Rufy3 (RUN and FYVE domain containing 3) - Rat Genome Database

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Gene: Rufy3 (RUN and FYVE domain containing 3) Rattus norvegicus
Analyze
Symbol: Rufy3
Name: RUN and FYVE domain containing 3
RGD ID: 1565242
Description: Predicted to enable metal ion binding activity. Involved in negative regulation of axonogenesis. Located in several cellular components, including growth cone; lamellipodium; and perikaryon. Orthologous to human RUFY3 (RUN and FYVE domain containing 3); INTERACTS WITH 3,3',4,4',5-pentachlorobiphenyl; bisphenol A; Brodifacoum.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: rap2 interacting protein x; rap2-interacting protein x; Ripx; RUN and FYVE domain-containing protein 3; singar; Singar1; singar2; single axon-regulated protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21419,431,530 - 19,506,531 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1419,432,524 - 19,507,004 (-)Ensembl
Rnor_6.01421,058,575 - 21,144,775 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1421,058,595 - 21,128,505 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01420,968,402 - 21,040,629 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41421,022,765 - 21,070,152 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1418,782,702 - 18,829,205 (-)NCBICelera
Cytogenetic Map14p22NCBI
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

Cellular Component
axon  (IBA,ISO,ISS)
cell junction  (IEA)
cytoplasm  (IBA,ISO,ISS)
cytosol  (IEA,ISO)
dendrite  (IBA,IDA,ISO,ISS)
endomembrane system  (IEA)
filopodium  (IDA)
growth cone  (IDA,ISO)
lamellipodium  (IDA)
membrane  (IEA)
neuronal cell body  (IBA,ISO)
perikaryon  (IDA,ISO)

Molecular Function

References

Additional References at PubMed
PMID:15489334   PMID:22871113   PMID:23206279   PMID:23904609   PMID:24720729   PMID:25766321  


