Picalm (phosphatidylinositol binding clathrin assembly protein) - Rat Genome Database

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Gene: Picalm (phosphatidylinositol binding clathrin assembly protein) Rattus norvegicus
Analyze
Symbol: Picalm
Name: phosphatidylinositol binding clathrin assembly protein
RGD ID: 621054
Description: Exhibits several functions, including SH3 domain binding activity; identical protein binding activity; and phosphatidylinositol binding activity. Involved in several processes, including generation of neurons; positive regulation of dendrite extension; and positive regulation of transport. Localizes to several cellular components, including Schaffer collateral - CA1 synapse; cytoplasmic vesicle; and synaptic membrane. Predicted to colocalize with AP-2 adaptor complex and perinuclear region of cytoplasm. Human ortholog(s) of this gene implicated in acute myeloid leukemia. Orthologous to human PICALM (phosphatidylinositol binding clathrin assembly protein); INTERACTS WITH ammonium chloride; amphetamine; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Calm; clathrin assembly lymphoid myeloid leukemia protein; clathrin-assembly lymphoid leukemia protein; clathrin-assembly lymphoid myeloid leukemia protein; MGC114290; phosphatidylinositol-binding clathrin assembly protein; rCALM
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
mRatBN7.21144,056,415 - 144,138,045 (+)NCBI
Rnor_6.0 Ensembl1154,377,247 - 154,458,425 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01154,377,229 - 154,458,966 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01160,681,689 - 160,763,382 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41146,754,085 - 146,834,197 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11146,832,490 - 146,912,603 (+)NCBI
Celera1142,288,691 - 142,367,949 (+)NCBICelera
Cytogenetic Map1q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Biological Process
amyloid-beta clearance by transcytosis  (IEA,ISO)
axonogenesis  (IEA,IMP,ISO)
clathrin coat assembly  (IDA,IEA,ISO)
clathrin-coated pit assembly  (IEA,ISO)
clathrin-dependent endocytosis  (IBA,IEA,ISO,ISS)
dendrite morphogenesis  (IEA,IMP,ISO)
endocytosis  (IEA,ISO)
endosomal transport  (IEA,ISO)
hemopoiesis  (IEA,ISO)
iron ion homeostasis  (IEA,ISO,ISS)
learning or memory  (IEA,ISO)
membrane bending  (IEA,ISO)
modulation of age-related behavioral decline  (IEA,ISO)
negative regulation of gene expression  (IEA,ISO,ISS)
negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process  (IEA,ISO,ISS)
negative regulation of protein localization to cell surface  (IEA,ISO)
negative regulation of protein localization to plasma membrane  (IEA,ISO)
negative regulation of receptor-mediated endocytosis  (IEA,ISO)
positive regulation of amyloid-beta formation  (IEA,ISO,ISS)
positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process  (IEA,ISO,ISS)
positive regulation of axonogenesis  (IMP)
positive regulation of dendrite extension  (IMP)
positive regulation of GTPase activity  (IEA,ISO)
positive regulation of neuron death  (IEA,ISO,ISS)
positive regulation of synaptic vesicle clustering  (IMP)
positive regulation of synaptic vesicle endocytosis  (IMP)
positive regulation of transcription, DNA-templated  (IEA,ISO)
receptor internalization  (IEA,ISO)
receptor-mediated endocytosis  (ISO,ISS)
regulation of amyloid-beta formation  (ISO)
regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process  (ISO,ISS)
regulation of endocytosis  (IMP,ISO)
regulation of protein localization  (ISO)
regulation of protein transport  (IMP)
regulation of synaptic vesicle endocytosis  (IMP)
regulation of synaptic vesicle transport  (IMP)
regulation of terminal button organization  (IMP)
regulation of vesicle size  (IEA,ISO)
synaptic vesicle budding from presynaptic endocytic zone membrane  (IBA)
synaptic vesicle endocytosis  (IDA,IMP)
synaptic vesicle maturation  (IEA,ISO,ISS)
vesicle budding from membrane  (IBA,IEA,ISO)
vesicle cargo loading  (IEA,ISO,ISS)
vesicle-mediated transport  (IMP)

Molecular Function

References

