Fgd3 (FYVE, RhoGEF and PH domain containing 3) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Fgd3 (FYVE, RhoGEF and PH domain containing 3) Rattus norvegicus
Analyze
Symbol: Fgd3
Name: FYVE, RhoGEF and PH domain containing 3
RGD ID: 1311725
Description: Predicted to have metal ion binding activity. Predicted to be involved in cytoskeleton organization and filopodium assembly. Predicted to localize to cytoplasm. Orthologous to human FGD3 (FYVE, RhoGEF and PH domain containing 3); INTERACTS WITH acetamide; bisphenol A; DDT.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: FYVE, RhoGEF and PH domain-containing protein 3; LOC361223
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
mRatBN7.21715,324,848 - 15,387,271 (+)NCBI
Rnor_6.0 Ensembl1715,749,978 - 15,800,401 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01715,737,962 - 15,800,403 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01717,807,528 - 17,855,077 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41721,292,539 - 21,343,264 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11721,306,219 - 21,342,775 (+)NCBI
Celera1715,067,402 - 15,115,963 (+)NCBICelera
Cytogenetic Map17p14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Biological Process

Cellular Component
cytoplasm  (IBA)
cytoskeleton  (IEA)

Molecular Function

References

Additional References at PubMed
PMID:10721717  


Genomics

Comparative Map Data
Fgd3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21715,324,848 - 15,387,271 (+)NCBI
Rnor_6.0 Ensembl1715,749,978 - 15,800,401 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01715,737,962 - 15,800,403 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01717,807,528 - 17,855,077 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41721,292,539 - 21,343,264 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11721,306,219 - 21,342,775 (+)NCBI
Celera1715,067,402 - 15,115,963 (+)NCBICelera
Cytogenetic Map17p14NCBI
FGD3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl992,947,523 - 93,036,236 (+)EnsemblGRCh38hg38GRCh38
GRCh38992,947,523 - 93,036,236 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37995,709,805 - 95,798,515 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36994,749,422 - 94,838,339 (+)NCBINCBI36hg18NCBI36
Celera966,151,416 - 66,240,262 (+)NCBI
Cytogenetic Map9q22.31NCBI
HuRef965,386,766 - 65,475,463 (+)NCBIHuRef
CHM1_1995,856,394 - 95,945,176 (+)NCBICHM1_1
Fgd3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391349,415,030 - 49,473,783 (-)NCBIGRCm39mm39
GRCm39 Ensembl1349,415,030 - 49,473,787 (-)Ensembl
GRCm381349,261,554 - 49,320,313 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1349,261,554 - 49,320,311 (-)EnsemblGRCm38mm10GRCm38
MGSCv371349,358,479 - 49,404,577 (-)NCBIGRCm37mm9NCBIm37
MGSCv361349,275,047 - 49,321,145 (-)NCBImm8
Celera1350,352,639 - 50,398,634 (-)NCBICelera
Cytogenetic Map13A5NCBI
cM Map1325.18NCBI
Fgd3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555154,968,504 - 5,025,633 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555154,967,862 - 5,025,604 (-)NCBIChiLan1.0ChiLan1.0
FGD3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1992,138,743 - 92,226,835 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl992,138,743 - 92,226,835 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0964,071,083 - 64,159,854 (+)NCBIMhudiblu_PPA_v0panPan3
FGD3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1198,624,529 - 98,696,916 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl198,625,138 - 98,648,839 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha199,018,508 - 99,048,949 (-)NCBI
ROS_Cfam_1.0199,241,437 - 99,271,847 (-)NCBI
UMICH_Zoey_3.1198,854,618 - 98,885,002 (-)NCBI
UNSW_CanFamBas_1.0198,589,955 - 98,620,404 (-)NCBI
UU_Cfam_GSD_1.0199,345,579 - 99,375,989 (-)NCBI
Fgd3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049448,165,569 - 8,206,669 (+)NCBI
SpeTri2.0NW_0049364872,385,732 - 2,422,326 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
FGD3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl342,540,550 - 42,622,702 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1342,457,072 - 42,587,585 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
FGD3
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.112103,368,267 - 103,424,194 (+)NCBI
ChlSab1.1 Ensembl12103,368,236 - 103,424,504 (+)Ensembl
Fgd3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248683,507,448 - 3,560,639 (-)NCBI

