Yju2 (YJU2 splicing factor) - Rat Genome Database

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Gene: Yju2 (YJU2 splicing factor) Rattus norvegicus
Analyze
Symbol: Yju2
Name: YJU2 splicing factor
RGD ID: 1589601
Description: Predicted to enable metal ion binding activity. Predicted to be involved in RNA splicing. Predicted to be part of U2-type catalytic step 1 spliceosome. Orthologous to human YJU2 (YJU2 splicing factor homolog); INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; bisphenol A; paracetamol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Ccdc94; coiled-coil domain containing 94; coiled-coil domain-containing protein 94; LOC501285; MGC156684; similar to CG8435-PA; splicing factor YJU2; YJU2 splicing factor homolog
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
GRCr89876,790 - 886,687 (+)NCBIGRCr8
mRatBN7.29789,603 - 799,505 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl9789,606 - 799,496 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx91,236,798 - 1,246,612 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.096,583,974 - 6,593,798 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.095,541,835 - 5,551,650 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0911,098,914 - 11,108,806 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl911,098,924 - 11,108,741 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0910,084,078 - 10,093,964 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera97,706,956 - 7,716,779 (-)NCBICelera
Cytogenetic Map9q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
amenorrhea  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:29301961  


Genomics

Comparative Map Data
Yju2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr89876,790 - 886,687 (+)NCBIGRCr8
mRatBN7.29789,603 - 799,505 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl9789,606 - 799,496 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx91,236,798 - 1,246,612 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.096,583,974 - 6,593,798 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.095,541,835 - 5,551,650 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0911,098,914 - 11,108,806 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl911,098,924 - 11,108,741 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0910,084,078 - 10,093,964 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera97,706,956 - 7,716,779 (-)NCBICelera
Cytogenetic Map9q11NCBI
YJU2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38194,247,080 - 4,269,088 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl194,247,080 - 4,269,088 (+)EnsemblGRCh38hg38GRCh38
GRCh37194,247,077 - 4,269,085 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36194,198,111 - 4,220,085 (+)NCBINCBI36Build 36hg18NCBI36
Celera194,186,494 - 4,208,470 (+)NCBICelera
Cytogenetic Map19p13.3NCBI
HuRef194,010,325 - 4,032,247 (+)NCBIHuRef
CHM1_1194,246,732 - 4,268,702 (+)NCBICHM1_1
T2T-CHM13v2.0194,229,720 - 4,252,363 (+)NCBIT2T-CHM13v2.0
Yju2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391756,266,187 - 56,274,951 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1756,266,099 - 56,275,285 (+)EnsemblGRCm39 Ensembl
GRCm381755,959,187 - 55,967,951 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1755,959,099 - 55,968,285 (+)EnsemblGRCm38mm10GRCm38
MGSCv371756,098,610 - 56,107,374 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361755,552,467 - 55,561,574 (+)NCBIMGSCv36mm8
Celera1759,377,714 - 59,386,478 (+)NCBICelera
Cytogenetic Map17DNCBI
cM Map1729.08NCBI
Yju2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554954,592,523 - 4,606,005 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554954,591,242 - 4,605,403 (-)NCBIChiLan1.0ChiLan1.0
YJU2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2208,644,495 - 8,666,464 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1197,874,484 - 7,896,519 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0193,270,432 - 3,292,457 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1194,217,448 - 4,239,684 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl194,217,457 - 4,239,684 (+)Ensemblpanpan1.1panPan2
YJU2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12055,367,512 - 55,380,755 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2055,368,480 - 55,380,679 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2055,095,555 - 55,108,798 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02056,026,737 - 56,039,990 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2056,026,667 - 56,039,942 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12055,086,676 - 55,099,906 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02055,567,887 - 55,581,120 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02055,766,561 - 55,779,809 (-)NCBIUU_Cfam_GSD_1.0
Yju2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118215,395,972 - 215,407,869 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365882,427,126 - 2,440,939 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365882,426,786 - 2,438,811 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
YJU2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl274,509,739 - 74,528,300 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1274,507,830 - 74,528,333 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2275,001,394 - 75,022,973 (-)NCBISscrofa10.2Sscrofa10.2susScr3
YJU2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.163,995,769 - 4,013,288 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660814,200,131 - 4,223,532 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Yju2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248285,381,617 - 5,397,782 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248285,381,387 - 5,397,893 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Yju2
17 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:503
Count of miRNA genes:264
Interacting mature miRNAs:311
Transcripts:ENSRNOT00000072357
Prediction methods:Microtar, 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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10054141Gmadr4Adrenal mass QTL 42.450.0074adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)9114209783Rat
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9125661317Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9137999212Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9137999212Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9137999212Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9140594091Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9143718459Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9143718459Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat

