Nif3l1 (NGG1 interacting factor 3 like 1) - Rat Genome Database
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Gene: Nif3l1 (NGG1 interacting factor 3 like 1) Rattus norvegicus
Analyze
Symbol: Nif3l1
Name: NGG1 interacting factor 3 like 1
RGD ID: 1310329
Description: Predicted to have identical protein binding activity and transcription factor binding activity. Predicted to be involved in negative regulation of nucleic acid-templated transcription; neuron differentiation; and positive regulation of transcription, DNA-templated. Predicted to localize to mitochondrion and nucleus. Orthologous to human NIF3L1 (NGG1 interacting factor 3 like 1); INTERACTS WITH bisphenol A; endosulfan; flutamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: GTP cyclohydrolase I; LOC301431; Ngg1 interacting factor 3-like 1; Ngg1 interacting factor 3-like 1 (S. pombe); NIF3 NGG1 interacting factor 3-like 1; NIF3 NGG1 interacting factor 3-like 1 (S. cerevisiae); NIF3 NGG1 interacting factor 3-like 1 (S. pombe); NIF3-like protein 1; putative GTP cyclohydrolase 1 type 2 Nif3l1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2959,980,101 - 60,001,490 (+)NCBI
Rnor_6.0 Ensembl965,331,290 - 65,349,141 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0965,329,143 - 65,349,280 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0965,136,444 - 65,156,450 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4957,105,338 - 57,122,976 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1957,252,319 - 57,269,957 (+)NCBI
Celera957,425,453 - 57,443,091 (+)NCBICelera
Cytogenetic Map9q31NCBI
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
cytoplasm  (IBA,IEA,ISO,ISS)
mitochondrion  (IBA)
nucleus  (IEA,ISO,ISS)

Molecular Function

References

Additional References at PubMed
PMID:11124544   PMID:12477932   PMID:12522100   PMID:12951069   PMID:15163635   PMID:16189514   PMID:18614015   PMID:25416956   PMID:31515488  


Genomics

Comparative Map Data
Nif3l1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2959,980,101 - 60,001,490 (+)NCBI
Rnor_6.0 Ensembl965,331,290 - 65,349,141 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0965,329,143 - 65,349,280 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0965,136,444 - 65,156,450 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4957,105,338 - 57,122,976 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1957,252,319 - 57,269,957 (+)NCBI
Celera957,425,453 - 57,443,091 (+)NCBICelera
Cytogenetic Map9q31NCBI
NIF3L1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2200,889,327 - 200,903,938 (+)EnsemblGRCh38hg38GRCh38
GRCh382200,889,327 - 200,903,932 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372201,754,050 - 201,768,655 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362201,462,391 - 201,476,898 (+)NCBINCBI36hg18NCBI36
Build 342201,579,651 - 201,594,159NCBI
Celera2195,508,680 - 195,523,285 (+)NCBI
Cytogenetic Map2q33.1NCBI
HuRef2193,605,423 - 193,620,028 (+)NCBIHuRef
CHM1_12201,760,035 - 201,774,640 (+)NCBICHM1_1
Nif3l1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39158,484,310 - 58,501,435 (+)NCBIGRCm39mm39
GRCm38158,445,151 - 58,462,276 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl158,445,151 - 58,481,816 (+)EnsemblGRCm38mm10GRCm38
MGSCv37158,504,478 - 58,519,120 (+)NCBIGRCm37mm9NCBIm37
MGSCv36158,390,174 - 58,406,822 (+)NCBImm8
Celera158,965,880 - 58,980,507 (+)NCBICelera
Cytogenetic Map1C1.3NCBI
Nif3l1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955403628,924 - 640,703 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955403628,069 - 640,703 (-)NCBIChiLan1.0ChiLan1.0
NIF3L1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12B206,303,865 - 206,319,810 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B206,303,931 - 206,319,810 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02B88,145,137 - 88,161,319 (+)NCBIMhudiblu_PPA_v0panPan3
NIF3L1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl3710,083,104 - 10,107,050 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.13710,082,823 - 10,136,647 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Nif3l1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936726194,873 - 212,487 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NIF3L1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15104,583,809 - 104,606,972 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.115104,583,736 - 104,606,507 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215115,686,849 - 115,691,851 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NIF3L1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11086,545,392 - 86,593,386 (+)NCBI
ChlSab1.1 Ensembl1086,545,014 - 86,564,263 (+)Ensembl
Nif3l1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624889273,072 - 284,777 (-)NCBI

