Synj1 (synaptojanin 1) - Rat Genome Database

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Gene: Synj1 (synaptojanin 1) Rattus norvegicus
Analyze
Symbol: Synj1
Name: synaptojanin 1
RGD ID: 69434
Description: Exhibits phosphatase activity; protein C-terminus binding activity; and protein domain specific binding activity. Involved in several processes, including nervous system development; positive regulation of receptor-mediated endocytosis; and response to retinoic acid. Localizes to several cellular components, including clathrin coat of coated pit; parallel fiber to Purkinje cell synapse; and synaptic membrane. Colocalizes with microtubule. Human ortholog(s) of this gene implicated in Parkinson's disease; Parkinson's disease 20; and developmental and epileptic encephalopathy 53. Orthologous to human SYNJ1 (synaptojanin 1); PARTICIPATES IN altered clathrin-dependent synaptic vesicle endocytosis; clathrin-dependent synaptic vesicle endocytosis; ephrin - ephrin receptor bidirectional signaling axis; INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: synaptic inositol 1,4,5-trisphosphate 5-phosphatase 1; synaptic inositol-1,4,5-trisphosphate 5-phosphatase 1; synaptojanin-1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21130,192,629 - 30,269,277 (-)NCBI
Rnor_6.0 Ensembl1131,104,787 - 31,180,642 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01131,105,784 - 31,181,573 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01134,717,258 - 34,792,366 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41130,921,834 - 30,998,609 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11130,921,975 - 30,966,053 (-)NCBI
Celera1129,860,879 - 29,935,097 (-)NCBICelera
Cytogenetic Map11q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

References

References - curated
1. Adayev T, etal., Biochem Biophys Res Commun. 2006 Dec 29;351(4):1060-5. doi: 10.1016/j.bbrc.2006.10.169. Epub 2006 Nov 7.
2. Cestra G, etal., Proc Natl Acad Sci U S A. 2005 Feb 1;102(5):1731-6. Epub 2005 Jan 19.
3. de Heuvel E, etal., J Biol Chem. 1997 Mar 28;272(13):8710-6.
4. Drouet V and Lesage S, Biomed Res Int. 2014;2014:289728. doi: 10.1155/2014/289728. Epub 2014 Sep 16.
5. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
6. GOA data from the GO Consortium
7. Haffner C, etal., FEBS Lett. 1997 Dec 15;419(2-3):175-80.
8. Herrera F, etal., Cell Death Differ. 2009 Jun;16(6):910-20. Epub 2009 Mar 13.
9. Hunn BH, etal., Trends Neurosci. 2015 Mar;38(3):178-88. doi: 10.1016/j.tins.2014.12.009. Epub 2015 Jan 29.
10. Irie F, etal., Nat Cell Biol. 2005 May;7(5):501-9. Epub 2005 Apr 10.
11. Krendel M, etal., FEBS Lett. 2007 Feb 20;581(4):644-50. Epub 2007 Jan 18.
12. Kudo M, etal., Brain Res Mol Brain Res. 1999 Feb 5;64(2):179-85.
13. Lee SY, etal., Proc Natl Acad Sci U S A. 2004 Jan 13;101(2):546-51. Epub 2004 Jan 2.
14. McPherson PS, etal., J Biol Chem. 1994 Dec 2;269(48):30132-9.
15. McPherson PS, etal., Nature 1996 Jan 25;379(6563):353-7.
16. MGD data from the GO Consortium
17. NCBI rat LocusLink and RefSeq merged data July 26, 2002
18. Nemoto Y, etal., J Biol Chem 2001 Nov 2;276(44):41133-42.
19. OMIM Disease Annotation Pipeline
20. Park J, etal., J Cell Sci. 2010 May 15;123(Pt 10):1742-50. doi: 10.1242/jcs.064170. Epub 2010 Apr 27.
21. Pipeline to import KEGG annotations from KEGG into RGD
22. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
23. Pipeline to import SMPDB annotations from SMPDB into RGD
24. Qualmann B, etal., Mol Biol Cell 1999 Feb;10(2):501-13.
25. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
26. RGD automated import pipeline for gene-chemical interactions
27. Ringstad N, etal., J Biol Chem. 2001 Nov 2;276(44):40424-30. doi: 10.1074/jbc.M106338200. Epub 2001 Aug 22.
28. Ringstad N, etal., Proc Natl Acad Sci U S A 1997 Aug 5;94(16):8569-74.
29. Saheki Y and De Camilli P, Cold Spring Harb Perspect Biol. 2012 Sep 1;4(9):a005645. doi: 10.1101/cshperspect.a005645.
30. So CW, etal., Leukemia. 2000 Apr;14(4):594-601.
31. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
32. Woscholski R Methods Enzymol 2002;345:335-45.
33. Woscholski R, etal., FEBS Lett 1998 Jul 31;432(1-2):5-8.
Additional References at PubMed
PMID:8798761   PMID:9195986   PMID:9341169   PMID:9694653   PMID:9813051   PMID:10535736   PMID:11879655   PMID:12481038   PMID:12606338   PMID:17762867   PMID:18093523   PMID:18591654  
PMID:18987319   PMID:20448150   PMID:22099461   PMID:22511594   PMID:22871113   PMID:29476059   PMID:30053369  