Position Markers
BF402796  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01715,750,992 - 15,751,115NCBIRnor6.0
Rnor_5.01717,808,557 - 17,808,680UniSTSRnor5.0
RGSC_v3.41721,293,568 - 21,293,691UniSTSRGSC3.4
Celera1715,068,431 - 15,068,554UniSTS
RH 3.4 Map17174.7UniSTS
Cytogenetic Map17p14UniSTS
BE120617  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01715,795,991 - 15,796,196NCBIRnor6.0
Rnor_5.01717,852,224 - 17,852,429UniSTSRnor5.0
RGSC_v3.41721,340,411 - 21,340,616UniSTSRGSC3.4
Celera1715,113,096 - 15,113,301UniSTS
RH 3.4 Map17176.1UniSTS
Cytogenetic Map17p14UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590316Scort21Serum corticosterone level QTL 214.750.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17124787908Rat
10401807Kidm52Kidney mass QTL 52kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17132230361Rat
70184BpQTLcluster14Blood pressure QTL cluster 143.38arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)17133303755Rat
631207Niddm41Non-insulin dependent diabetes mellitus QTL 41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)17138243814Rat
1354658Spl8Serum phospholipid level QTL 83.8blood VLDL phospholipid amount (VT:0010507)blood very low density lipoprotein phospholipid level (CMO:0001571)17163676140Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17173413148Rat
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17173413148Rat
1641902Colcr7Colorectal carcinoma resistance QTL 73.350.0044intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)1751977023422380Rat
1300123Bp194Blood pressure QTL 1942.82arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1751977036283402Rat
2324619Coatc4Coat color QTL 40.001coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)17333697224030841Rat
2324619Coatc4Coat color QTL 40.001coat/hair pigmentation trait (VT:0010463)pigmented dorsal coat/hair area to total dorsal coat/hair area ratio (CMO:0001811)17333697224030841Rat
1354613Kidm14Kidney mass QTL 146.2kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)17333697237790462Rat
1354596Bw32Body weight QTL 324.5body mass (VT:0001259)body weight (CMO:0000012)17333697263676140Rat
1354638Insul1Insulin level QTL 14.8blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)17333697273413148Rat
1354651Lmblg2Limb length QTL 26tibia length (VT:0004357)tibia length (CMO:0000450)17333697273413148Rat
1354630Cm34Cardiac mass QTL 348.7heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)17333697273413148Rat
631499Stl1Serum triglyceride level QTL 13.6blood triglyceride amount (VT:0002644)blood triglyceride level (CMO:0000118)17341403928073589Rat
2293648Bmd31Bone mineral density QTL 314.50.0001femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)17471606727691136Rat
2293664Bmd28Bone mineral density QTL 285.10.0001femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)17471606727691136Rat
2303627Vencon8Ventilatory control QTL 80.001respiration trait (VT:0001943)tidal volume (CMO:0000222)17519104750191047Rat
10054088Scort28Serum corticosterone level QTL 282.040.0102blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17519104750191047Rat
1581553Pur14Proteinuria QTL 145.30.0001total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)17842446716620067Rat
1582224Epfw4Epididymal fat weight QTL 43.50.0058epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)17973026321491085Rat
1582225Bw67Body weight QTL 676.20.0001body mass (VT:0001259)body weight (CMO:0000012)17973026321491085Rat
1582226Bw64Body weight QTL 644.20.0017body mass (VT:0001259)body weight (CMO:0000012)17973026321491085Rat
1582241Bw70Body weight QTL 704.60.0003body mass (VT:0001259)body weight (CMO:0000012)17973026321491085Rat
1582245Bw73Body weight QTL 734.60.0004body mass (VT:0001259)body weight (CMO:0000012)17973026321491085Rat
1582258Bw76Body weight QTL 764.60.0005body mass (VT:0001259)body weight (CMO:0000012)17973026321491085Rat
1582199Insul5Insulin level QTL 53.40.0119blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)17973026321491085Rat
1582208Kidm32Kidney mass QTL 323.90.0018kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17973026321491085Rat
2303561Bw91Body weight QTL 912body mass (VT:0001259)body weight (CMO:0000012)17982730454827304Rat
2300002Iddm36Insulin dependent diabetes mellitus QTL 361.98blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)171052970942542027Rat
1549900Iddm20Insulin dependent diabetes mellitus QTL 203.7pancreas integrity trait (VT:0010560)percentage of study population developing diabetes mellitus during a period of time (CMO:0001114)171400967923316697Rat
1331720Rf43Renal function QTL 432.881kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)171574375522711729Rat
1331765Hrtrt15Heart rate QTL 154.094heart pumping trait (VT:2000009)heart rate (CMO:0000002)171574375561036897Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:238
Count of miRNA genes:167
Interacting mature miRNAs:184
Transcripts:ENSRNOT00000067311
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 2 8 19 36 13 2 4
Low 1 43 49 41 41 8 8 38 22 39 7 8
Below cutoff 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000067311   ⟹   ENSRNOP00000063011
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1715,749,978 - 15,798,844 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000089310   ⟹   ENSRNOP00000072384
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1715,762,030 - 15,800,401 (+)Ensembl
RefSeq Acc Id: NM_001108409   ⟹   NP_001101879
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21715,336,822 - 15,385,712 (+)NCBI
Rnor_6.01715,749,963 - 15,798,844 (+)NCBI
Rnor_5.01717,807,528 - 17,855,077 (+)NCBI
RGSC_v3.41721,292,539 - 21,343,264 (+)RGD
Celera1715,067,402 - 15,115,963 (+)RGD
Sequence:
RefSeq Acc Id: XM_008771543   ⟹   XP_008769765
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21715,336,279 - 15,387,271 (+)NCBI
Rnor_6.01715,749,406 - 15,800,403 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008771544   ⟹   XP_008769766
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21715,347,178 - 15,387,271 (+)NCBI
Rnor_6.01715,760,413 - 15,800,403 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008771545   ⟹   XP_008769767
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21715,324,848 - 15,387,271 (+)NCBI
Rnor_6.01715,737,962 - 15,800,403 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008771546   ⟹   XP_008769768
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21715,348,546 - 15,387,271 (+)NCBI
Rnor_6.01715,761,653 - 15,800,403 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039095863   ⟹   XP_038951791
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21715,336,270 - 15,372,014 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001101879   ⟸   NM_001108409
- UniProtKB: D3ZS34 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008769767   ⟸   XM_008771545
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K2U9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008769765   ⟸   XM_008771543
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K2U9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008769766   ⟸   XM_008771544
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K2U9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008769768   ⟸   XM_008771546
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K2U9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000063011   ⟸   ENSRNOT00000067311
RefSeq Acc Id: ENSRNOP00000072384   ⟸   ENSRNOT00000089310
RefSeq Acc Id: XP_038951791   ⟸   XM_039095863
- Peptide Label: isoform X2
Protein Domains
DH   FYVE-type   PH