Position Markers
RH134827  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0965,348,774 - 65,348,991NCBIRnor6.0
Rnor_5.0965,156,068 - 65,156,285UniSTSRnor5.0
RGSC_v3.4957,122,823 - 57,123,040UniSTSRGSC3.4
Celera957,442,938 - 57,443,155UniSTS
RH 3.4 Map9479.08UniSTS
Cytogenetic Map9q31UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9105522293442944Rat
631680Cm11Cardiac mass QTL 113.10.00089heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)92488509969885099Rat
70186Niddm26Non-insulin dependent diabetes mellitus QTL 263.87blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)92569234292741406Rat
631643Bp120Blood pressure QTL 12030.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)92569237370692373Rat
1300180Bw14Body weight QTL 143.776body mass (VT:0001259)body weight (CMO:0000012)92748603666757620Rat
7207814Bmd91Bone mineral density QTL 913.5femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)92748615588333183Rat
70218Cm28Cardiac mass QTL 288.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)92907507983686404Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)929075079122095297Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)929466970107878528Rat
1641894Alcrsp12Alcohol response QTL 12response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)93238513377385133Rat
7411571Bw138Body weight QTL 13814.30.001body mass (VT:0001259)body weight gain (CMO:0000420)93764235182642351Rat
7411656Foco26Food consumption QTL 269.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)93764235182642351Rat
1598834Memor11Memory QTL 112.5exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)94126103490024806Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)94126103498606834Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)941261034102531865Rat
6903941Pur31Proteinuria QTL 310.036total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)94657976991579769Rat
11353949Bp393Blood pressure QTL 393arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94657976991579769Rat
61352Bp34Blood pressure QTL 345arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94695242783686153Rat
10058949Gmadr5Adrenal mass QTL 520.014adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)94724896594124663Rat
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)95417754299177542Rat
1598849Memor17Memory QTL 172.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)95488504176677636Rat
2303170Bp332Blood pressure QTL 3323.730.027arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)96081029882732466Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)961186278106186278Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)96173092382890620Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)96173092382890620Rat
2303180Bp333Blood pressure QTL 3330.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)96173092382890620Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)963270073107878387Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:81
Count of miRNA genes:50
Interacting mature miRNAs:62
Transcripts:ENSRNOT00000018014, ENSRNOT00000058667
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.


