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 have metal ion binding activity. Involved in negative regulation of axonogenesis. Localizes to 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: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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
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
GRCh37471,570,647 - 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 - 71,710,366 (+)NCBICHM1_1
Rufy3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39588,711,305 - 88,799,276 (+)NCBIGRCm39mm39
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
CanFam3.1 Ensembl1360,007,056 - 60,078,617 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11360,007,041 - 60,079,198 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Rufy3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1719,214,051 - 19,316,840 (+)NCBI
ChlSab1.1 Ensembl719,232,434 - 19,300,550 (+)Ensembl
Rufy3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248902,032,980 - 2,135,922 (+)NCBI

Position Markers
RH131654  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
Cytogenetic Map14p22UniSTS
RH 3.4 Map14285.4UniSTS
RH132885  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
Cytogenetic Map14p22UniSTS
RH 3.4 Map14292.4UniSTS
RH134531  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
Cytogenetic Map14p22UniSTS
RH 3.4 Map14289.9UniSTS
BG376722  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
Cytogenetic Map14p22UniSTS
RH 3.4 Map14285.4UniSTS
BI295036  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
Cytogenetic Map14p22UniSTS
RH 3.4 Map14293.6UniSTS
AW529895  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
Cytogenetic Map14p22UniSTS
RH 3.4 Map14285.3UniSTS


QTLs in Region (Rnor_6.0)
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)14127597761Rat
2300183Bmd60Bone mineral density QTL 605.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14127597761Rat
619619Rf4Renal disease susceptibility QTL 44.10.002total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14134403399Rat
9589814Gluco67Glucose level QTL 674.540.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)14141333960Rat
7411573Bw139Body weight QTL 1394.70.001body mass (VT:0001259)body weight gain (CMO:0000420)14141333960Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14142766285Rat
1300114Srn2Serum renin concentration QTL 23.27blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)14483323323004027Rat
70195Mcs8Mammary carcinoma susceptibility QTL 84.28mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)14483323326466248Rat
1331740Bw26Body weight QTL 263.028body mass (VT:0001259)body weight (CMO:0000012)14483323333040042Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14975643572854397Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin141053997755539977Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)141053997755539977Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)141072926861873323Rat
2302277Gluco38Glucose level QTL 385.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141268042430155192Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1412680424106641756Rat
631212Bw5Body weight QTL55.43retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)141268061332593926Rat
1300140Srn3Serum renin concentration QTL 33.19blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)141633698833163485Rat
631528Scl11Serum cholesterol level QTL 114.9blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)141915991938289187Rat
71117Niddm17Non-insulin dependent diabetes mellitus QTL 172.35blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)141916189343957503Rat
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)141919154143957628Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)142018938665189386Rat
61420Pia6Pristane induced arthritis QTL 64.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)142026622343957628Rat

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
  XR_001841024 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AABR07014547 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07014548 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07014549 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01078483 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01078484 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01078485 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  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

Reference Sequences
RefSeq Acc Id: ENSRNOT00000004776   ⟹   ENSRNOP00000004776
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1421,070,593 - 21,128,505 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000020608   ⟹   ENSRNOP00000020608
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1421,070,610 - 21,127,868 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092172   ⟹   ENSRNOP00000073742
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1421,058,595 - 21,127,875 (-)Ensembl
RefSeq Acc Id: NM_001025127   ⟹   NP_001020298
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
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
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
Rnor_6.01421,058,575 - 21,129,353 (-)NCBI
Rnor_5.01420,968,402 - 21,040,629 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006250784   ⟹   XP_006250846
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01421,058,575 - 21,118,015 (-)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
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
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
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
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
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
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
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
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
Rnor_6.01421,058,575 - 21,132,526 (-)NCBI
Sequence:
RefSeq Acc Id: XR_001841024
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01421,058,575 - 21,144,771 (-)NCBI
Sequence:
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_006250846   ⟸   XM_006250784
- Peptide Label: isoform X10
- 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
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 (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)
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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 (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/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 (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)
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
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565242 AgrOrtholog
Ensembl Genes ENSRNOG00000003428 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000004776 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000020608 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000073742 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000004776 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000020608 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000092172 ENTREZGENE, 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
UniGene Rn.228806 ENTREZGENE
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