References - curated
1. Bushlin I, etal., J Neurosci. 2008 Oct 8;28(41):10257-71. doi: 10.1523/JNEUROSCI.2471-08.2008.
2. Ford MG, etal., Science. 2001 Feb 9;291(5506):1051-5.
3. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4. GOA data from the GO Consortium
5. Hasse S, etal., Histochem Cell Biol. 2006 Aug;126(2):219-29. Epub 2006 Apr 20.
6. Kim HL and Kim JA, Exp Mol Med. 2000 Dec 31;32(4):222-6.
7. Kim HL and Lee SC, Exp Mol Med 1999 Dec 31;31(4):191-6.
8. Kim JA, etal., Exp Mol Med. 2000 Jun 30;32(2):93-9.
9. Koo SJ, etal., Proc Natl Acad Sci U S A. 2011 Aug 16;108(33):13540-5. doi: 10.1073/pnas.1107067108. Epub 2011 Aug 1.
10. Miller SE, etal., Cell. 2011 Nov 23;147(5):1118-31. doi: 10.1016/j.cell.2011.10.038.
11. Miller SE, etal., Dev Cell. 2015 Apr 20;33(2):163-75. doi: 10.1016/j.devcel.2015.03.002.
12. NCBI rat LocusLink and RefSeq merged data July 26, 2002
13. OMIM Disease Annotation Pipeline
14. Petralia RS and Yao PJ, J Comp Neurol. 2007 Sep 20;504(3):314-27.
15. Petralia RS, etal., Neuromolecular Med. 2013 Mar;15(1):49-60. doi: 10.1007/s12017-012-8194-x. Epub 2012 Aug 1.
16. RGD automated data pipeline
17. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
18. RGD automated import pipeline for gene-chemical interactions
19. Wechsler DS, etal., Genes Chromosomes Cancer. 2003 Jan;36(1):26-36.
20. Yao PJ, etal., J Comp Neurol. 2005 Jan 3;481(1):58-69.
Additional References at PubMed
PMID:10436022   PMID:11425879   PMID:12477932   PMID:12832620   PMID:14985334   PMID:15182197   PMID:16262731   PMID:16491119   PMID:18182011   PMID:19946888   PMID:20653035   PMID:21221849  
PMID:22539346   PMID:22952941   PMID:23589030   PMID:24577224   PMID:25468996   PMID:26005850   PMID:30053369  


Genomics

Comparative Map Data
Picalm
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21144,056,415 - 144,138,045 (+)NCBI
Rnor_6.0 Ensembl1154,377,247 - 154,458,425 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01154,377,229 - 154,458,966 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01160,681,689 - 160,763,382 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41146,754,085 - 146,834,197 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11146,832,490 - 146,912,603 (+)NCBI
Celera1142,288,691 - 142,367,949 (+)NCBICelera
Cytogenetic Map1q32NCBI
PICALM
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1185,957,175 - 86,069,882 (-)EnsemblGRCh38hg38GRCh38
GRCh381185,957,175 - 86,069,860 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371185,668,218 - 85,780,902 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361185,346,133 - 85,457,756 (-)NCBINCBI36hg18NCBI36
Build 341185,346,133 - 85,457,756NCBI
Celera1182,977,768 - 83,089,435 (-)NCBI
Cytogenetic Map11q14.2NCBI
HuRef1181,965,384 - 82,078,030 (-)NCBIHuRef
CHM1_11185,553,010 - 85,665,742 (-)NCBICHM1_1
Picalm
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39789,779,418 - 89,858,655 (+)NCBIGRCm39mm39
GRCm39 Ensembl789,779,421 - 89,862,673 (+)Ensembl
GRCm38790,130,192 - 90,209,447 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl790,130,213 - 90,213,465 (+)EnsemblGRCm38mm10GRCm38
MGSCv37797,278,742 - 97,357,442 (+)NCBIGRCm37mm9NCBIm37
MGSCv36790,005,424 - 90,084,124 (+)NCBImm8
Celera787,455,394 - 87,534,538 (+)NCBICelera
Cytogenetic Map7D3NCBI
cM Map750.47NCBI
Picalm
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554146,871,520 - 6,969,208 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554146,871,220 - 6,970,569 (+)NCBIChiLan1.0ChiLan1.0
PICALM
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11184,619,241 - 84,730,516 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1184,619,241 - 84,730,684 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01181,011,324 - 81,122,352 (-)NCBIMhudiblu_PPA_v0panPan3
PICALM
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12113,437,819 - 13,540,167 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2113,437,925 - 13,539,616 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2113,303,451 - 13,405,757 (+)NCBI
ROS_Cfam_1.02113,619,410 - 13,719,561 (+)NCBI
UMICH_Zoey_3.12113,405,869 - 13,508,626 (+)NCBI
UNSW_CanFamBas_1.02113,478,428 - 13,581,047 (+)NCBI
UU_Cfam_GSD_1.02113,531,568 - 13,633,911 (+)NCBI
Picalm
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494772,186,022 - 72,286,358 (-)NCBI
SpeTri2.0NW_00493649813,785,638 - 13,885,931 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PICALM
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl919,835,938 - 20,104,632 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1919,835,934 - 19,947,239 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2922,107,100 - 22,184,702 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PICALM