Genomics

Comparative Map Data
Rufy3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21419,431,530 - 19,506,531 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1419,432,524 - 19,507,004 (-)Ensembl
Rnor_6.01421,058,575 - 21,144,775 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1421,058,595 - 21,128,505 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01420,968,402 - 21,040,629 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41421,022,765 - 21,070,152 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1418,782,702 - 18,829,205 (-)NCBICelera
Cytogenetic Map14p22NCBI
RUFY3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl470,704,204 - 70,808,619 (+)EnsemblGRCh38hg38GRCh38
GRCh38470,704,204 - 70,808,619 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37471,570,456 - 71,674,336 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36471,806,560 - 71,891,789 (+)NCBINCBI36hg18NCBI36
Celera468,927,653 - 69,031,337 (+)NCBI
Cytogenetic Map4q13.3NCBI
HuRef467,374,309 - 67,478,077 (+)NCBIHuRef
CHM1_1471,606,608 - 71,710,363 (+)NCBICHM1_1
Rufy3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39588,711,305 - 88,799,276 (+)NCBIGRCm39mm39
GRCm39 Ensembl588,712,899 - 88,799,251 (+)Ensembl
GRCm38588,564,505 - 88,651,417 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl588,565,040 - 88,651,392 (+)EnsemblGRCm38mm10GRCm38
MGSCv37589,012,599 - 89,071,721 (+)NCBIGRCm37mm9NCBIm37
MGSCv36589,658,135 - 89,717,257 (+)NCBImm8
Celera586,733,200 - 86,791,895 (+)NCBICelera
Cytogenetic Map5E1NCBI
cM Map543.77NCBI
Rufy3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554472,211,262 - 2,266,008 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554472,200,788 - 2,266,008 (-)NCBIChiLan1.0ChiLan1.0
RUFY3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1459,762,339 - 59,846,574 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl459,762,053 - 59,846,574 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0453,415,742 - 53,516,600 (-)NCBIMhudiblu_PPA_v0panPan3
RUFY3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11360,007,041 - 60,079,198 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1360,007,056 - 60,078,617 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1359,741,413 - 59,813,528 (+)NCBI
ROS_Cfam_1.01360,813,185 - 60,885,065 (+)NCBI
UMICH_Zoey_3.11360,427,868 - 60,499,800 (+)NCBI
UNSW_CanFamBas_1.01359,919,548 - 59,991,670 (+)NCBI
UU_Cfam_GSD_1.01361,067,046 - 61,138,949 (+)NCBI
Rufy3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528515,535,254 - 15,594,049 (-)NCBI
SpeTri2.0NW_0049365983,987,287 - 4,046,019 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RUFY3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl867,495,033 - 67,582,143 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1867,494,552 - 67,582,144 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2871,403,191 - 71,490,372 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RUFY3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1719,214,051 - 19,316,840 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl719,232,434 - 19,300,550 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660843,562,094 - 3,671,841 (-)NCBIVero_WHO_p1.0
Rufy3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248902,032,980 - 2,135,922 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH131654  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21419,431,907 - 19,432,110 (+)MAPPERmRatBN7.2
Rnor_6.01421,058,953 - 21,059,155NCBIRnor6.0
Rnor_5.01420,968,780 - 20,968,982UniSTSRnor5.0
RGSC_v3.41421,011,126 - 21,011,328UniSTSRGSC3.4
Celera1418,771,078 - 18,771,280UniSTS
RH 3.4 Map14285.4UniSTS
Cytogenetic Map14p22UniSTS
RH132885  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21419,441,212 - 19,441,424 (+)MAPPERmRatBN7.2
Rnor_6.01421,068,258 - 21,068,469NCBIRnor6.0
Rnor_5.01420,978,085 - 20,978,296UniSTSRnor5.0
RGSC_v3.41421,020,431 - 21,020,642UniSTSRGSC3.4
Celera1418,780,368 - 18,780,579UniSTS
RH 3.4 Map14292.4UniSTS
Cytogenetic Map14p22UniSTS
RH134531  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21419,441,569 - 19,441,752 (+)MAPPERmRatBN7.2
Rnor_6.01421,068,615 - 21,068,797NCBIRnor6.0
Rnor_5.01420,978,442 - 20,978,624UniSTSRnor5.0
RGSC_v3.41421,020,788 - 21,020,970UniSTSRGSC3.4
Celera1418,780,725 - 18,780,907UniSTS
RH 3.4 Map14289.9UniSTS
Cytogenetic Map14p22UniSTS
BG376722  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21419,432,743 - 19,432,885 (+)MAPPERmRatBN7.2
Rnor_6.01421,059,789 - 21,059,930NCBIRnor6.0
Rnor_5.01420,969,616 - 20,969,757UniSTSRnor5.0
RGSC_v3.41421,011,962 - 21,012,103UniSTSRGSC3.4
Celera1418,771,914 - 18,772,055UniSTS
RH 3.4 Map14285.4UniSTS
Cytogenetic Map14p22UniSTS
BI295036  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21419,488,641 - 19,488,777 (+)MAPPERmRatBN7.2
Rnor_6.01421,126,671 - 21,126,806NCBIRnor6.0
Rnor_5.01421,036,498 - 21,036,633UniSTSRnor5.0
RGSC_v3.41421,068,318 - 21,068,453UniSTSRGSC3.4
Celera1418,827,375 - 18,827,510UniSTS
RH 3.4 Map14293.6UniSTS
Cytogenetic Map14p22UniSTS
AW529895  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21419,435,598 - 19,435,803 (+)MAPPERmRatBN7.2
Rnor_6.01421,062,644 - 21,062,848NCBIRnor6.0
Rnor_5.01420,972,471 - 20,972,675UniSTSRnor5.0
RGSC_v3.41421,014,817 - 21,015,021UniSTSRGSC3.4
Celera1418,774,754 - 18,774,958UniSTS
RH 3.4 Map14285.3UniSTS
Cytogenetic Map14p22UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2300159Bmd61Bone mineral density QTL 615.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
2300183Bmd60Bone mineral density QTL 605.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
619619Rf4Renal disease susceptibility QTL 44.10.002total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14132754612Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
1300114Srn2Serum renin concentration QTL 23.27blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)14381307421217635Rat
70195Mcs8Mammary carcinoma susceptibility QTL 84.28mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)14381307424531477Rat
1331740Bw26Body weight QTL 263.028body mass (VT:0001259)body weight (CMO:0000012)14381307430767156Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14826709053267090Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14826709053267090Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)14908897839057237Rat
2302277Gluco38Glucose level QTL 385.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062228035204Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
631212Bw5Body weight QTL55.43retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)141103081230320092Rat
1300140Srn3Serum renin concentration QTL 33.19blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)141487516830883947Rat
631528Scl11Serum cholesterol level QTL 114.9blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)141757341219726296Rat
71117Niddm17Non-insulin dependent diabetes mellitus QTL 172.35blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)141759376142336881Rat
631262Tcas4Tongue tumor susceptibility QTL 47.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)141762256142337007Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)141854133263541332Rat
61420Pia6Pristane induced arthritis QTL 64.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)141863134542337007Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:116
Count of miRNA genes:88
Interacting mature miRNAs:89
Transcripts:ENSRNOT00000004776, ENSRNOT00000020608
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 35 51 35 19 35 8 10 74 35 41 11 8
Low 8 6 6 6 1
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001025127 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006250781 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006250782 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006250783 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006250784 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008770044 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008770045 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008770046 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008770047 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008770048 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599283 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599284 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599285 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599286 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092170 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092171 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092173 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001841024 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC089952 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474060 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EF538802 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EF577045 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000250 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000004776   ⟹   ENSRNOP00000004776