Genomics

Comparative Map Data
Synj1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21130,192,629 - 30,269,277 (-)NCBI
Rnor_6.0 Ensembl1131,104,787 - 31,180,642 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01131,105,784 - 31,181,573 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01134,717,258 - 34,792,366 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41130,921,834 - 30,998,609 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11130,921,975 - 30,966,053 (-)NCBI
Celera1129,860,879 - 29,935,097 (-)NCBICelera
Cytogenetic Map11q11NCBI
SYNJ1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2132,628,759 - 32,728,040 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl2132,628,759 - 32,728,048 (-)EnsemblGRCh38hg38GRCh38
GRCh382132,628,759 - 32,731,247 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372134,001,069 - 34,100,351 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362132,922,944 - 33,022,148 (-)NCBINCBI36hg18NCBI36
Build 342132,922,943 - 33,022,105NCBI
Celera2119,184,699 - 19,284,009 (-)NCBI
Cytogenetic Map21q22.11NCBI
HuRef2119,410,440 - 19,509,720 (-)NCBIHuRef
CHM1_12133,562,725 - 33,661,992 (-)NCBICHM1_1
Synj1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391690,732,980 - 90,810,543 (-)NCBIGRCm39mm39
GRCm39 Ensembl1690,732,980 - 90,808,196 (-)Ensembl
GRCm381690,936,092 - 91,013,727 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1690,936,092 - 91,011,308 (-)EnsemblGRCm38mm10GRCm38
MGSCv371690,936,342 - 91,011,553 (-)NCBIGRCm37mm9NCBIm37
MGSCv361690,824,951 - 90,900,361 (-)NCBImm8
Celera1692,017,943 - 92,093,156 (-)NCBICelera
Cytogenetic Map16C3.3NCBI
Synj1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540732,093,479 - 32,175,795 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540732,094,076 - 32,175,676 (-)NCBIChiLan1.0ChiLan1.0
SYNJ1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12132,368,949 - 32,466,994 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2132,368,949 - 32,466,994 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02118,990,526 - 19,088,839 (-)NCBIMhudiblu_PPA_v0panPan3
SYNJ1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13127,308,169 - 27,399,226 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3127,308,169 - 27,399,197 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3127,301,124 - 27,392,150 (-)NCBI
ROS_Cfam_1.03127,428,088 - 27,497,209 (-)NCBI
UMICH_Zoey_3.13127,372,989 - 27,463,773 (-)NCBI
UNSW_CanFamBas_1.03127,384,757 - 27,475,496 (-)NCBI
UU_Cfam_GSD_1.03127,892,120 - 27,983,140 (-)NCBI
Synj1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440497127,901,843 - 27,983,289 (-)NCBI
SpeTri2.0NW_0049365009,484,571 - 9,565,980 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SYNJ1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13196,230,089 - 196,330,465 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113196,230,101 - 196,330,512 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213206,240,582 - 206,342,113 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SYNJ1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1259,421,561 - 59,523,076 (+)NCBI
ChlSab1.1 Ensembl259,422,110 - 59,523,176 (+)Ensembl
Synj1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474520,881,312 - 20,984,242 (-)NCBI

Position Markers
D11Rat98  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21130,223,187 - 30,223,321 (+)MAPPER
Rnor_6.01131,135,608 - 31,135,741NCBIRnor6.0
Rnor_5.01134,746,400 - 34,746,533UniSTSRnor5.0
RGSC_v3.41130,952,088 - 30,952,222RGDRGSC3.4
RGSC_v3.41130,952,089 - 30,952,222UniSTSRGSC3.4
RGSC_v3.11130,951,995 - 30,952,129RGD
Celera1129,890,048 - 29,890,179UniSTS
SHRSP x BN Map118.2299RGD
SHRSP x BN Map118.2299UniSTS
Cytogenetic Map11q11UniSTS
RH127638  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21130,192,908 - 30,193,103 (+)MAPPER
Rnor_6.01131,105,092 - 31,105,286NCBIRnor6.0
Rnor_5.01134,716,566 - 34,716,760UniSTSRnor5.0
RGSC_v3.41130,921,142 - 30,921,336UniSTSRGSC3.4
Celera1129,860,187 - 29,860,381UniSTS
RH 3.4 Map11181.4UniSTS
Cytogenetic Map11q11UniSTS
RH143404  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21130,193,171 - 30,193,366 (+)MAPPER
Rnor_6.01131,105,355 - 31,105,549NCBIRnor6.0
Rnor_5.01134,716,829 - 34,717,023UniSTSRnor5.0
RGSC_v3.41130,921,405 - 30,921,599UniSTSRGSC3.4
Celera1129,860,450 - 29,860,644UniSTS
RH 3.4 Map11182.7UniSTS
Cytogenetic Map11q11UniSTS
REN82086  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21130,245,465 - 30,245,690 (+)MAPPER
Rnor_6.01131,157,885 - 31,158,109NCBIRnor6.0
Rnor_5.01134,768,677 - 34,768,901UniSTSRnor5.0
RGSC_v3.41130,974,366 - 30,974,590UniSTSRGSC3.4
Celera1129,912,321 - 29,912,545UniSTS
Cytogenetic Map11q11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1598842Glom10Glomerulus QTL 103.4kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)11133867429Rat
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11172720192Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)1132503169342559Rat
1641927Alcrsp10Alcohol response QTL 10alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)11935127454351274Rat
2290451Scl58Serum cholesterol level QTL 583.48blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)111136730644444347Rat
724517Uae18Urinary albumin excretion QTL 183.7urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)111632197346583360Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111901627290463843Rat
10755497Bp388Blood pressure QTL 3882.76arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)111947517979734728Rat
1598811Bp291Blood pressure QTL 2911.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)112194422966944229Rat
1598841Memor7Memory QTL 7exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)112194422966944229Rat
634341Bw121Body weight QTL 1213.56abdominal fat pad mass (VT:1000711)abdominal fat pad weight (CMO:0000088)112204314944444112Rat
10058952Gmadr6Adrenal mass QTL 62.290.0072adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)112540112970401129Rat
9590313Scort20Serum corticosterone level QTL 206.510.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)112572003870720038Rat
9589032Epfw10Epididymal fat weight QTL 109.290.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)112572003870720038Rat
8694376Bw156Body weight QTL 1562.250.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112572003870720038Rat
8694424Bw162Body weight QTL 1623.80.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112572003870720038Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112831466586994795Rat
1300130Rf20Renal function QTL 204.44kidney glomerulus integrity trait (VT:0010546)kidney glomerulus diameter (CMO:0001166)113043533963186373Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)113043533986714631Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:559
Count of miRNA genes:206
Interacting mature miRNAs:256
Transcripts:ENSRNOT00000002812, ENSRNOT00000052033, ENSRNOT00000065535
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 12 28 12 19 12 72 23 29 11
Low 31 29 29 29 8 11 2 12 12 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_053476 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088690 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088691 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088692 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088693 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088694 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088695 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088696 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088697 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088698 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088699 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088700 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088701 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088702 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088704 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088705 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088706 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC094784 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC120732 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ006855 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473989 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214527 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230618 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232801 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000222 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U45479 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U91836 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000002812   ⟹   ENSRNOP00000002812
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1131,105,799 - 31,180,642 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000052033   ⟹   ENSRNOP00000045019
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1131,104,787 - 31,180,636 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000065535   ⟹   ENSRNOP00000060346
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1131,106,934 - 31,180,616 (-)Ensembl
RefSeq Acc Id: NM_053476   ⟹   NP_445928
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21130,192,629 - 30,269,206 (-)NCBI
Rnor_6.01131,105,784 - 31,181,573 (-)NCBI
Rnor_5.01134,717,258 - 34,792,366 (-)NCBI
RGSC_v3.41130,921,834 - 30,998,609 (-)RGD
Celera1129,860,879 - 29,935,097 (-)RGD
Sequence:
RefSeq Acc Id: XM_039088690   ⟹   XP_038944618
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21130,192,629 - 30,269,277 (-)NCBI
RefSeq Acc Id: XM_039088691   ⟹   XP_038944619
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21130,192,629 - 30,269,277 (-)NCBI
RefSeq Acc Id: XM_039088692   ⟹   XP_038944620
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21130,192,629 - 30,269,277 (-)NCBI
RefSeq Acc Id: XM_039088693   ⟹   XP_038944621
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21130,192,629 - 30,269,277 (-)NCBI
RefSeq Acc Id: XM_039088694   ⟹   XP_038944622
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21130,192,629 - 30,269,277 (-)NCBI
RefSeq Acc Id: XM_039088695   ⟹   XP_038944623
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21130,192,629 - 30,269,277 (-)NCBI
RefSeq Acc Id: XM_039088696   ⟹   XP_038944624
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21130,192,629 - 30,269,276 (-)NCBI
RefSeq Acc Id: XM_039088697   ⟹   XP_038944625
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21130,192,629 - 30,269,276 (-)NCBI
RefSeq Acc Id: XM_039088698   ⟹   XP_038944626
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21130,195,121 - 30,269,277 (-)NCBI
RefSeq Acc Id: XM_039088699   ⟹   XP_038944627
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21130,195,405 - 30,269,277 (-)NCBI
RefSeq Acc Id: XM_039088700   ⟹   XP_038944628
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21130,196,149 - 30,269,277 (-)NCBI
RefSeq Acc Id: XM_039088701   ⟹   XP_038944629
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21130,195,405 - 30,269,277 (-)NCBI
RefSeq Acc Id: XM_039088702   ⟹   XP_038944630
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21130,196,978 - 30,269,277 (-)NCBI
RefSeq Acc Id: XM_039088704   ⟹   XP_038944632
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21130,192,629 - 30,269,277 (-)NCBI
RefSeq Acc Id: XM_039088705   ⟹   XP_038944633
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21130,195,121 - 30,269,276 (-)NCBI
RefSeq Acc Id: XM_039088706   ⟹   XP_038944634
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21130,192,629 - 30,234,785 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_445928   ⟸   NM_053476
- UniProtKB: Q62910 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000002812   ⟸   ENSRNOT00000002812
RefSeq Acc Id: ENSRNOP00000060346   ⟸   ENSRNOT00000065535
RefSeq Acc Id: ENSRNOP00000045019   ⟸   ENSRNOT00000052033
RefSeq Acc Id: XP_038944619   ⟸   XM_039088691
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038944632   ⟸   XM_039088704
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038944620   ⟸   XM_039088692
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038944623   ⟸   XM_039088695
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038944621   ⟸   XM_039088693
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038944622   ⟸   XM_039088694
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038944618   ⟸   XM_039088690
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038944625   ⟸   XM_039088697
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038944624   ⟸   XM_039088696
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038944634   ⟸   XM_039088706
- Peptide Label: isoform X13
RefSeq Acc Id: XP_038944626   ⟸   XM_039088698
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038944633   ⟸   XM_039088705
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038944629   ⟸   XM_039088701
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038944627   ⟸   XM_039088699
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038944628   ⟸   XM_039088700
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038944630   ⟸   XM_039088702
- Peptide Label: isoform X10
Protein Domains
RRM   SAC

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
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 (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:69434 AgrOrtholog
BIND 129614
  130419
  130567
  130570
  134435
Ensembl Genes ENSRNOG00000002051 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000002812 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000045019 UniProtKB/TrEMBL
  ENSRNOP00000060346 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000002812 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000052033 UniProtKB/TrEMBL
  ENSRNOT00000065535 UniProtKB/Swiss-Prot
Gene3D-CATH 3.30.70.330 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.60.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro DUF1866 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Endo/exonu/phosph_ase_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Endo/exonuclease/phosphatase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IPPc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nucleotide-bd_a/b_plait_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RBD_domain_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RRM_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SAC_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SYNJ1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SYNJ1_RRM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:85238 UniProtKB/Swiss-Prot
NCBI Gene 85238 ENTREZGENE
PANTHER PTHR11200:SF158 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam DUF1866 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Exo_endo_phos UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Syja_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Synj1 PhenoGen
PROSITE RRM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SAC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART DUF1866 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IPPc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF54928 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF56219 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC228838
UniProt D4ABN3_RAT UniProtKB/TrEMBL
  Q62910 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary O89092 UniProtKB/Swiss-Prot
  Q62911 UniProtKB/Swiss-Prot
  Q810Z8 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Synj1  synaptojanin 1      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_homology amino-terminal domain has homology with yeast Sac1, which plays a role in phospholipid metabolism and in actin cytoskeleton function 69388
gene_physical_interaction binds the SH3 domain of the presynaptic protein amphiphysin 69388