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

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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 NAD(P)HX epimerase activity. Predicted to be active in mitochondrion. Orthologous to human YJEFN3 (YjeF N-terminal domain containing 3); INTERACTS WITH 6-propyl-2-thiouracil; amitrole; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
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
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81619,567,565 - 19,573,667 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1619,558,947 - 19,573,956 (+)EnsemblGRCr8
mRatBN7.21619,533,742 - 19,539,759 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1619,533,788 - 19,539,728 (+)EnsemblmRatBN7.2
Rnor_6.01621,282,355 - 21,288,656 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1621,282,467 - 21,288,406 (+)Ensemblrn6Rnor6.0
Rnor_5.01621,198,438 - 21,204,519 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41620,011,423 - 20,024,519 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1619,722,785 - 19,729,087 (+)NCBICelera
Cytogenetic Map16p14NCBI
JBrowse:




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

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

Genomics

Comparative Map Data
Yjefn3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81619,567,565 - 19,573,667 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1619,558,947 - 19,573,956 (+)EnsemblGRCr8
mRatBN7.21619,533,742 - 19,539,759 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1619,533,788 - 19,539,728 (+)EnsemblmRatBN7.2
Rnor_6.01621,282,355 - 21,288,656 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1621,282,467 - 21,288,406 (+)Ensemblrn6Rnor6.0
Rnor_5.01621,198,438 - 21,204,519 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41620,011,423 - 20,024,519 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
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 - 19,537,584 (+)Ensemblhg38GRCh38
GRCh371919,639,720 - 19,648,390 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361919,500,720 - 19,509,393 (+)NCBIBuild 36Build 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 EnsemblGRCm39
GRCm38869,887,788 - 69,893,983 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl869,887,788 - 69,902,712 (-)Ensemblmm10GRCm38
MGSCv37872,411,716 - 72,417,874 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
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 (-)Ensembl
ChiLan1.0NW_0049555242,421,350 - 2,426,509 (-)NCBIChiLan1.0ChiLan1.0
YJEFN3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22024,378,339 - 24,399,970 (+)NCBINHGRI_mPanPan1-v2
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 (+)EnsemblpanPan2panpan1.1
YJEFN3
(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 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2043,630,796 - 43,638,600 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02044,201,209 - 44,209,016 (-)NCBIROS_Cfam_1.0ROS_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_1.0UU_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 Ensembl
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 (-)EnsemblsusScr11Sscrofa11.1
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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046249082,319,805 - 2,325,264 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Yjefn3
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11312,155,846 - 12,162,004 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Yjefn3
27 total Variants
miRNA Target Status (No longer updated)

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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1549842Bp248Blood pressure QTL 2480.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1638712345387123Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16133425095Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16139568015Rat
737819Hcas4Hepatocarcinoma susceptibility QTL 44.43liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)16423421253708481Rat
631517Scl9Serum cholesterol level QTL 93.3blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)161574800625801629Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16474422249744222Rat
61405Niddm6Non-insulin dependent diabetes mellitus QTL 63.660.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)16126734272Rat
631830Alc7Alcohol consumption QTL 72.9consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16126734272Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16435482249354822Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)longest distance run on treadmill (CMO:0001406)1638712345387123Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)16423421249757901Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16423421266955197Rat
1600369Hcas8Hepatocarcinoma susceptibility QTL 8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)161627818427244292Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16139568015Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1683908666195506Rat
2306902Bp339Blood pressure QTL 3390.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16338679049757901Rat
1300133Rf24Renal function QTL 243.64blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)16338679026128267Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)1683908666195506Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1683908666195506Rat
634355Rends4Renal damage susceptibility QTL 40.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)16126734272Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161773081872536785Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1683908652786090Rat
2301406Kidm39Kidney mass QTL 390.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)161590580260905802Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1683908666195506Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)16330168348301683Rat

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

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
13 8 50 129 56 55 24 34 24 6 198 109 3 106 46 65 31 9 9

Sequence


Ensembl Acc Id: ENSRNOT00000027980   ⟹   ENSRNOP00000027980
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1619,558,947 - 19,570,041 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000065345   ⟹   ENSRNOP00000061892
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1619,567,689 - 19,573,956 (+)Ensembl
mRatBN7.2 Ensembl1619,533,788 - 19,539,728 (+)Ensembl
Rnor_6.0 Ensembl1621,282,467 - 21,288,406 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000128440   ⟹   ENSRNOP00000099759
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1619,567,689 - 19,573,666 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000160028   ⟹   ENSRNOP00000102553
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1619,558,947 - 19,572,479 (+)Ensembl
RefSeq Acc Id: XM_039094888   ⟹   XP_038950816
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81619,567,625 - 19,573,667 (+)NCBI
mRatBN7.21619,533,742 - 19,539,759 (+)NCBI
RefSeq Acc Id: XM_063275930   ⟹   XP_063132000
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81619,567,625 - 19,573,667 (+)NCBI
RefSeq Acc Id: XM_573886   ⟹   XP_573886
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81619,567,565 - 19,573,667 (+)NCBI
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:
RefSeq Acc Id: XP_573886   ⟸   XM_573886
- Peptide Label: isoform X2
- Sequence:
Ensembl Acc Id: ENSRNOP00000061892   ⟸   ENSRNOT00000065345
RefSeq Acc Id: XP_038950816   ⟸   XM_039094888
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063132000   ⟸   XM_063275930
- Peptide Label: isoform X3
Ensembl Acc Id: ENSRNOP00000027980   ⟸   ENSRNOT00000027980
Ensembl Acc Id: ENSRNOP00000102553   ⟸   ENSRNOT00000160028
Ensembl Acc Id: ENSRNOP00000099759   ⟸   ENSRNOT00000128440

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 ENSRNOT00000027980.9 UniProtKB/TrEMBL
  ENSRNOT00000065345 ENTREZGENE
  ENSRNOT00000065345.5 UniProtKB/TrEMBL
  ENSRNOT00000128440.1 UniProtKB/TrEMBL
  ENSRNOT00000160028.1 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.10260 UniProtKB/TrEMBL
InterPro GRIM-19 UniProtKB/TrEMBL
  YjeF_N UniProtKB/TrEMBL
  YjeF_N_dom_sf UniProtKB/TrEMBL
  YJEFN_prot_eukaryotes UniProtKB/TrEMBL
NCBI Gene 498608 ENTREZGENE
PANTHER NADH DEHYDROGENASE [UBIQUINONE] 1 ALPHA SUBCOMPLEX SUBUNIT 13 UniProtKB/TrEMBL
  NADH DEHYDROGENASE UBIQUINONE 1 ALPHA SUBCOMPLEX SUBUNIT 13 UniProtKB/TrEMBL
  PTHR13232 UniProtKB/TrEMBL
  YJEF N-TERMINAL DOMAIN-CONTAINING PROTEIN 3 UniProtKB/TrEMBL
Pfam GRIM-19 UniProtKB/TrEMBL
  YjeF_N UniProtKB/TrEMBL
PhenoGen Yjefn3 PhenoGen
PROSITE YJEF_N UniProtKB/TrEMBL
RatGTEx ENSRNOG00000039191 RatGTEx
Superfamily-SCOP YjeF_N UniProtKB/TrEMBL
UniProt A0ABK0LD16_RAT UniProtKB/TrEMBL
  A0ABK0LE67_RAT UniProtKB/TrEMBL
  D3ZE15_RAT UniProtKB/TrEMBL
  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