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1177,214,391 - 77,325,626 (-)NCBI
ChlSab1.1 Ensembl177,213,836 - 77,324,875 (-)Ensembl
Vero_WHO_p1.0NW_02366604348,400,453 - 48,511,604 (+)NCBI
Picalm
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248453,875,601 - 3,990,347 (+)NCBI

Position Markers
RH66557  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01154,458,117 - 154,458,279NCBIRnor6.0
Rnor_5.01160,762,577 - 160,762,739UniSTSRnor5.0
RGSC_v3.41146,835,123 - 146,835,285UniSTSRGSC3.4
Celera1142,368,875 - 142,369,037UniSTS
Cytogenetic Map1q32UniSTS
SHGC-24065  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X105,158,590 - 105,158,716NCBIRnor6.0
Rnor_6.01154,458,277 - 154,458,403NCBIRnor6.0
Rnor_5.01160,762,736 - 160,762,863NCBIRnor5.0
Rnor_5.0X105,051,438 - 105,051,565NCBIRnor5.0
RGSC_v3.41146,835,283 - 146,835,409UniSTSRGSC3.4
RGSC_v3.4X121,797,723 - 121,797,849UniSTSRGSC3.4
Celera1142,369,035 - 142,369,161UniSTS
CeleraX98,568,913 - 98,569,039UniSTS
Cytogenetic Map1q32UniSTS
Cytogenetic MapXq34UniSTS
RH136706  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01154,397,011 - 154,397,228NCBIRnor6.0
Rnor_5.01160,701,471 - 160,701,688UniSTSRnor5.0
RGSC_v3.41146,773,591 - 146,773,808UniSTSRGSC3.4
Celera1142,308,197 - 142,308,414UniSTS
RH 3.4 Map11122.99UniSTS
Cytogenetic Map1q32UniSTS
Picalm  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01154,458,082 - 154,458,231NCBIRnor6.0
Rnor_5.01160,762,542 - 160,762,691UniSTSRnor5.0
RGSC_v3.41146,835,088 - 146,835,237UniSTSRGSC3.4
Celera1142,368,840 - 142,368,989UniSTS
Cytogenetic Map1q32UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70209Niddm23Non-insulin dependent diabetes mellitus QTL 232.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)199983293216325819Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134993530173445086Rat
71118Thym1Thymus enlargement QTL 110.170.001thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)1153655976198655976Rat
631199Cm23Cardiac mass QTL 234.60.0004heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)1124603592188289386Rat
631202Gluco13Glucose level QTL 130.0001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1139523928170246858Rat
631205Bp196Blood pressure QTL 19640.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1126240667217054291Rat
631206Niddm40Non-insulin dependent diabetes mellitus QTL 40blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1144723107174343537Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)158354072161711996Rat
61442Strs1Sensitivity to stroke QTL 17.4cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)1133946489178946489Rat
724521Uae1Urinary albumin excretion QTL 13.80.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)194201400184846632Rat
724529Cm16Cardiac mass QTL 162.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)190804143161321256Rat
724550Thym3Thymus enlargement QTL 37.820.001thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)1153655976198655976Rat
724562Rends1Renal damage susceptibility QTL 10.05kidney glomerulus integrity trait (VT:0010546)index of glomerular damage (CMO:0001135)1137787261236763528Rat
724567Tcas6Tongue tumor susceptibility QTL 66.85tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)195304961156446783Rat
1331749Hrtrt11Heart rate QTL 112.973heart pumping trait (VT:2000009)heart rate (CMO:0000002)199983293216213510Rat
1331751Bp199Blood pressure QTL 1993.60022arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)199983293198656062Rat
631654Bp107Blood pressure QTL 107arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1133076978178076978Rat
1331793Bp200Blood pressure QTL 2003.71601arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)199983293188289386Rat
2303591Gluco41Glucose level QTL 412blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1109634374154634374Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149578577169852184Rat
731168Bp154Blood pressure QTL 1543.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1100131562236763528Rat
738006Anxrr14Anxiety related response QTL 1440.00035locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)1141296374186296374Rat
738028Anxrr12Anxiety related response QTL 124.90.00001locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)1141296374186296374Rat
631496Bp97Blood pressure QTL 973.08arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1113593576158593576Rat
631519Pia11Pristane induced arthritis QTL 115.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1153656062198656062Rat
631544Bp84Blood pressure QTL 845.6arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1130779148198585664Rat
631549Bp89Blood pressure QTL 895.7arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1130779320219238476Rat