Transcriptome

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

Promoters
RGD ID:13700356
Promoter ID:EPDNEW_R10878
Type:single initiation site
Name:Fgd3_1
Description:FYVE, RhoGEF and PH domain containing 3
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_6.01715,749,972 - 15,750,032EPDNEW

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)
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
WKY/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
WKY/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
WN/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311725 AgrOrtholog
Ensembl Genes ENSRNOG00000016225 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000063011 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000072384 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000067311 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000089310 UniProtKB/TrEMBL
Gene3D-CATH 1.20.900.10 UniProtKB/TrEMBL
  2.30.29.30 UniProtKB/TrEMBL
  3.30.40.10 UniProtKB/TrEMBL
InterPro DBL_dom_sf UniProtKB/TrEMBL
  DH-domain UniProtKB/TrEMBL
  FGD1-4_PH2 UniProtKB/TrEMBL
  PH_type UniProtKB/TrEMBL
  Pleckstrin_homology UniProtKB/TrEMBL
  Znf_FYVE UniProtKB/TrEMBL
  Znf_FYVE-rel UniProtKB/TrEMBL
  Znf_FYVE_PHD UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
KEGG Report rno:361223 UniProtKB/TrEMBL
NCBI Gene 361223 ENTREZGENE
Pfam FYVE UniProtKB/TrEMBL
  PF00169 UniProtKB/TrEMBL
  RhoGEF UniProtKB/TrEMBL
PhenoGen Fgd3 PhenoGen
PROSITE DH_2 UniProtKB/TrEMBL
  PH_DOMAIN UniProtKB/TrEMBL
  ZF_FYVE UniProtKB/TrEMBL
SMART FYVE UniProtKB/TrEMBL
  RhoGEF UniProtKB/TrEMBL
  SM00233 UniProtKB/TrEMBL
Superfamily-SCOP DH-domain UniProtKB/TrEMBL
  FYVE_PHD_ZnF UniProtKB/TrEMBL
UniProt A0A0G2K2U9 ENTREZGENE, UniProtKB/TrEMBL
  D3ZS34 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Fgd3  FYVE, RhoGEF and PH domain containing 3   Fgd3_predicted  FYVE, RhoGEF and PH domain containing 3 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Fgd3_predicted  FYVE, RhoGEF and PH domain containing 3 (predicted)      Symbol and Name status set to approved 70820 APPROVED