Yjefn3 (YjeF N-terminal domain containing 3) - Rat Genome Database

Send us a Message



 Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes QTLs Strains Markers Community Projects Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap)  (beta) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease COVID-19 Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes GERRC (Gene Editing Rat Resource Center) Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Yjefn3 (YjeF N-terminal domain containing 3) Rattus norvegicus
Analyze
Symbol: Yjefn3
Name: YjeF N-terminal domain containing 3
RGD ID: 1563236
Description: Predicted to enable NADHX epimerase activity. Orthologous to human YJEFN3 (YjeF N-terminal domain containing 3); INTERACTS WITH 6-propyl-2-thiouracil; amitrole; bisphenol A.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC498608; RGD1563236; similar to BC028663 protein; yjeF N-terminal domain-containing protein 3
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
mRatBN7.21619,533,742 - 19,539,759 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1619,533,788 - 19,539,728 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01621,282,355 - 21,288,656 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1621,282,467 - 21,288,406 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01621,198,438 - 21,204,519 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41620,011,423 - 20,024,519 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1619,722,785 - 19,729,087 (+)NCBICelera
Cytogenetic Map16p14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

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

Genomics

Comparative Map Data
Yjefn3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21619,533,742 - 19,539,759 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1619,533,788 - 19,539,728 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01621,282,355 - 21,288,656 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1621,282,467 - 21,288,406 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01621,198,438 - 21,204,519 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41620,011,423 - 20,024,519 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1619,722,785 - 19,729,087 (+)NCBICelera
Cytogenetic Map16p14NCBI
YJEFN3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381919,528,911 - 19,537,581 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1919,528,861 - 19,537,581 (+)EnsemblGRCh38hg38GRCh38
GRCh371919,639,720 - 19,648,390 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361919,500,720 - 19,509,393 (+)NCBINCBI36Build 36hg18NCBI36
Celera1919,543,732 - 19,552,455 (+)NCBICelera
Cytogenetic Map19p13.11NCBI
HuRef1919,201,895 - 19,210,613 (+)NCBIHuRef
CHM1_11919,640,582 - 19,649,297 (+)NCBICHM1_1
T2T-CHM13v2.01919,666,386 - 19,675,069 (+)NCBIT2T-CHM13v2.0
Yjefn3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39870,340,438 - 70,346,633 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl870,340,438 - 70,355,362 (-)EnsemblGRCm39 Ensembl
GRCm38869,887,788 - 69,893,983 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl869,887,788 - 69,902,712 (-)EnsemblGRCm38mm10GRCm38
MGSCv37872,411,716 - 72,417,874 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36872,816,476 - 72,822,964 (-)NCBIMGSCv36mm8
Celera872,446,530 - 72,452,678 (-)NCBICelera
Cytogenetic Map8B3.3NCBI
cM Map834.02NCBI
Yjefn3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555242,421,350 - 2,426,509 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555242,421,350 - 2,426,509 (-)NCBIChiLan1.0ChiLan1.0
YJEFN3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan11923,384,523 - 23,406,420 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01918,966,788 - 18,976,052 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11919,964,456 - 19,973,200 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1919,964,456 - 19,973,200 (+)Ensemblpanpan1.1panPan2
CILP2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12043,713,245 - 43,721,494 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2043,703,274 - 43,722,505 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2043,630,796 - 43,638,600 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02044,201,209 - 44,209,016 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2044,201,267 - 44,210,473 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12043,438,804 - 43,446,608 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02043,848,230 - 43,856,014 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02044,123,841 - 44,131,653 (-)NCBIUU_Cfam_GSD_1.0
Yjefn3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118202,388,092 - 202,396,603 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365961,937,225 - 1,946,500 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049365961,937,234 - 1,945,742 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
YJEFN3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl258,392,514 - 58,401,070 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1258,392,515 - 58,401,408 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2258,296,551 - 58,305,491 (+)NCBISscrofa10.2Sscrofa10.2susScr3
YJEFN3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1617,990,831 - 18,000,433 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660741,301,951 - 1,311,550 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Yjefn3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249082,319,698 - 2,325,339 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046249082,319,805 - 2,325,264 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Yjefn3
11 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:58
Count of miRNA genes:55
Interacting mature miRNAs:57
Transcripts:ENSRNOT00000065345
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
1600369Hcas8Hepatocarcinoma susceptibility QTL 8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)16122477621Rat
631830Alc7Alcohol consumption QTL 72.9consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16126727669Rat
634355Rends4Renal damage susceptibility QTL 40.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)16126727669Rat
1582235Insul8Insulin level QTL 83.30.0063blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)16126727669Rat
9590151Scort8Serum corticosterone level QTL 88.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)16130836262Rat
2302380Slep6Serum leptin concentration QTL 63.36blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16132139025Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16133418960Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16139533930Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16139533930Rat
631561Hcuc2Hepatic copper content QTL 22.8liver copper amount (VT:0003065)liver total copper weight (CMO:0001507)16139533949Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)16143534949Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16144588133Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16144977551Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1683223646053497Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)1683223659492508Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1683223659492508Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1683223659492508Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1683223659492508Rat
1300133Rf24Renal function QTL 243.64blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)16338015021361552Rat
2306902Bp339Blood pressure QTL 3390.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16338015043025077Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)16422760943025077Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16422760943025077Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)16422760943025077Rat
737819Hcas4Hepatocarcinoma susceptibility QTL 44.43liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)16422760946975965Rat
61405Niddm6Non-insulin dependent diabetes mellitus QTL 63.660.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)16422760948972724Rat
61338Bp23Blood pressure QTL 234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16422760949227609Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16422760960252231Rat
631517Scl9Serum cholesterol level QTL 93.3blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)161572643321034895Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
70215Niddm29Non-insulin dependent diabetes mellitus QTL 293.54blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)161900443575226532Rat

