Arfgef1 (ADP ribosylation factor guanine nucleotide exchange factor 1) - Rat Genome Database
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Gene: Arfgef1 (ADP ribosylation factor guanine nucleotide exchange factor 1) Rattus norvegicus
Analyze
Symbol: Arfgef1
Name: ADP ribosylation factor guanine nucleotide exchange factor 1
RGD ID: 1560793
Description: Predicted to have guanyl-nucleotide exchange factor activity; myosin binding activity; and protein kinase A regulatory subunit binding activity. Involved in neuron projection development and positive regulation of protein kinase B signaling. Localizes to trans-Golgi network. Orthologous to human ARFGEF1 (ADP ribosylation factor guanine nucleotide exchange factor 1); INTERACTS WITH bisphenol A; DDT; glafenine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: ADP-ribosylation factor guanine nucleotide-exchange factor 1; ADP-ribosylation factor guanine nucleotide-exchange factor 1(brefeldin A-inhibited); BIG1; brefeldin A-inhibited GEP 1; brefeldin A-inhibited guanine nucleotide-exchange protein 1; LOC312915; RGD1560793; similar to brefeldin A-inhibited guanine nucleotide-exchange protein 1
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
mRatBN7.258,982,061 - 9,076,326 (+)NCBI
Rnor_6.0 Ensembl58,666,200 - 8,760,458 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.058,666,046 - 8,760,458 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0513,474,381 - 13,568,680 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.458,498,644 - 8,592,918 (+)NCBIRGSC3.4rn4RGSC3.4
Celera58,494,495 - 8,587,878 (+)NCBICelera
Cytogenetic Map5q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References

Additional References at PubMed
PMID:10716990   PMID:12571360   PMID:14973189   PMID:17227842   PMID:18292223   PMID:20360857   PMID:22084092   PMID:22871113   PMID:23220274   PMID:24198228  


Genomics

Comparative Map Data
Arfgef1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.258,982,061 - 9,076,326 (+)NCBI
Rnor_6.0 Ensembl58,666,200 - 8,760,458 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.058,666,046 - 8,760,458 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0513,474,381 - 13,568,680 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.458,498,644 - 8,592,918 (+)NCBIRGSC3.4rn4RGSC3.4
Celera58,494,495 - 8,587,878 (+)NCBICelera
Cytogenetic Map5q11NCBI
ARFGEF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl867,173,511 - 67,343,781 (-)EnsemblGRCh38hg38GRCh38
GRCh38867,174,298 - 67,343,824 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37868,109,893 - 68,256,016 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36868,272,451 - 68,418,466 (-)NCBINCBI36hg18NCBI36
Build 34868,272,450 - 68,418,466NCBI
Celera864,103,297 - 64,249,319 (-)NCBI
Cytogenetic Map8q13.2NCBI
HuRef863,601,813 - 63,748,371 (-)NCBIHuRef
CHM1_1868,165,896 - 68,311,968 (-)NCBICHM1_1
Arfgef1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39110,207,732 - 10,303,306 (-)NCBIGRCm39mm39
GRCm39 Ensembl110,207,796 - 10,302,895 (-)Ensembl
GRCm38110,137,507 - 10,232,670 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl110,137,571 - 10,232,670 (-)EnsemblGRCm38mm10GRCm38
MGSCv37110,127,588 - 10,222,751 (-)NCBIGRCm37mm9NCBIm37
MGSCv36110,122,721 - 10,218,159 (-)NCBImm8
Celera110,111,100 - 10,206,279 (-)NCBICelera
Cytogenetic Map1A2NCBI
Arfgef1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544411,986,595 - 12,110,172 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495544411,986,595 - 12,110,172 (+)NCBIChiLan1.0ChiLan1.0
ARFGEF1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1865,402,117 - 65,546,014 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl865,403,386 - 65,545,789 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0863,740,512 - 63,884,189 (-)NCBIMhudiblu_PPA_v0panPan3
ARFGEF1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2916,708,820 - 16,852,844 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12916,712,872 - 16,852,478 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Arfgef1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049364966,807,388 - 6,914,960 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ARFGEF1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl467,466,014 - 67,639,442 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1467,465,517 - 67,613,611 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2473,526,804 - 73,674,463 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ARFGEF1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1863,058,504 - 63,204,238 (-)NCBI
ChlSab1.1 Ensembl863,057,200 - 63,204,292 (-)Ensembl
Arfgef1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474424,010,609 - 24,144,474 (+)NCBI