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 28 33 17 19 17 1 1 74 34 39 11 1
Low 15 24 24 24 7 10 1 2 7
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001024763 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006244958 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006244960 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006244961 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006244962 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006244963 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017596361 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083306 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083307 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083308 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083310 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005488870 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC123462 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC097437 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC097992 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473965 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000214 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000018014   ⟹   ENSRNOP00000018014
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl965,331,374 - 65,349,141 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000058667   ⟹   ENSRNOP00000055461
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl965,331,290 - 65,348,926 (+)Ensembl
RefSeq Acc Id: NM_001024763   ⟹   NP_001019934
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2959,982,289 - 59,999,928 (+)NCBI
Rnor_6.0965,331,290 - 65,348,927 (+)NCBI
Rnor_5.0965,136,444 - 65,156,450 (+)NCBI
RGSC_v3.4957,105,338 - 57,122,976 (+)RGD
Celera957,425,453 - 57,443,091 (+)RGD
Sequence:
RefSeq Acc Id: XM_006244958   ⟹   XP_006245020
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2959,980,104 - 60,000,144 (+)NCBI
Rnor_6.0965,329,146 - 65,348,816 (+)NCBI
Rnor_5.0965,136,444 - 65,156,450 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006244960   ⟹   XP_006245022
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2959,980,104 - 60,000,144 (+)NCBI
Rnor_6.0965,329,156 - 65,348,816 (+)NCBI
Rnor_5.0965,136,444 - 65,156,450 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006244961   ⟹   XP_006245023
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2959,980,104 - 60,000,159 (+)NCBI
Rnor_6.0965,329,147 - 65,349,280 (+)NCBI
Rnor_5.0965,136,444 - 65,156,450 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006244962   ⟹   XP_006245024
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2959,980,101 - 60,000,144 (+)NCBI
Rnor_6.0965,329,143 - 65,348,816 (+)NCBI
Rnor_5.0965,136,444 - 65,156,450 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006244963   ⟹   XP_006245025
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2959,980,104 - 59,999,928 (+)NCBI
Rnor_6.0965,329,144 - 65,348,927 (+)NCBI
Rnor_5.0965,136,444 - 65,156,450 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596361   ⟹   XP_017451850
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2959,981,252 - 60,000,144 (+)NCBI
Rnor_6.0965,330,318 - 65,348,816 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039083306   ⟹   XP_038939234
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2959,981,252 - 60,000,144 (+)NCBI
RefSeq Acc Id: XM_039083307   ⟹   XP_038939235
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2959,980,104 - 60,001,490 (+)NCBI
RefSeq Acc Id: XM_039083308   ⟹   XP_038939236
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2959,981,252 - 60,000,144 (+)NCBI
RefSeq Acc Id: XM_039083310   ⟹   XP_038939238
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2959,980,104 - 59,991,404 (+)NCBI
RefSeq Acc Id: XR_001839652
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0965,329,143 - 65,342,584 (+)NCBI
Sequence:
RefSeq Acc Id: XR_005488870
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2959,980,104 - 59,987,910 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001019934   ⟸   NM_001024763
- UniProtKB: Q4V8D5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006245025   ⟸   XM_006244963
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006245024   ⟸   XM_006244962
- Peptide Label: isoform X2
- UniProtKB: Q4V7D6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006245023   ⟸   XM_006244961
- Peptide Label: isoform X2
- UniProtKB: Q4V7D6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006245020   ⟸   XM_006244958
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006245022   ⟸   XM_006244960
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017451850   ⟸   XM_017596361
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000018014   ⟸   ENSRNOT00000018014
RefSeq Acc Id: ENSRNOP00000055461   ⟸   ENSRNOT00000058667
RefSeq Acc Id: XP_038939235   ⟸   XM_039083307
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038939238   ⟸   XM_039083310
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038939234   ⟸   XM_039083306
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038939236   ⟸   XM_039083308
- Peptide Label: isoform X2