1641895Bp298Blood pressure QTL 298arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1130779148199254774Rat
1598850Bp297Blood pressure QTL 2972.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1131334152176334152Rat
1598853Memor3Memory QTL 34.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)1153834077232297227Rat
1598866Bp287Blood pressure QTL 2875.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1131334152176334152Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149578693217054291Rat
634348Bp138Blood pressure QTL 138arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1133076978184188922Rat
1578770Stresp23Stress response QTL 23kidney sympathetic nerve activity (VT:0004050)stimulated renal sympathetic nerve activity to basal renal sympathetic nerve activity ratio (CMO:0001786)1130779148199254774Rat
1578780Cm52Cardiac mass QTL 523.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)182788437239853971Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)149147799156446783Rat
1300158Bp173Blood pressure QTL 1733.48arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)1122614824201146953Rat
1354591Cm36Cardiac mass QTL 364.1heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1108986301219232156Rat
1354606Bp246Blood pressure QTL 2463.6arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)1108986301238830534Rat
1354615Cm32Cardiac mass QTL 325.2heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)1108986301219232156Rat
1354623Rf46Renal function QTL 463.8blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)1108986301161784422Rat
1558645Bw55Body weight QTL 553.20.004body mass (VT:0001259)body weight (CMO:0000012)1144395993189395993Rat
1358189Cstrr1Cold stress response QTL 10.0001catecholamine amount (VT:0010543)urine norepinephrine level (CMO:0001629)1130779148199254774Rat
2313060Bss71Bone structure and strength QTL 712.60.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)1124090312169090312Rat
1358902Bw47Body weight QTL 471.67body mass (VT:0001259)body weight (CMO:0000012)194201400197187904Rat
2293140Bp313Blood pressure QTL 313arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1129208943174208943Rat
61341Bp26Blood pressure QTL 26arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1137787261236763528Rat
61346Rf2Renal disease susceptibility QTL 23.7urine protein amount (VT:0005160)urine protein level (CMO:0000591)1111446783156446783Rat
61348Bp30Blood pressure QTL 302.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1154337847215828102Rat
61370Mcs3Mammary carcinoma susceptibility QTL 32.15mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1108057233167517487Rat
61399Tcat1Tongue tumor resistance QTL 13.3tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 5 mm (CMO:0001879)1111446783156446783Rat
6893347Bw98Body weight QTL 980.20.53body mass (VT:0001259)body weight (CMO:0000012)1144395993189395993Rat
6893361Bw104Body weight QTL 1040.590.27body mass (VT:0001259)body weight (CMO:0000012)1144395993189395993Rat
8655649Arrd1Age-related retinal degeneration QTL 14.89retinal layer morphology trait (VT:0003727)percentage of study population developing retinopathy during a period of time (CMO:0002453)1106002252202571904Rat
7794788Mcs32Mammary carcinoma susceptibility QTL 322.61mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)1122614824262664716Rat
9685799Bp375Blood pressure QTL 375arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1133076978178076978Rat
9590300Scort16Serum corticosterone level QTL 164.390.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1110620749155620749Rat
9685802Bp376Blood pressure QTL 376arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1134089429179089429Rat
7771612Cm80Cardiac mass QTL 808.4heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)1144634295241482368Rat
7421630Bp362Blood pressure QTL 3620.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1125875758262433692Rat
8694370Bw154Body weight QTL 1548.910.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)1110620749155620749Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)135377692217372257Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:16
Count of miRNA genes:15
Interacting mature miRNAs:15
Transcripts:ENSRNOT00000025415
Prediction methods: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 43 57 41 19 41 8 10 74 35 41 11 8
Low 1
