074081   ⟹   ENSRNOP00000067005
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl209,742,906 - 9,753,832 (-)Ensembl
Rnor_6.0 Ensembl2010,396,621 - 10,407,554 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000100283   ⟹   ENSRNOP00000086374
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl209,742,906 - 9,753,811 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000108169   ⟹   ENSRNOP00000082509
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl209,742,905 - 9,751,124 (-)Ensembl
RefSeq Acc Id: NM_001044291   ⟹   NP_001037756
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8209,744,206 - 9,755,094 (-)NCBI
mRatBN7.2209,742,904 - 9,753,792 (-)NCBI
Rnor_6.02010,396,652 - 10,407,540 (-)NCBI
Rnor_5.02012,582,585 - 12,593,487 (-)NCBI
Celera2011,256,755 - 11,267,643 (-)RGD
Sequence:
RefSeq Acc Id: XM_006256228   ⟹   XP_006256290
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8209,744,206 - 9,755,146 (-)NCBI
mRatBN7.2209,742,904 - 9,753,840 (-)NCBI
Rnor_6.02010,396,652 - 10,407,564 (-)NCBI
Rnor_5.02012,582,585 - 12,593,487 (-)NCBI
Sequence:
RefSeq Acc Id: XM_063279519   ⟹   XP_063135589
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8209,744,206 - 9,752,055 (-)NCBI
RefSeq Acc Id: NP_001037756   ⟸   NM_001044291
- UniProtKB: Q3KR55 (UniProtKB/TrEMBL),   M0RBR0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006256290   ⟸   XM_006256228
- Peptide Label: isoform X1
- UniProtKB: A6JK09 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000067005   ⟸   ENSRNOT00000074081
Ensembl Acc Id: ENSRNOP00000086374   ⟸   ENSRNOT00000100283
Ensembl Acc Id: ENSRNOP00000082509   ⟸   ENSRNOT00000108169
RefSeq Acc Id: XP_063135589   ⟸   XM_063279519
- Peptide Label: isoform X2
Protein Domains
C3H1-type   RRM

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q3KR55-F1-model_v2 AlphaFold Q3KR55 1-239 view protein structure

Transcriptome

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

Promoters
RGD ID:13701479
Promoter ID:EPDNEW_R12002
Type:initiation region
Name:U2af1_1
Description:U2 small nuclear RNA auxiliary factor 1
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_6.02010,407,507 - 10,407,567EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1584190 AgrOrtholog
BioCyc Gene G2FUF-4305 BioCyc
Ensembl Genes ENSRNOG00000045860 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000074081.3 UniProtKB/TrEMBL
  ENSRNOT00000100283.1 UniProtKB/TrEMBL
  ENSRNOT00000108169.1 UniProtKB/TrEMBL
Gene3D-CATH 3.30.70.330 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7374686 IMAGE-MGC_LOAD
InterPro Nucleotide-bd_a/b_plait_sf UniProtKB/TrEMBL
  RBD_domain_sf UniProtKB/TrEMBL
  RRM_dom_euk UniProtKB/TrEMBL
  RRM_RNP1 UniProtKB/TrEMBL
  U2_small UniProtKB/TrEMBL
  Znf_CCCH UniProtKB/TrEMBL
KEGG Report rno:687575 UniProtKB/TrEMBL
MGC_CLONE MGC:125109 IMAGE-MGC_LOAD
NCBI Gene 687575 ENTREZGENE
PANTHER SPLICING FACTOR U2AF 35 KDA SUBUNIT-RELATED UniProtKB/TrEMBL
  U2_small UniProtKB/TrEMBL
Pfam RRM_1 UniProtKB/TrEMBL
  zf-CCCH UniProtKB/TrEMBL
PhenoGen U2af1 PhenoGen
PRINTS U2AUXFACTOR UniProtKB/TrEMBL
PROSITE RRM UniProtKB/TrEMBL
  ZF_C3H1 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000045860 RatGTEx
SMART RRM UniProtKB/TrEMBL
  RRM_1 UniProtKB/TrEMBL
  ZnF_C3H1 UniProtKB/TrEMBL
Superfamily-SCOP SSF54928 UniProtKB/TrEMBL
UniProt A0A8I5ZV21_RAT UniProtKB/TrEMBL
  A0A8I6A5Q2_RAT UniProtKB/TrEMBL
  A6JK09 ENTREZGENE, UniProtKB/TrEMBL
  M0RBR0 ENTREZGENE, UniProtKB/TrEMBL
  Q3KR55 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-08-16 U2af1  U2 small nuclear RNA auxiliary factor 1  LOC687575  similar to Splicing factor U2AF 35 kDa subunit (U2 auxiliary factor 35 kDa subunit) (U2 snRNP auxiliary factor small subunit)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC687575  similar to Splicing factor U2AF 35 kDa subunit (U2 auxiliary factor 35 kDa subunit) (U2 snRNP auxiliary factor small subunit)      Symbol and Name status set to provisional 70820 PROVISIONAL