Markers in Region
RH138721  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21619,527,608 - 19,527,728 (+)MAPPERmRatBN7.2
Rnor_6.01621,276,287 - 21,276,406NCBIRnor6.0
Rnor_5.01621,192,371 - 21,192,490UniSTSRnor5.0
RGSC_v3.41620,012,399 - 20,012,518UniSTSRGSC3.4
Celera1619,716,717 - 19,716,836UniSTS
RH 3.4 Map16238.5UniSTS
Cytogenetic Map16p14UniSTS


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
Low 9 6 27 3 8 4
Below cutoff 1 40 22 15 13 15 6 8 47 26 31 7 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000065345   ⟹   ENSRNOP00000061892
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1619,533,788 - 19,539,728 (+)Ensembl
Rnor_6.0 Ensembl1621,282,467 - 21,288,406 (+)Ensembl
RefSeq Acc Id: XM_039094888   ⟹   XP_038950816
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21619,533,742 - 19,539,759 (+)NCBI
RefSeq Acc Id: XM_573886   ⟹   XP_573886
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21619,533,742 - 19,539,759 (+)NCBI
Rnor_6.01621,282,355 - 21,288,656 (+)NCBI
Rnor_5.01621,198,438 - 21,204,519 (+)NCBI
RGSC_v3.41620,011,423 - 20,024,519 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs XP_038950816 (Get FASTA)   NCBI Sequence Viewer  
  XP_573886 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL90631 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000061892
  ENSRNOP00000061892.4
Reference Protein Sequences
RefSeq Acc Id: XP_573886   ⟸   XM_573886
- Peptide Label: isoform X2
- UniProtKB: F1M695 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000061892   ⟸   ENSRNOT00000065345
RefSeq Acc Id: XP_038950816   ⟸   XM_039094888
- Peptide Label: isoform X1
Protein Domains
YjeF N-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1M695-F1-model_v2 AlphaFold F1M695 1-250 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:1563236 AgrOrtholog
BioCyc Gene G2FUF-11744 BioCyc
Ensembl Genes ENSRNOG00000039191 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000065345 ENTREZGENE
  ENSRNOT00000065345.4 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.10260 UniProtKB/TrEMBL
InterPro YjeF_N UniProtKB/TrEMBL
  YjeF_N_dom_sf UniProtKB/TrEMBL
  YJEFN_prot_eukaryotes UniProtKB/TrEMBL
NCBI Gene 498608 ENTREZGENE
PANTHER PTHR13232 UniProtKB/TrEMBL
  YJEF N-TERMINAL DOMAIN-CONTAINING PROTEIN 3 UniProtKB/TrEMBL
Pfam YjeF_N UniProtKB/TrEMBL
PhenoGen Yjefn3 PhenoGen
PROSITE YJEF_N UniProtKB/TrEMBL
RatGTEx ENSRNOG00000039191 RatGTEx
Superfamily-SCOP YjeF_N UniProtKB/TrEMBL
UniProt F1M695 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-09 Yjefn3  YjeF N-terminal domain containing 3  RGD1563236  similar to BC028663 protein   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1563236  similar to BC028663 protein   RGD1563236_predicted  similar to BC028663 protein (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1563236_predicted  similar to BC028663 protein (predicted)  LOC498608  similar to BC028663 protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC498608  similar to BC028663 protein      Symbol and Name status set to provisional 70820 PROVISIONAL