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_053554 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006229669 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006229670 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006229671 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006229672 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006229673 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006229674 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006229675 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006229676 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006229677 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006229678 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006229679 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006229680 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006229681 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006229682 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006229683 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006229684 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006229685 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039093093 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF041373 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF041374 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY699717 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY706215 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY724477 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC100142 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473956 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215390 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222766 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227108 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232530 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000041 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000025415   ⟹   ENSRNOP00000025415
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1154,377,529 - 154,457,089 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000084268   ⟹   ENSRNOP00000068834
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1154,377,447 - 154,457,287 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000091470   ⟹   ENSRNOP00000069185
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1154,377,505 - 154,457,191 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092086   ⟹   ENSRNOP00000075591
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1154,377,505 - 154,457,191 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092945   ⟹   ENSRNOP00000076067
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1154,377,247 - 154,458,425 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000093052   ⟹   ENSRNOP00000076050
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1154,446,156 - 154,457,391 (+)Ensembl
RefSeq Acc Id: NM_053554   ⟹   NP_446006
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21144,056,761 - 144,136,323 (+)NCBI
Rnor_6.01154,377,505 - 154,457,191 (+)NCBI
Rnor_5.01160,681,689 - 160,763,382 (+)NCBI
RGSC_v3.41146,754,085 - 146,834,197 (+)RGD
Celera1142,288,691 - 142,367,949 (+)RGD
Sequence:
RefSeq Acc Id: XM_006229669   ⟹   XP_006229731
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21144,056,415 - 144,138,045 (+)NCBI
Rnor_6.01154,377,230 - 154,458,966 (+)NCBI
Rnor_5.01160,681,689 - 160,763,382 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006229670   ⟹   XP_006229732
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21144,056,416 - 144,138,045 (+)NCBI
Rnor_6.01154,377,230 - 154,458,966 (+)NCBI
Rnor_5.01160,681,689 - 160,763,382 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006229671   ⟹   XP_006229733
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21144,056,415 - 144,138,045 (+)NCBI
Rnor_6.01154,377,229 - 154,458,966 (+)NCBI
Rnor_5.01160,681,689 - 160,763,382 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006229672   ⟹   XP_006229734
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21144,056,416 - 144,138,045 (+)NCBI
Rnor_6.01154,377,230 - 154,458,966 (+)NCBI
Rnor_5.01160,681,689 - 160,763,382 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006229673   ⟹   XP_006229735
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21144,056,417 - 144,138,045 (+)NCBI
Rnor_6.01154,377,230 - 154,458,966 (+)NCBI
Rnor_5.01160,681,689 - 160,763,382 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006229674   ⟹   XP_006229736
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21144,056,416 - 144,138,045 (+)NCBI
Rnor_6.01154,377,230 - 154,458,966 (+)NCBI
Rnor_5.01160,681,689 - 160,763,382 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006229675   ⟹   XP_006229737
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21144,056,416 - 144,138,045 (+)NCBI
Rnor_6.01154,377,230 - 154,458,966 (+)NCBI
Rnor_5.01160,681,689 - 160,763,382 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006229676   ⟹   XP_006229738
