Pacsin2 (protein kinase C and casein kinase substrate in neurons 2) - Rat Genome Database

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Gene: Pacsin2 (protein kinase C and casein kinase substrate in neurons 2) Rattus norvegicus
Analyze
Symbol: Pacsin2
Name: protein kinase C and casein kinase substrate in neurons 2
RGD ID: 69411
Description: Predicted to have cytoskeletal protein binding activity; identical protein binding activity; and phosphatidic acid binding activity. Predicted to be involved in several processes, including caveolin-mediated endocytosis; plasma membrane organization; and protein localization to endosome. Predicted to localize to several cellular components, including caveola; nuclear speck; and recycling endosome membrane. Orthologous to human PACSIN2 (protein kinase C and casein kinase substrate in neurons 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: protein kinase C and casein kinase substrate in neurons 2 protein; SdpII; SdpIIsyndapin II; synaptic dynamin-associated protein II; syndapin 2; syndapin II; syndapin-2; syndapin-II
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
mRatBN7.27114,505,525 - 114,599,087 (-)NCBI
Rnor_6.0 Ensembl7124,223,633 - 124,317,379 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.07124,224,210 - 124,317,407 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.07124,214,202 - 124,307,009 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47121,484,248 - 121,546,498 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17121,487,482 - 121,579,686 (+)NCBI
Celera7110,819,040 - 110,881,274 (-)NCBICelera
Cytogenetic Map7q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:10431838   PMID:11082044   PMID:15930129   PMID:16189514   PMID:19056867   PMID:20188097   PMID:21423176   PMID:21610094   PMID:23376485   PMID:23596323   PMID:23793062   PMID:23918399  
PMID:24013648   PMID:25416956   PMID:25468996   PMID:28235806   PMID:31515488  


Genomics

Comparative Map Data
Pacsin2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27114,505,525 - 114,599,087 (-)NCBI
Rnor_6.0 Ensembl7124,223,633 - 124,317,379 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.07124,224,210 - 124,317,407 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.07124,214,202 - 124,307,009 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47121,484,248 - 121,546,498 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17121,487,482 - 121,579,686 (+)NCBI
Celera7110,819,040 - 110,881,274 (-)NCBICelera
Cytogenetic Map7q34NCBI
PACSIN2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2242,835,412 - 43,015,149 (-)EnsemblGRCh38hg38GRCh38
GRCh382242,869,766 - 43,015,149 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372243,265,772 - 43,411,155 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362241,596,880 - 41,672,991 (-)NCBINCBI36hg18NCBI36
Build 342241,590,274 - 41,735,649NCBI
Celera2227,176,274 - 27,321,760 (-)NCBI
Cytogenetic Map22q13.2NCBI
HuRef2226,224,672 - 26,369,391 (-)NCBIHuRef
CHM1_12243,225,547 - 43,371,023 (-)NCBICHM1_1
Pacsin2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391583,259,808 - 83,348,816 (-)NCBIGRCm39mm39
GRCm39 Ensembl1583,259,808 - 83,348,807 (-)Ensembl
GRCm381583,375,607 - 83,464,610 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1583,375,607 - 83,464,606 (-)EnsemblGRCm38mm10GRCm38
MGSCv371583,206,037 - 83,295,036 (-)NCBIGRCm37mm9NCBIm37
MGSCv361583,203,884 - 83,260,585 (-)NCBImm8
Celera1585,508,985 - 85,597,984 (-)NCBICelera
Cytogenetic Map15E1NCBI
Pacsin2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541328,116,961 - 28,140,810 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541328,119,769 - 28,209,258 (-)NCBIChiLan1.0ChiLan1.0
PACSIN2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12241,908,922 - 42,052,327 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2241,908,922 - 41,999,692 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02223,757,565 - 23,900,837 (-)NCBIMhudiblu_PPA_v0panPan3
PACSIN2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11022,512,058 - 22,648,553 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1022,512,077 - 22,647,322 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1022,448,532 - 22,584,797 (+)NCBI
ROS_Cfam_1.01023,256,673 - 23,393,490 (+)NCBI
UMICH_Zoey_3.11022,975,693 - 23,111,993 (+)NCBI
UNSW_CanFamBas_1.01023,294,958 - 23,431,287 (+)NCBI
UU_Cfam_GSD_1.01023,469,880 - 23,606,571 (+)NCBI
Pacsin2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049456,129,392 - 6,241,034 (+)NCBI