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1419,432,524 - 19,490,474 (-)Ensembl
Rnor_6.0 Ensembl1421,070,593 - 21,128,505 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000020608   ⟹   ENSRNOP00000020608
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1419,432,524 - 19,489,839 (-)Ensembl
Rnor_6.0 Ensembl1421,070,610 - 21,127,868 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092172   ⟹   ENSRNOP00000073742
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1419,432,524 - 19,489,839 (-)Ensembl
Rnor_6.0 Ensembl1421,058,595 - 21,127,875 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000100042   ⟹   ENSRNOP00000093326
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1419,443,548 - 19,507,004 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000103075   ⟹   ENSRNOP00000096851
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1419,432,524 - 19,507,004 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000109188   ⟹   ENSRNOP00000078674
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1419,432,524 - 19,479,766 (-)Ensembl
RefSeq Acc Id: NM_001025127   ⟹   NP_001020298
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21419,443,547 - 19,490,474 (-)NCBI
Rnor_6.01421,070,592 - 21,128,505 (-)NCBI
Rnor_5.01420,968,402 - 21,040,629 (-)NCBI
RGSC_v3.41421,022,765 - 21,070,152 (-)RGD
Celera1418,782,702 - 18,829,205 (-)RGD
Sequence:
RefSeq Acc Id: XM_006250781   ⟹   XP_006250843
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21419,431,530 - 19,491,033 (-)NCBI
Rnor_6.01421,058,575 - 21,129,354 (-)NCBI
Rnor_5.01420,968,402 - 21,040,629 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006250782   ⟹   XP_006250844
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21419,431,530 - 19,482,693 (-)NCBI
Rnor_6.01421,058,575 - 21,120,875 (-)NCBI
Rnor_5.01420,968,402 - 21,040,629 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006250783   ⟹   XP_006250845
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21419,431,530 - 19,491,029 (-)NCBI
Rnor_6.01421,058,575 - 21,129,353 (-)NCBI
Rnor_5.01420,968,402 - 21,040,629 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008770044   ⟹   XP_008768266
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21419,431,530 - 19,506,531 (-)NCBI
Rnor_6.01421,058,575 - 21,144,774 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008770045   ⟹   XP_008768267
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21419,431,530 - 19,506,355 (-)NCBI
Rnor_6.01421,058,575 - 21,144,643 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008770046   ⟹   XP_008768268
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21419,431,530 - 19,482,692 (-)NCBI
Rnor_6.01421,058,575 - 21,120,875 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008770047   ⟹   XP_008768269
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21419,441,493 - 19,506,355 (-)NCBI
Rnor_6.01421,068,538 - 21,144,643 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008770048   ⟹   XP_008768270
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21419,441,493 - 19,491,029 (-)NCBI
Rnor_6.01421,068,538 - 21,129,349 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017599283   ⟹   XP_017454772
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21419,431,530 - 19,506,531 (-)NCBI
Rnor_6.01421,058,575 - 21,144,775 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017599284   ⟹   XP_017454773
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21419,431,530 - 19,506,531 (-)NCBI
Rnor_6.01421,058,575 - 21,144,774 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017599285   ⟹   XP_017454774
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21419,431,530 - 19,491,041 (-)NCBI
Rnor_6.01421,058,575 - 21,129,356 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017599286   ⟹   XP_017454775
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21419,431,530 - 19,497,294 (-)NCBI
Rnor_6.01421,058,575 - 21,132,526 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039092170   ⟹   XP_038948098
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21419,431,530 - 19,491,332 (-)NCBI
RefSeq Acc Id: XM_039092171   ⟹   XP_038948099
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21419,431,530 - 19,490,012 (-)NCBI
RefSeq Acc Id: XM_039092173   ⟹   XP_038948101
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21419,441,493 - 19,506,530 (-)NCBI
RefSeq Acc Id: XR_001841024
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21419,431,530 - 19,506,531 (-)NCBI
Rnor_6.01421,058,575 - 21,144,771 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001020298 (Get FASTA)   NCBI Sequence Viewer  
  XP_006250843 (Get FASTA)   NCBI Sequence Viewer  
  XP_006250844 (Get FASTA)   NCBI Sequence Viewer  
  XP_006250845 (Get FASTA)   NCBI Sequence Viewer  
  XP_008768266 (Get FASTA)   NCBI Sequence Viewer  
  XP_008768267 (Get FASTA)   NCBI Sequence Viewer  
  XP_008768268 (Get FASTA)   NCBI Sequence Viewer  
  XP_008768269 (Get FASTA)   NCBI Sequence Viewer  
  XP_008768270 (Get FASTA)   NCBI Sequence Viewer  
  XP_017454772 (Get FASTA)   NCBI Sequence Viewer  
  XP_017454773 (Get FASTA)   NCBI Sequence Viewer  
  XP_017454774 (Get FASTA)   NCBI Sequence Viewer  
  XP_017454775 (Get FASTA)   NCBI Sequence Viewer  
  XP_038948098 (Get FASTA)   NCBI Sequence Viewer  
  XP_038948099 (Get FASTA)   NCBI Sequence Viewer  
  XP_038948101 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH89952 (Get FASTA)   NCBI Sequence Viewer  
  ABP99060 (Get FASTA)   NCBI Sequence Viewer  
  ABQ45403 (Get FASTA)   NCBI Sequence Viewer  
  EDL88518 (Get FASTA)   NCBI Sequence Viewer  
  EDL88519 (Get FASTA)   NCBI Sequence Viewer  
  EDL88520 (Get FASTA)   NCBI Sequence Viewer  
  EDL88521 (Get FASTA)   NCBI Sequence Viewer  
  EDL88522 (Get FASTA)   NCBI Sequence Viewer  
  EDL88523 (Get FASTA)   NCBI Sequence Viewer  
  EDL88524 (Get FASTA)   NCBI Sequence Viewer  
  EDL88525 (Get FASTA)   NCBI Sequence Viewer  
  Q5FVJ0 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001020298   ⟸   NM_001025127
- UniProtKB: Q5FVJ0 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006250845   ⟸   XM_006250783
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_006250843   ⟸   XM_006250781
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_006250844   ⟸   XM_006250782
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_008768267   ⟸   XM_008770045
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_008768266   ⟸   XM_008770044
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008768268   ⟸   XM_008770046
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_008768269   ⟸   XM_008770047
- Peptide Label: isoform X11
- Sequence:
RefSeq Acc Id: XP_008768270   ⟸   XM_008770048
- Peptide Label: isoform X12
- UniProtKB: Q5FVJ0 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017454772   ⟸   XM_017599283
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017454773   ⟸   XM_017599284
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017454775   ⟸   XM_017599286
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017454774   ⟸   XM_017599285
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: ENSRNOP00000073742   ⟸   ENSRNOT00000092172
RefSeq Acc Id: ENSRNOP00000004776   ⟸   ENSRNOT00000004776
RefSeq Acc Id: ENSRNOP00000020608   ⟸   ENSRNOT00000020608
RefSeq Acc Id: XP_038948098   ⟸   XM_039092170
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038948099   ⟸   XM_039092171
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038948101   ⟸   XM_039092173
- Peptide Label: isoform X10
RefSeq Acc Id: ENSRNOP00000093326   ⟸   ENSRNOT00000100042
RefSeq Acc Id: ENSRNOP00000078674   ⟸   ENSRNOT00000109188
RefSeq Acc Id: ENSRNOP00000096851   ⟸   ENSRNOT00000103075
Protein Domains
RUN