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21144,056,418 - 144,138,045 (+)NCBI
Rnor_6.01154,377,231 - 154,458,966 (+)NCBI
Rnor_5.01160,681,689 - 160,763,382 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006229677   ⟹   XP_006229739
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21144,056,419 - 144,138,045 (+)NCBI
Rnor_6.01154,377,231 - 154,458,966 (+)NCBI
Rnor_5.01160,681,689 - 160,763,382 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006229678   ⟹   XP_006229740
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21144,056,419 - 144,138,045 (+)NCBI
Rnor_6.01154,377,232 - 154,458,922 (+)NCBI
Rnor_5.01160,681,689 - 160,763,382 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006229679   ⟹   XP_006229741
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21144,056,417 - 144,138,045 (+)NCBI
Rnor_6.01154,377,231 - 154,458,966 (+)NCBI
Rnor_5.01160,681,689 - 160,763,382 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006229680   ⟹   XP_006229742
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21144,056,418 - 144,138,045 (+)NCBI
Rnor_6.01154,377,232 - 154,458,966 (+)NCBI
Rnor_5.01160,681,689 - 160,763,382 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006229681   ⟹   XP_006229743
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21144,056,418 - 144,138,045 (+)NCBI
Rnor_6.01154,377,232 - 154,458,966 (+)NCBI
Rnor_5.01160,681,689 - 160,763,382 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006229682   ⟹   XP_006229744
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21144,056,419 - 144,138,045 (+)NCBI
Rnor_6.01154,377,232 - 154,458,966 (+)NCBI
Rnor_5.01160,681,689 - 160,763,382 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006229683   ⟹   XP_006229745
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21144,056,419 - 144,138,045 (+)NCBI
Rnor_6.01154,377,233 - 154,458,966 (+)NCBI
Rnor_5.01160,681,689 - 160,763,382 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006229684   ⟹   XP_006229746
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21144,056,420 - 144,138,045 (+)NCBI
Rnor_6.01154,377,233 - 154,458,966 (+)NCBI
Rnor_5.01160,681,689 - 160,763,382 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006229685   ⟹   XP_006229747
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21144,056,420 - 144,138,045 (+)NCBI
Rnor_6.01154,377,234 - 154,458,922 (+)NCBI
Rnor_5.01160,681,689 - 160,763,382 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039093093   ⟹   XP_038949021
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21144,056,419 - 144,104,507 (+)NCBI
Protein Sequences
Protein RefSeqs NP_446006 (Get FASTA)   NCBI Sequence Viewer  
  XP_006229731 (Get FASTA)   NCBI Sequence Viewer  
  XP_006229732 (Get FASTA)   NCBI Sequence Viewer  
  XP_006229733 (Get FASTA)   NCBI Sequence Viewer  
  XP_006229734 (Get FASTA)   NCBI Sequence Viewer  
  XP_006229735 (Get FASTA)   NCBI Sequence Viewer  
  XP_006229736 (Get FASTA)   NCBI Sequence Viewer  
  XP_006229737 (Get FASTA)   NCBI Sequence Viewer  
  XP_006229738 (Get FASTA)   NCBI Sequence Viewer  
  XP_006229739 (Get FASTA)   NCBI Sequence Viewer  
  XP_006229740 (Get FASTA)   NCBI Sequence Viewer  
  XP_006229741 (Get FASTA)   NCBI Sequence Viewer  
  XP_006229742 (Get FASTA)   NCBI Sequence Viewer  
  XP_006229743 (Get FASTA)   NCBI Sequence Viewer  
  XP_006229744 (Get FASTA)   NCBI Sequence Viewer  
  XP_006229745 (Get FASTA)   NCBI Sequence Viewer  
  XP_006229746 (Get FASTA)   NCBI Sequence Viewer  
  XP_006229747 (Get FASTA)   NCBI Sequence Viewer  
  XP_038949021 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAB97078 (Get FASTA)   NCBI Sequence Viewer  
  AAB97079 (Get FASTA)   NCBI Sequence Viewer  
  AAI00143 (Get FASTA)   NCBI Sequence Viewer  
  AAU06231 (Get FASTA)   NCBI Sequence Viewer  
  AAU10101 (Get FASTA)   NCBI Sequence Viewer  
  EDM18554 (Get FASTA)   NCBI Sequence Viewer  
  EDM18555 (Get FASTA)   NCBI Sequence Viewer  
  EDM18556 (Get FASTA)   NCBI Sequence Viewer  
  EDM18557 (Get FASTA)   NCBI Sequence Viewer  
  EDM18558 (Get FASTA)   NCBI Sequence Viewer  
  O55012 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_446006   ⟸   NM_053554
- UniProtKB: O55012 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006229734   ⟸   XM_006229672
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_006229733   ⟸   XM_006229671
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006229736   ⟸   XM_006229674
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_006229731   ⟸   XM_006229669
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006229735   ⟸   XM_006229673
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_006229737   ⟸   XM_006229675