SpeTri2.0NW_004936718739,133 - 850,775 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PACSIN2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl55,853,377 - 5,985,171 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.155,853,377 - 5,985,174 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.253,320,905 - 3,358,652 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PACSIN2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11925,412,627 - 25,553,919 (-)NCBI
ChlSab1.1 Ensembl1925,412,394 - 25,435,169 (-)Ensembl
Vero_WHO_p1.0NW_02366604599,894,616 - 100,039,255 (+)NCBI
Pacsin2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247525,927,096 - 6,041,458 (+)NCBI

Position Markers
D7Rat128  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27114,527,811 - 114,528,048 (+)MAPPER
Rnor_6.07124,246,491 - 124,246,733NCBIRnor6.0
Rnor_5.07124,236,483 - 124,236,725UniSTSRnor5.0
RGSC_v3.47121,523,977 - 121,524,220RGDRGSC3.4
RGSC_v3.47121,523,978 - 121,524,220UniSTSRGSC3.4
RGSC_v3.17121,558,207 - 121,558,450RGD
Celera7110,841,297 - 110,841,485UniSTS
SHRSP x BN Map766.86RGD
SHRSP x BN Map766.86UniSTS
Cytogenetic Map7q34UniSTS
RH127347  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27114,505,611 - 114,505,816 (+)MAPPER
Rnor_6.07124,224,290 - 124,224,494NCBIRnor6.0
Rnor_5.07124,214,282 - 124,214,486UniSTSRnor5.0
RGSC_v3.47121,546,216 - 121,546,420UniSTSRGSC3.4
Celera7110,819,118 - 110,819,322UniSTS
RH 3.4 Map7911.9UniSTS
Cytogenetic Map7q34UniSTS
RH141067  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27114,506,637 - 114,506,847 (+)MAPPER
Rnor_6.07124,225,317 - 124,225,526NCBIRnor6.0
Rnor_5.07124,215,309 - 124,215,518UniSTSRnor5.0
RGSC_v3.47121,545,185 - 121,545,394UniSTSRGSC3.4
Celera7110,820,145 - 110,820,354UniSTS
RH 3.4 Map7909.6UniSTS
Cytogenetic Map7q34UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)72920071124838025Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)748118835128611831Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)750704769128085642Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)751251919145729302Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)771448715145729302Rat
631540Bw9Body weight QTL 94.5body mass (VT:0001259)body weight (CMO:0000012)777428105127748511Rat
634331Pia17Pristane induced arthritis QTL 174.7joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)781645773140745067Rat
7411607Foco15Food consumption QTL 150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)785595369130595369Rat
7411654Foco25Food consumption QTL 259.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)785595369130595369Rat
1331768Kidm10Kidney mass QTL 104.62096kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)788365265133365265Rat
1331728Bp214Blood pressure QTL 2142.825arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)788365265134673427Rat
2317052Aia17Adjuvant induced arthritis QTL 172.13joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)791018361136018361Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)791832949145158140Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)791832949145158140Rat
71114Niddm14Non-insulin dependent diabetes mellitus QTL 144.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)793726906138726906Rat
2298475Eau6Experimental allergic uveoretinitis QTL 60.0029uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)793726906138726906Rat
1558655Swd4Spike wave discharge measurement QTL 43.680.0002brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge severity grade (CMO:0001988)796630946141630946Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)7100028953145729302Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)7100160423140335001Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)7100192194145192194Rat
2313102Bmd79Bone mineral density QTL 792.30.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)7103815550126525386Rat
1357336Gluco6Glucose level QTL 63.4blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)7103867802126080176Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)7106564316145729302Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7111519266143965591Rat
70159Bp61Blood pressure QTL 610.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7112429186126525386Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7114825174145729302Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7115922628145729302Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7120746024145692398Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7121654760145729302Rat
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7121986439143965591Rat
1357339Stl14Serum triglyceride level QTL 143.450.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7122421276143965415Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:225
Count of miRNA genes:55
Interacting mature miRNAs:63
Transcripts:ENSRNOT00000013398, ENSRNOT00000013428, ENSRNOT00000067913
