Ngef (neuronal guanine nucleotide exchange factor) - Rat Genome Database
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Gene: Ngef (neuronal guanine nucleotide exchange factor) Rattus norvegicus
Analyze
Symbol: Ngef
Name: neuronal guanine nucleotide exchange factor
RGD ID: 1309055
Description: Predicted to have ephrin receptor binding activity and guanyl-nucleotide exchange factor activity. Predicted to be involved in several processes, including ephrin receptor signaling pathway; negative regulation of dendritic spine morphogenesis; and synapse pruning. Predicted to localize to glutamatergic synapse. Orthologous to human NGEF (neuronal guanine nucleotide exchange factor); PARTICIPATES IN ephrin - ephrin receptor bidirectional signaling axis; INTERACTS WITH (+)-schisandrin B; 1,2-dimethylhydrazine; 17beta-estradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Besh3; brain-enriched SH3-domain protein Besh3; eph-interacting exchange protein; ephexin-1; LOC360451
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
mRatBN7.2988,146,956 - 88,244,454 (-)NCBI
Rnor_6.0 Ensembl994,569,286 - 94,601,852 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0994,569,286 - 94,601,852 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0994,290,729 - 94,323,295 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4986,294,206 - 86,327,765 (-)NCBIRGSC3.4rn4RGSC3.4
Celera985,556,597 - 85,590,171 (-)NCBICelera
Cytogenetic Map9q35NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (EXP)
17beta-estradiol  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-amino-2-deoxy-D-glucopyranose  (ISO)
3,3',4,4'-tetrachlorobiphenyl  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
8-Br-cAMP  (ISO)
acetamide  (EXP)
acrylamide  (EXP)
aflatoxin B1  (ISO)
aldehydo-D-glucosamine  (ISO)
ammonium chloride  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
belinostat  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[a]pyrene diol epoxide I  (ISO)
beta-D-glucosamine  (ISO)
bisphenol A  (EXP)
bisphenol F  (ISO)
butanal  (ISO)
carbon nanotube  (ISO)
carmustine  (EXP)
choline  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
clothianidin  (ISO)
cobalt dichloride  (EXP)
copper(II) sulfate  (ISO)
cyclosporin A  (ISO)
daunorubicin  (ISO)
dibenz[a,h]anthracene  (ISO)
diethylstilbestrol  (ISO)
dorsomorphin  (ISO)
endosulfan  (EXP)
entinostat  (ISO)
flavonoids  (EXP)
folic acid  (ISO)
fonofos  (ISO)
genistein  (ISO)
glafenine  (EXP)
L-methionine  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
methotrexate  (EXP)
methylmercury chloride  (ISO)
p-toluidine  (EXP)
panobinostat  (ISO)
paracetamol  (ISO)
parathion  (ISO)
pentanal  (ISO)
perfluorooctane-1-sulfonic acid  (EXP)
phenformin  (EXP)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
propanal  (ISO)
propiconazole  (ISO)
quercetin  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
tamoxifen  (ISO)
terbufos  (ISO)
tetrachloromethane  (EXP,ISO)
tioguanine  (EXP)
tributylstannane  (ISO)
troglitazone  (ISO)
urethane  (ISO)
valproic acid  (ISO)
zearalenone  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:10777665   PMID:11336673   PMID:15057822   PMID:15489334   PMID:15848799   PMID:17143272   PMID:20949525   PMID:22871113  


Genomics

Comparative Map Data
Ngef
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2988,146,956 - 88,244,454 (-)NCBI
Rnor_6.0 Ensembl994,569,286 - 94,601,852 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0994,569,286 - 94,601,852 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0994,290,729 - 94,323,295 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4986,294,206 - 86,327,765 (-)NCBIRGSC3.4rn4RGSC3.4
Celera985,556,597 - 85,590,171 (-)NCBICelera
Cytogenetic Map9q35NCBI
NGEF
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2232,878,701 - 233,013,256 (-)EnsemblGRCh38hg38GRCh38
GRCh382232,878,686 - 233,013,256 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372233,743,411 - 233,877,966 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362233,451,655 - 233,586,182 (-)NCBINCBI36hg18NCBI36
Celera2227,507,672 - 227,643,202 (-)NCBI
Cytogenetic Map2q37.1NCBI
HuRef2225,592,253 - 225,726,431 (-)NCBIHuRef
CHM1_12233,749,324 - 233,883,758 (-)NCBICHM1_1
Ngef
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39187,404,551 - 87,501,661 (-)NCBIGRCm39mm39
GRCm39 Ensembl187,404,556 - 87,501,592 (-)Ensembl
GRCm38187,476,829 - 87,573,870 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl187,476,834 - 87,573,870 (-)EnsemblGRCm38mm10GRCm38
MGSCv37189,373,404 - 89,470,445 (-)NCBIGRCm37mm9NCBIm37
MGSCv36189,308,005 - 89,341,517 (-)NCBImm8
Celera190,442,498 - 90,539,911 (-)NCBICelera
Cytogenetic Map1DNCBI
cM Map144.42NCBI
Ngef
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554533,082,628 - 3,186,039 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554533,082,826 - 3,186,039 (+)NCBIChiLan1.0ChiLan1.0
NGEF
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12B239,027,286 - 239,155,874 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B239,027,286 - 239,155,874 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02B120,110,441 - 120,153,934 (-)NCBIMhudiblu_PPA_v0panPan3
NGEF
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2544,474,174 - 44,547,872 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12544,473,422 - 44,547,838 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Ngef
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365254,250,389 - 4,282,041 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NGEF
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15133,332,718 - 133,460,166 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.115133,332,715 - 133,460,161 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215147,333,684 - 147,429,402 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NGEF
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.110118,911,019 - 118,959,259 (-)NCBI
Ngef
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248435,558,053 - 5,648,869 (-)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
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
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
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)95417754299177542Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)961186278106186278Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)963270073107878387Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)966757444112943287Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)96745166499920892Rat
1578757Pur6Proteinuria QTL 63.30.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)96745166499920892Rat
61385Edpm9Estrogen-dependent pituitary mass QTL 93.430.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)970241351115241351Rat
731171Glom6Glomerulus QTL 62.80.0003kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)970942881115942881Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)981411073119983851Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)98368615398164303Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)98368615398164303Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)98368615398164303Rat
724547Cm21Cardiac mass QTL 212.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)983686153111609081Rat
4889852Pur26Proteinuria QTL 26150.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)990024661107199079Rat
7794784Mcs31Mammary carcinoma susceptibility QTL 312.98mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)990024661119983851Rat
4889943Bss90Bone structure and strength QTL 904.1tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)99274129798606834Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:317
Count of miRNA genes:198
Interacting mature miRNAs:221
Transcripts:ENSRNOT00000022485
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.