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_006229732   ⟸   XM_006229670
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006229743   ⟸   XM_006229681
- Peptide Label: isoform X13
- Sequence:
RefSeq Acc Id: XP_006229741   ⟸   XM_006229679
- Peptide Label: isoform X11
- Sequence:
RefSeq Acc Id: XP_006229744   ⟸   XM_006229682
- Peptide Label: isoform X14
- Sequence:
RefSeq Acc Id: XP_006229739   ⟸   XM_006229677
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_006229742   ⟸   XM_006229680
- Peptide Label: isoform X12
- Sequence:
RefSeq Acc Id: XP_006229738   ⟸   XM_006229676
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_006229740   ⟸   XM_006229678
- Peptide Label: isoform X10
- UniProtKB: Q498N4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006229745   ⟸   XM_006229683
- Peptide Label: isoform X15
- UniProtKB: Q66SY1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006229746   ⟸   XM_006229684
- Peptide Label: isoform X16
- Sequence:
RefSeq Acc Id: XP_006229747   ⟸   XM_006229685
- Peptide Label: isoform X17
- UniProtKB: Q66WT9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000075591   ⟸   ENSRNOT00000092086
RefSeq Acc Id: ENSRNOP00000076067   ⟸   ENSRNOT00000092945
RefSeq Acc Id: ENSRNOP00000069185   ⟸   ENSRNOT00000091470
RefSeq Acc Id: ENSRNOP00000076050   ⟸   ENSRNOT00000093052
RefSeq Acc Id: ENSRNOP00000025415   ⟸   ENSRNOT00000025415
RefSeq Acc Id: ENSRNOP00000068834   ⟸   ENSRNOT00000084268
RefSeq Acc Id: XP_038949021   ⟸   XM_039093093
- Peptide Label: isoform X18
Protein Domains
ENTH

Transcriptome

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

Promoters
RGD ID:13690191
Promoter ID:EPDNEW_R711
Type:initiation region
Name:Picalm_1
Description:phosphatidylinositol binding clathrin assembly protein
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R712  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01154,377,220 - 154,377,280EPDNEW
RGD ID:13690195
Promoter ID:EPDNEW_R712
Type:initiation region
Name:Picalm_2
Description:phosphatidylinositol binding clathrin assembly protein
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R711  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01154,377,481 - 154,377,541EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 160736524 160736525 G A snv SBN/Ygl (MCW)
1 160736527 160736528 G T snv SBN/Ygl (MCW)
1 160736530 160736531 G A snv SBN/Ygl (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621054 AgrOrtholog
Ensembl Genes ENSRNOG00000018322 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000025415 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000068834 UniProtKB/TrEMBL
  ENSRNOP00000069185 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000075591 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000076050 UniProtKB/TrEMBL
  ENSRNOP00000076067 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000025415 UniProtKB/TrEMBL
  ENSRNOT00000084268 UniProtKB/TrEMBL
  ENSRNOT00000091470 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000092086 UniProtKB/TrEMBL
  ENSRNOT00000092945 UniProtKB/TrEMBL
  ENSRNOT00000093052 UniProtKB/TrEMBL
Gene3D-CATH 1.20.58.150 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  1.25.40.90 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7456159 IMAGE-MGC_LOAD
InterPro ANTH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Clathrin_AP_dom2 UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
  ENTH UniProtKB/TrEMBL
  ENTH_VHS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Epsin-like_N UniProtKB/Swiss-Prot
  PICALM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:89816 UniProtKB/Swiss-Prot
MGC_CLONE MGC:114290 IMAGE-MGC_LOAD
NCBI Gene 89816 ENTREZGENE
PANTHER PTHR22951:SF16 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam ANTH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Picalm PhenoGen
PROSITE ENTH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART ENTH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP ENTH_VHS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JTT2_RAT UniProtKB/TrEMBL
  A0A0G2JUQ5_RAT UniProtKB/TrEMBL
  A0A1B0GWW9_RAT UniProtKB/TrEMBL
  O55012 ENTREZGENE, UniProtKB/Swiss-Prot
  Q498N4 ENTREZGENE, UniProtKB/TrEMBL
  Q66SY1 ENTREZGENE, UniProtKB/TrEMBL
  Q66WT9 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary A0A0G2KAZ9 UniProtKB/TrEMBL
  E9PTD2 UniProtKB/TrEMBL
  O55011 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-02-26 Picalm  phosphatidylinositol binding clathrin assembly protein      Symbol and Name status set to approved 625702 APPROVED
2002-08-07 Picalm  phosphatidylinositol binding clathrin assembly protein      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression enriched in brain 633906
gene_protein 69 kD 633906