Prediction methods: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 43 56 40 19 40 2 5 74 35 41 11 2
Low 1 1 1 6 6 6
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_130740 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006242050 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006242051 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006242052 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006242053 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006242055 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006242058 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006242060 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008765660 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008765661 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008765662 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594626 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594627 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594628 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594629 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594630 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078304 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078305 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078306 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078307 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078308 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078309 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078310 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078311 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF139492 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF139493 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF139494 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF139495 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC070911 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473950 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230278 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000187 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000013398   ⟹   ENSRNOP00000013398
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7124,225,255 - 124,317,379 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000013428   ⟹   ENSRNOP00000013428
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7124,223,633 - 124,256,148 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000067913   ⟹   ENSRNOP00000060074
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7124,225,704 - 124,256,077 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000088125   ⟹   ENSRNOP00000072822
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7124,224,212 - 124,286,478 (-)Ensembl
RefSeq Acc Id: NM_130740   ⟹   NP_570096
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27114,505,534 - 114,567,653 (-)NCBI
Rnor_6.07124,224,212 - 124,286,478 (-)NCBI
Rnor_5.07124,214,202 - 124,307,009 (-)NCBI
RGSC_v3.47121,484,248 - 121,546,498 (+)RGD
Celera7110,819,040 - 110,881,274 (-)RGD
Sequence:
RefSeq Acc Id: XM_006242050   ⟹   XP_006242112
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27114,505,525 - 114,568,309 (-)NCBI
Rnor_6.07124,224,210 - 124,287,162 (-)NCBI
Rnor_5.07124,214,202 - 124,307,009 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006242051   ⟹   XP_006242113
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27114,506,576 - 114,599,087 (-)NCBI
Rnor_6.07124,225,255 - 124,317,403 (-)NCBI
Rnor_5.07124,214,202 - 124,307,009 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006242052   ⟹   XP_006242114
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27114,505,525 - 114,568,309 (-)NCBI
Rnor_6.07124,224,210 - 124,287,162 (-)NCBI
Rnor_5.07124,214,202 - 124,307,009 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006242053   ⟹   XP_006242115
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27114,505,525 - 114,599,087 (-)NCBI
Rnor_6.07124,224,210 - 124,317,407 (-)NCBI
Rnor_5.07124,214,202 - 124,307,009 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006242055   ⟹   XP_006242117
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27114,506,492 - 114,598,531 (-)NCBI
Rnor_6.07124,225,255 - 124,317,403 (-)NCBI
Rnor_5.07124,214,202 - 124,307,009 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006242058   ⟹   XP_006242120
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27114,506,576 - 114,598,504 (-)NCBI
Rnor_6.07124,225,255 - 124,317,403 (-)NCBI
Rnor_5.07124,214,202 - 124,307,009 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006242060   ⟹   XP_006242122
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27114,506,576 - 114,598,504 (-)NCBI
Rnor_6.07124,225,255 - 124,317,403 (-)NCBI