Markers in Region
RH134940  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.29799,190 - 799,410 (-)MAPPERmRatBN7.2
Rnor_6.0911,099,009 - 11,099,228NCBIRnor6.0
Rnor_5.0910,084,173 - 10,084,392UniSTSRnor5.0
Celera97,707,047 - 7,707,266UniSTS


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 30 40 25 19 25 74 30 34 11
Low 13 17 16 16 8 11 5 7 8
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000072357   ⟹   ENSRNOP00000067468
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl9789,606 - 799,496 (+)Ensembl
Rnor_6.0 Ensembl911,098,924 - 11,108,741 (-)Ensembl
RefSeq Acc Id: NM_001109673   ⟹   NP_001103143
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr89876,864 - 886,687 (+)NCBI
mRatBN7.29789,677 - 799,501 (+)NCBI
Rnor_6.0911,098,918 - 11,108,741 (-)NCBI
Rnor_5.0910,084,078 - 10,093,964 (-)NCBI
Celera97,706,956 - 7,716,779 (-)RGD
Sequence:
RefSeq Acc Id: XM_006244336   ⟹   XP_006244398
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr89876,790 - 886,687 (+)NCBI
mRatBN7.29789,603 - 799,505 (+)NCBI
Rnor_6.0911,098,914 - 11,108,806 (-)NCBI
Rnor_5.0910,084,078 - 10,093,964 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001103143 (Get FASTA)   NCBI Sequence Viewer  
  XP_006244398 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI29099 (Get FASTA)   NCBI Sequence Viewer  
  AAI69032 (Get FASTA)   NCBI Sequence Viewer  
  EDL83681 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000067468
  ENSRNOP00000067468.2
RefSeq Acc Id: NP_001103143   ⟸   NM_001109673
- UniProtKB: A2VD11 (UniProtKB/TrEMBL),   A6KR23 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006244398   ⟸   XM_006244336
- Peptide Label: isoform X1
- UniProtKB: A6KR23 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000067468   ⟸   ENSRNOT00000072357

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A2VD11-F1-model_v2 AlphaFold A2VD11 1-313 view protein structure

Transcriptome

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

Promoters
RGD ID:13696476
Promoter ID:EPDNEW_R7001
Type:initiation region
Name:Ccdc94_1
Description:coiled-coil domain containing 94
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_6.0911,108,774 - 11,108,834EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1589601 AgrOrtholog
BioCyc Gene G2FUF-28572 BioCyc
Ensembl Genes ENSRNOG00000047456 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000072357 ENTREZGENE
  ENSRNOT00000072357.2 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:8373484 IMAGE-MGC_LOAD
InterPro DUF572 UniProtKB/TrEMBL
  Yju2 UniProtKB/TrEMBL
KEGG Report rno:501285 UniProtKB/TrEMBL
MGC_CLONE MGC:156684 IMAGE-MGC_LOAD
NCBI Gene 501285 ENTREZGENE
PANTHER DUF572 UniProtKB/TrEMBL
  SPLICING FACTOR YJU2 UniProtKB/TrEMBL
Pfam DUF572 UniProtKB/TrEMBL
PhenoGen Yju2 PhenoGen
RatGTEx ENSRNOG00000047456 RatGTEx
UniProt A2VD11 ENTREZGENE, UniProtKB/TrEMBL
  A6KR23 ENTREZGENE, UniProtKB/TrEMBL
  M0RCY0_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-05-13 Yju2  YJU2 splicing factor  Yju2  YJU2 splicing factor homolog  Name changed 629549 APPROVED
2018-03-01 Yju2  YJU2 splicing factor homolog  Ccdc94  coiled-coil domain containing 94  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-05 Ccdc94  coiled-coil domain containing 94  LOC501285  similar to CG8435-PA  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC501285  similar to CG8435-PA      Symbol and Name status set to provisional 70820 PROVISIONAL