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 12 12 12 54 4 14
Low 9 36 29 5 29 5 8 20 27 21 11 5
Below cutoff 30 9 13 3 3 4 6 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000022485   ⟹   ENSRNOP00000022485
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl994,569,286 - 94,601,852 (-)Ensembl
RefSeq Acc Id: NM_001136241   ⟹   NP_001129713
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2988,146,956 - 88,180,387 (-)NCBI
Rnor_6.0994,569,286 - 94,601,852 (-)NCBI
Rnor_5.0994,290,729 - 94,323,295 (-)NCBI
RGSC_v3.4986,294,206 - 86,327,765 (-)RGD
Celera985,556,597 - 85,590,171 (-)RGD
Sequence:
RefSeq Acc Id: XM_039083015   ⟹   XP_038938943
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2988,146,956 - 88,244,454 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001129713 (Get FASTA)   NCBI Sequence Viewer  
  XP_038938943 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH78722 (Get FASTA)   NCBI Sequence Viewer  
  AAH91122 (Get FASTA)   NCBI Sequence Viewer  
  EDL75642 (Get FASTA)   NCBI Sequence Viewer  
  Q5BKC9 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001129713   ⟸   NM_001136241
- UniProtKB: G3V856 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000022485   ⟸   ENSRNOT00000022485
RefSeq Acc Id: XP_038938943   ⟸   XM_039083015
- Peptide Label: isoform X1
Protein Domains
DH   PH   SH3

Transcriptome

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

Promoters
RGD ID:13696836
Promoter ID:EPDNEW_R7361
Type:single initiation site
Name:Ngef_1
Description:neuronal guanine nucleotide exchange factor
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_6.0994,601,900 - 94,601,960EPDNEW

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)
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)
FHH/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
FHL/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)
FHL/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
GH/OmrMcwi (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)
GK/Ox (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
LE/Stm (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
LEW/Crl (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
LEW/NCrlBR (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
LH/MavRrrc (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
LL/MavRrrc (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
LN/MavRrrc (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
M520/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
MHS/Gib (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
MNS/Gib (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
MR/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
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309055 AgrOrtholog
Ensembl Genes ENSRNOG00000016653 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000022485 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000022485 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.20.900.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  2.30.29.30 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro DBL_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DH-domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ephexin-1_SH3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PH-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PH_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:246217 UniProtKB/TrEMBL
NCBI Gene 246217 ENTREZGENE
Pfam PF00169 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RhoGEF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ngef PhenoGen
PROSITE DH_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PH_DOMAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART RhoGEF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00233 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48065 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF50044 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt G3V856 ENTREZGENE, UniProtKB/TrEMBL
  NGEF_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q6AZ62_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-12-05 Ngef  neuronal guanine nucleotide exchange factor  Ngef_predicted  neuronal guanine nucleotide exchange factor (predicted)  Symbol and Name updated 1299863 APPROVED
2006-12-05 Ngef_predicted  neuronal guanine nucleotide exchange factor (predicted)  Besh3_retired    Data Merged 737654 APPROVED
2006-12-05 Besh3_retired    Besh3  brain-enriched SH3-domain protein Besh3  Symbol and Name updated 1299863 APPROVED
2005-01-12 Ngef_predicted  neuronal guanine nucleotide exchange factor (predicted)      Symbol and Name status set to approved 70820 APPROVED
2003-02-27 Besh3  brain-enriched SH3-domain protein Besh3      Symbol and Name status set to provisional 70820 PROVISIONAL