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
9 65138792 65138793 C T snv COP/CrCrl (MCW & UW), ZFDM (KyushuU), SBH/Ygl (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SBN/Ygl (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), LH/MavRrrc (KNAW), LL/MavRrrc (KNAW), LN/MavRrrc (KNAW), MR/N (KNAW), SR/JrHsd (KNAW), SS/Jr (KNAW), SS/JrHsdMcwi (KNAW), WAG/Rij (KNAW), BBDP/WorN (KNAW), SBH/Ygl (KNAW), SBN/Ygl (KNAW), SHR/NCrlPrin (KNAW), SHR/NHsd (KNAW), SHR/OlaIpcv (KNAW), SHR/OlaIpcvPrin (KNAW), SHRSP/Gcrc (KNAW), F344/NRrrc (Illumina) (KNAW), WKY/Gcrc (KNAW), WKY/N (KNAW), WKY/NCrl (KNAW), WKY/NHsd (KNAW), BUF/N (KNAW), DA/BklArbNsi (KNAW), F344/NRrrc (SOLiD) (KNAW), F344/NCrl (KNAW), F344/NHsd (KNAW), FHH/EurMcwi (KNAW), FHL/EurMcwi (KNAW), GK/Ox (KNAW), LEW/Crl (KNAW), LEW/NCrl (KNAW), MNS/Gib (KNAW), WN/N (KNAW), LE/OrlBarth (UDEL), Crl:SD (UDEL), BUF/MNa (KyushuU), NIG-III/Hok (KyushuU), F344/DuCrlCrlj (KyushuU), HTX/Kyo (KyushuU), F344/NSlc (KyushuU), RCS/Kyo (KyushuU), F344/Stm (KyushuU), HWY/Slc (KyushuU), F344/Jcl (KyushuU), BDIX/NemOda (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), KFRS3B/Kyo (KyushuU), ZF (KyushuU), GH/OmrMcwi (MCW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
9 65331498 65331499 C T snv COP/CrCrl (MCW & UW), WKY/NHsd (RGD), SBH/Ygl (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SBN/Ygl (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), CDR, CDS, Buf/N (MCW), F344/NRrrc (MCW), MR/N (MCW), WKY/N (MCW), WN/N (MCW), FHL/EurMcwi (RGD), BBDP/Wor (RGD), F344/NCrl (RGD), FHH/EurMcwi (RGD), GK/Ox (RGD), LEW/Crl (RGD), LEW/NCrlBR (RGD), LH/MavRrrc (RGD), LN/MavRrrc (RGD), LL/MavRrrc (RGD), MNS/Gib (RGD), SBH/Ygl (RGD), SBN/Ygl (RGD), SHR/NHsd (RGD), SHRSP/Gcrc (RGD), SR/JrHsd (RGD), SS/Jr (RGD), SS/JrHsdMcwi (RGD), WAG/Rij (RGD), WKY/NCrl (RGD), WKY/Gcrc (RGD), GH/OmrMcwi (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
9 57105546 57105547 C T snv SHR/OlaIpcv (ICL), DA/BklArbNsi (ICAHN), SHRSP/Gcrc (MDC), SS/JrHsdMcwi (MDC), BUF/N (KNAW), F344/NRrrc (KNAW), MR/N (KNAW), WKY/N (KNAW), WN/N (KNAW), SHR/OlaIpcv (KNAW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), BBDP/WorN (ICL), F344/NCrl (ICL), FHH/EurMcwi (ICL), FHL/EurMcwi (ICL), GK/Ox (ICL), LEW/Crl (ICL), LEW/NCrl (ICL), LH/MavRrrc (ICL), LL/MavRrrc (ICL), LN/MavRrrc (ICL), MNS/Gib (ICL), SBH/Ygl (ICL), SBN/Ygl (ICL), SHR/OlaIpcv (ICL), SHR/NHsd (ICL), SHRSP/Gcrc (ICL), SR/JrHsd (ICL), SS/Jr (ICL), SS/JrHsdMcwi (ICL), WAG/Rij (ICL), WKY/Gcrc (ICL), WKY/NHsd (ICL), WKY/NCrl (ICL), HCR/1Mco (UMich), LCR/1Mco (UMich), HCR/2Mco (UMich), LCR/2Mco (UMich), F344/NHsd (ICAHN), FHH/EurMcwi (MDC)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310329 AgrOrtholog
Ensembl Genes ENSRNOG00000013446 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000018014 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000055461 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000018014 UniProtKB/Swiss-Prot
  ENSRNOT00000058667 ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7446502 IMAGE-MGC_LOAD
  IMAGE:7455562 IMAGE-MGC_LOAD
InterPro GTP_cyclohydrolase_I/Nif3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GTP_cyclohydrolase_I/Nif3_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NIF3L1_animal UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:301431 UniProtKB/TrEMBL
MGC_CLONE MGC:114487 IMAGE-MGC_LOAD
  MGC:116136 IMAGE-MGC_LOAD
NCBI Gene 301431 ENTREZGENE
PANTHER PTHR13799 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam NIF3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Nif3l1 PhenoGen
PIRSF UCP037490_NIF3_euk UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF102705 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGRFAMs YbgI_SA1388 UniProtKB/Swiss-Prot
UniProt NIF3L_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q4V8D5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-30 Nif3l1  NGG1 interacting factor 3 like 1  Nif3l1  NIF3 NGG1 interacting factor 3-like 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-07-09 Nif3l1  NIF3 NGG1 interacting factor 3-like 1  Nif3l1  NIF3 NGG1 interacting factor 3-like 1 (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-12-06 Nif3l1  NIF3 NGG1 interacting factor 3-like 1 (S. cerevisiae)  Nif3l1  NIF3 NGG1 interacting factor 3-like 1 (S. pombe)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-24 Nif3l1  NIF3 NGG1 interacting factor 3-like 1 (S. pombe)  Nif3l1  Ngg1 interacting factor 3-like 1 (S. pombe)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Nif3l1  Ngg1 interacting factor 3-like 1 (S. pombe)  Nif3l1_predicted  Ngg1 interacting factor 3-like 1 (S. pombe) (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Nif3l1_predicted  Ngg1 interacting factor 3-like 1 (S. pombe) (predicted)      Symbol and Name status set to approved 70820 APPROVED