Transcriptome

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

Promoters
RGD ID:13699241
Promoter ID:EPDNEW_R9766
Type:initiation region
Name:Rufy3_1
Description:RUN and FYVE 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_6.01421,128,467 - 21,128,527EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/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)
ACI/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
ACI/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/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
BBDP/Wor (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
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (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
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/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
COP/CrCrl (MCW & UW)
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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)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/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
F344/NRrrc (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
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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:1565242 AgrOrtholog
Ensembl Genes ENSRNOG00000003428 Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000004776 UniProtKB/Swiss-Prot
  ENSRNOP00000020608 UniProtKB/Swiss-Prot
  ENSRNOP00000073742 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000004776 UniProtKB/Swiss-Prot
  ENSRNOT00000020608 UniProtKB/Swiss-Prot
  ENSRNOT00000092172 UniProtKB/TrEMBL
Gene3D-CATH 1.20.58.900 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.40.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7312240 IMAGE-MGC_LOAD
InterPro Run_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Run_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_FYVE UniProtKB/TrEMBL
  Znf_FYVE_PHD UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
KEGG Report rno:360921 UniProtKB/Swiss-Prot
MGC_CLONE MGC:109279 IMAGE-MGC_LOAD
NCBI Gene 360921 ENTREZGENE
Pfam RUN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Rufy3 PhenoGen
PROSITE RUN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART FYVE UniProtKB/TrEMBL
  RUN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF140741 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF57903 UniProtKB/TrEMBL
UniProt A0A0G2K6A9_RAT UniProtKB/TrEMBL
  Q5FVJ0 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary A5HLX7 UniProtKB/Swiss-Prot
  A5JUR6 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-07 Rufy3  RUN and FYVE domain containing 3  Ripx  rap2 interacting protein x  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-02-09 Ripx  rap2 interacting protein x      Symbol and Name status set to provisional 70820 PROVISIONAL