Rnor_5.07124,214,202 - 124,307,009 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008765660   ⟹   XP_008763882
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27114,505,525 - 114,537,290 (-)NCBI
Rnor_6.07124,224,210 - 124,249,352 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008765661   ⟹   XP_008763883
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.07124,224,210 - 124,286,414 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008765662   ⟹   XP_008763884
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27114,505,525 - 114,599,087 (-)NCBI
Rnor_6.07124,224,210 - 124,317,407 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017594626   ⟹   XP_017450115
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.07124,224,210 - 124,249,352 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017594627   ⟹   XP_017450116
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27114,505,525 - 114,599,087 (-)NCBI
Rnor_6.07124,224,210 - 124,301,112 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017594628   ⟹   XP_017450117
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.07124,224,210 - 124,249,352 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017594629   ⟹   XP_017450118
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.07124,224,210 - 124,249,352 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017594630   ⟹   XP_017450119
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.07124,224,210 - 124,287,163 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039078304   ⟹   XP_038934232
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27114,505,525 - 114,529,068 (-)NCBI
RefSeq Acc Id: XM_039078305   ⟹   XP_038934233
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27114,505,525 - 114,559,102 (-)NCBI
RefSeq Acc Id: XM_039078306   ⟹   XP_038934234
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27114,505,525 - 114,588,481 (-)NCBI
RefSeq Acc Id: XM_039078307   ⟹   XP_038934235
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27114,505,525 - 114,529,076 (-)NCBI
RefSeq Acc Id: XM_039078308   ⟹   XP_038934236
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27114,506,492 - 114,598,561 (-)NCBI
RefSeq Acc Id: XM_039078309   ⟹   XP_038934237
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27114,505,534 - 114,582,237 (-)NCBI
RefSeq Acc Id: XM_039078310   ⟹   XP_038934238
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27114,505,525 - 114,599,087 (-)NCBI
RefSeq Acc Id: XM_039078311   ⟹   XP_038934239
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27114,505,525 - 114,537,466 (-)NCBI
Protein Sequences
Protein RefSeqs NP_570096 (Get FASTA)   NCBI Sequence Viewer  
  XP_006242112 (Get FASTA)   NCBI Sequence Viewer  
  XP_006242113 (Get FASTA)   NCBI Sequence Viewer  
  XP_006242114 (Get FASTA)   NCBI Sequence Viewer  
  XP_006242115 (Get FASTA)   NCBI Sequence Viewer  
  XP_006242117 (Get FASTA)   NCBI Sequence Viewer  
  XP_006242120 (Get FASTA)   NCBI Sequence Viewer  
  XP_006242122 (Get FASTA)   NCBI Sequence Viewer  
  XP_008763882 (Get FASTA)   NCBI Sequence Viewer  
  XP_008763884 (Get FASTA)   NCBI Sequence Viewer  
  XP_017450116 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934232 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934233 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934234 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934235 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934236 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934237 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934238 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934239 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAF22211 (Get FASTA)   NCBI Sequence Viewer  
  AAF22212 (Get FASTA)   NCBI Sequence Viewer  
  AAF22213 (Get FASTA)   NCBI Sequence Viewer  
  AAF22214 (Get FASTA)   NCBI Sequence Viewer  
  AAH70911 (Get FASTA)   NCBI Sequence Viewer  
  EDM15628 (Get FASTA)   NCBI Sequence Viewer  
  EDM15629 (Get FASTA)   NCBI Sequence Viewer  
  EDM15630 (Get FASTA)   NCBI Sequence Viewer  
  EDM15631 (Get FASTA)   NCBI Sequence Viewer  
  Q9QY17 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_570096   ⟸   NM_130740
- UniProtKB: Q9QY17 (UniProtKB/Swiss-Prot),   Q6IRI3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006242115   ⟸   XM_006242053
- Peptide Label: isoform X3
- UniProtKB: Q9QY17 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006242122   ⟸   XM_006242060
- Peptide Label: isoform X8
- UniProtKB: Q9QY17 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006242117   ⟸   XM_006242055
- Peptide Label: isoform X5
- UniProtKB: Q9QY17 (UniProtKB/Swiss-Prot),   Q6IRI3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006242120   ⟸   XM_006242058
- Peptide Label: isoform X7