Position Markers
BE114642  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.058,729,509 - 8,729,660NCBIRnor6.0
Rnor_5.0513,537,846 - 13,537,997UniSTSRnor5.0
RGSC_v3.458,561,946 - 8,562,097UniSTSRGSC3.4
Celera58,556,939 - 8,557,090UniSTS
RH 3.4 Map555.3UniSTS
Cytogenetic Map5q11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5189432042Rat
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5193273395Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51136640934Rat
2312562Pur18Proteinuria QTL 182.60.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5152509833001026Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)5152509878720537Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5166658771552720Rat
2313085Bss59Bone structure and strength QTL 592.90.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)5325132926252076Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5325132948722188Rat
61462Niddm10Non-insulin dependent diabetes mellitus QTL 103.90.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)5452573847978104Rat
631827Alc4Alcohol consumption QTL 43.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)5787561118592319Rat
2293666Bmd38Bone mineral density QTL 384.4femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)5863228553632285Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:129
Count of miRNA genes:101
Interacting mature miRNAs:108
Transcripts:ENSRNOT00000007766
Prediction methods:Microtar, 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 40 52 36 19 36 8 10 74 35 41 11 8
Low 3 5 5 5 1
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000007766   ⟹   ENSRNOP00000007766
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl58,666,200 - 8,760,458 (+)Ensembl
RefSeq Acc Id: NM_001277056   ⟹   NP_001263985
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.258,982,061 - 9,076,326 (+)NCBI
Rnor_6.058,666,200 - 8,760,458 (+)NCBI
Rnor_5.0513,474,381 - 13,568,680 (+)NCBI
Celera58,494,495 - 8,587,878 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017593322   ⟹   XP_017448811
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.258,982,180 - 9,074,896 (+)NCBI
Rnor_6.058,666,046 - 8,759,039 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001263985 (Get FASTA)   NCBI Sequence Viewer  
  XP_017448811 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein D4A631 (Get FASTA)   NCBI Sequence Viewer  
  EDM11544 (Get FASTA)   NCBI Sequence Viewer  
  EDM11545 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001263985   ⟸   NM_001277056
- UniProtKB: D4A631 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017448811   ⟸   XM_017593322
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000007766   ⟸   ENSRNOT00000007766
Protein Domains
SEC7

Transcriptome

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

Promoters
RGD ID:13693533
Promoter ID:EPDNEW_R4058
Type:single initiation site
Name:Arfgef1_1
Description:ADP ribosylation factor guanine nucleotide exchange factor 1
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_6.058,666,295 - 8,666,355EPDNEW

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)
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: SBH/Ygl sequenced by MCW
SBH/Ygl (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
SBN/Ygl (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: SBN/Ygl sequenced by MCW
SBN/Ygl (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
SHR/NHsd (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
SHRSP/Gcrc (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
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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
WAG/Rij (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
WKY/Gcrc (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
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:1560793 AgrOrtholog
Ensembl Genes ENSRNOG00000005703 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000007766 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000007766 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.1000.11 UniProtKB/Swiss-Prot
InterPro ARM-type_fold UniProtKB/Swiss-Prot
  DCB_dom UniProtKB/Swiss-Prot
  Sec7_C UniProtKB/Swiss-Prot
  Sec7_C_sf UniProtKB/Swiss-Prot
  Sec7_dom UniProtKB/Swiss-Prot
  Sec7_dom_sf UniProtKB/Swiss-Prot
  Sec7_N UniProtKB/Swiss-Prot
KEGG Report rno:312915 UniProtKB/Swiss-Prot
NCBI Gene 312915 ENTREZGENE
Pfam DCB UniProtKB/Swiss-Prot
  DUF1981 UniProtKB/Swiss-Prot
  Sec7 UniProtKB/Swiss-Prot
  Sec7_N UniProtKB/Swiss-Prot
PhenoGen Arfgef1 PhenoGen
PROSITE SEC7 UniProtKB/Swiss-Prot
SMART Sec7 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF48371 UniProtKB/Swiss-Prot
  SSF48425 UniProtKB/Swiss-Prot
UniProt BIG1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-25 Arfgef1  ADP ribosylation factor guanine nucleotide exchange factor 1  Arfgef1  ADP-ribosylation factor guanine nucleotide-exchange factor 1(brefeldin A-inhibited)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Arfgef1  ADP-ribosylation factor guanine nucleotide-exchange factor 1(brefeldin A-inhibited)   Arfgef1_predicted  ADP-ribosylation factor guanine nucleotide-exchange factor 1(brefeldin A-inhibited) (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Arfgef1_predicted  ADP-ribosylation factor guanine nucleotide-exchange factor 1(brefeldin A-inhibited) (predicted)  RGD1560793_predicted  similar to brefeldin A-inhibited guanine nucleotide-exchange protein 1 (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-07 RGD1560793_predicted  similar to brefeldin A-inhibited guanine nucleotide-exchange protein 1 (predicted)  LOC312915  similar to brefeldin A-inhibited guanine nucleotide-exchange protein 1  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC312915  similar to brefeldin A-inhibited guanine nucleotide-exchange protein 1      Symbol and Name status set to provisional 70820 PROVISIONAL