- UniProtKB: Q9QY17 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006242113   ⟸   XM_006242051
- Peptide Label: isoform X3
- UniProtKB: Q9QY17 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006242114   ⟸   XM_006242052
- Peptide Label: isoform X3
- UniProtKB: Q9QY17 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006242112   ⟸   XM_006242050
- Peptide Label: isoform X3
- UniProtKB: Q9QY17 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008763884   ⟸   XM_008765662
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_008763883   ⟸   XM_008765661
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_008763882   ⟸   XM_008765660
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017450116   ⟸   XM_017594627
- Peptide Label: isoform X3
- UniProtKB: Q9QY17 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017450119   ⟸   XM_017594630
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_017450118   ⟸   XM_017594629
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_017450115   ⟸   XM_017594626
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017450117   ⟸   XM_017594628
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: ENSRNOP00000060074   ⟸   ENSRNOT00000067913
RefSeq Acc Id: ENSRNOP00000013428   ⟸   ENSRNOT00000013428
RefSeq Acc Id: ENSRNOP00000013398   ⟸   ENSRNOT00000013398
RefSeq Acc Id: ENSRNOP00000072822   ⟸   ENSRNOT00000088125
RefSeq Acc Id: XP_038934238   ⟸   XM_039078310
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038934234   ⟸   XM_039078306
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038934233   ⟸   XM_039078305
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038934239   ⟸   XM_039078311
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038934235   ⟸   XM_039078307
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038934232   ⟸   XM_039078304
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038934237   ⟸   XM_039078309
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038934236   ⟸   XM_039078308
- Peptide Label: isoform X5
Protein Domains
F-BAR   SH3

Transcriptome

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

Promoters
RGD ID:13695546
Promoter ID:EPDNEW_R6071
Type:initiation region
Name:Pacsin2_2
Description:protein kinase C and casein kinase substrate in neurons 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R6072  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.07124,286,505 - 124,286,565EPDNEW
RGD ID:13695558
Promoter ID:EPDNEW_R6072
Type:initiation region
Name:Pacsin2_1
Description:protein kinase C and casein kinase substrate in neurons 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R6071  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.07124,317,422 - 124,317,482EPDNEW

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:69411 AgrOrtholog
Ensembl Genes ENSRNOG00000009756 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000013398 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000013428 UniProtKB/TrEMBL
  ENSRNOP00000060074 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000072822 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000013398 UniProtKB/Swiss-Prot
  ENSRNOT00000013428 UniProtKB/TrEMBL
  ENSRNOT00000067913 UniProtKB/Swiss-Prot
  ENSRNOT00000088125 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.20.1270.60 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7104542 IMAGE-MGC_LOAD
InterPro AH/BAR_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  F_BAR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FCH_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PACSIN1/PACSIN2_SH3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PACSIN2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PACSIN2_F-BAR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:124461 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:91517 IMAGE-MGC_LOAD
NCBI Gene 124461 ENTREZGENE
PANTHER PTHR23065:SF14 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam FCH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pacsin2 PhenoGen
PRINTS SH3DOMAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE F_BAR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART FCH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF103657 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF50044 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC230697
  TC230698
UniProt PACN2_RAT UniProtKB/Swiss-Prot
  Q6IRI3 ENTREZGENE, UniProtKB/TrEMBL
  Q9QY17 ENTREZGENE
  R9PXU3_RAT UniProtKB/TrEMBL
UniProt Secondary Q9QY18 UniProtKB/Swiss-Prot
  Q9QY19 UniProtKB/Swiss-Prot
  Q9QY20 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Pacsin2  protein kinase C and casein kinase substrate in neurons 2      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference