Ptbp1 (polypyrimidine tract binding protein 1) - Rat Genome Database

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Gene: Ptbp1 (polypyrimidine tract binding protein 1) Rattus norvegicus
Analyze
Symbol: Ptbp1
Name: polypyrimidine tract binding protein 1
RGD ID: 62047
Description: Enables nucleic acid binding activity and single-stranded DNA endodeoxyribonuclease activity. Involved in several processes, including mRNA metabolic process; positive regulation of cellular component organization; and positive regulation of gene expression. Located in cytoplasm; neuron projection terminus; and nucleus. Orthologous to human PTBP1 (polypyrimidine tract binding protein 1); PARTICIPATES IN spliceosome pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene; 7,12-dimethyltetraphene.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: heterogeneous nuclear ribonucleoprotein I; hnRNP I; polypyrimidine tract binding protein ; polypyrimidine tract-binding protein 1; Ptb; PTB1; Pybp; Pybp1; Pybp2; pyrimidine binding protein 1; pyrimidine binding protein 2; pyrimidine-binding protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.279,842,574 - 9,852,332 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl79,842,574 - 9,852,397 (-)Ensembl
Rnor_6.0712,663,965 - 12,673,723 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl712,663,965 - 12,673,718 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0712,833,687 - 12,843,445 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4711,355,538 - 11,365,188 (-)NCBIRGSC3.4rn4RGSC3.4
Celera78,017,276 - 8,027,027 (-)NCBICelera
Cytogenetic Map7q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,6-dinitrotoluene  (EXP)
2-methylcholine  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
7,12-dimethyltetraphene  (EXP)
aconitine  (EXP)
acrylamide  (EXP,ISO)
AM-251  (ISO)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[b]fluoranthene  (ISO)
bisphenol A  (EXP,ISO)
bleomycin A2  (EXP)
bortezomib  (ISO)
cadmium dichloride  (EXP)
carbon nanotube  (ISO)
cefaloridine  (EXP)
choline  (ISO)
chrysene  (ISO)
cisplatin  (EXP,ISO)
clofibric acid  (EXP)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
coumestrol  (ISO)
Cuprizon  (EXP)
diazinon  (ISO)
dibutyl phthalate  (EXP)
dicrotophos  (ISO)
dorsomorphin  (ISO)
Enterolactone  (ISO)
enzyme inhibitor  (ISO)
flutamide  (EXP)
folic acid  (ISO)
gentamycin  (EXP)
glutathione  (EXP)
hydrogen cyanide  (ISO)
isoflavones  (EXP)
ivermectin  (ISO)
L-methionine  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
mercury atom  (ISO)
mercury(0)  (ISO)
methotrexate  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
paracetamol  (ISO)
pentachlorophenol  (ISO)
perfluorooctanoic acid  (ISO)
phenobarbital  (ISO)
PhIP  (EXP)
potassium cyanide  (ISO)
quercetin  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium fluoride  (ISO)
Soman  (EXP)
testosterone enanthate  (ISO)
tetrachloromethane  (ISO)
tetraphene  (ISO)
trimellitic anhydride  (ISO)
triptonide  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IDA)
neuron projection terminus  (IDA)
nucleus  (IBA,IDA,IEA,ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Brunel F, etal., Nucleic Acids Res 1991 Oct 11;19(19):5237-45.
2. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. GOA data from the GO Consortium
4. Gooding C, etal., J Biol Chem 2003 Apr 25;278(17):15201-7. Epub 2003 Feb 10.
5. Gooding C, etal., Nucleic Acids Res. 2013 May;41(9):4765-82. doi: 10.1093/nar/gkt168. Epub 2013 Mar 19.
6. Haldar D, etal., Biochemistry 2002 Oct 1;41(39):11628-41.
7. Jansen-Durr P, etal., Nucleic Acids Res. 1992 Mar 25;20(6):1243-9.
8. Knoch KP, etal., Nat Cell Biol. 2004 Mar;6(3):207-14. Epub 2004 Feb 22.
9. Kornblihtt AR, etal., Nat Rev Mol Cell Biol. 2013 Mar;14(3):153-65. doi: 10.1038/nrm3525. Epub 2013 Feb 6.
10. Liu H, etal., RNA 2002 Feb;8(2):137-49.
11. Ma S, etal., Biochim Biophys Acta. 2007 Jun;1773(6):912-23. Epub 2007 Feb 22.
12. Majumder M, etal., Mol Cell Biol. 2009 May;29(10):2899-912. doi: 10.1128/MCB.01774-08. Epub 2009 Mar 9.
13. MGD data from the GO Consortium
14. NCBI rat LocusLink and RefSeq merged data July 26, 2002
15. RGD automated data pipeline
16. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
17. RGD automated import pipeline for gene-chemical interactions
18. Shukla S, etal., RNA. 2005 Nov;11(11):1725-36. Epub 2005 Sep 21.
19. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
20. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
21. Tillmar L, etal., J Biol Chem. 2002 Jan 11;277(2):1099-106. Epub 2001 Nov 5.
22. Zhang J, etal., Cell Death Differ. 2009 Nov;16(11):1460-8. doi: 10.1038/cdd.2009.87. Epub 2009 Jul 10.
Additional References at PubMed
PMID:10716735   PMID:15009664   PMID:16260624   PMID:16282332   PMID:16459313   PMID:17679093   PMID:18335065   PMID:19946888   PMID:20458337   PMID:21518792   PMID:21518806   PMID:22082260  
PMID:22658674   PMID:22681889   PMID:23636947   PMID:23853098   PMID:24530304   PMID:24625528   PMID:25800779  


Genomics

Comparative Map Data
Ptbp1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.279,842,574 - 9,852,332 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl79,842,574 - 9,852,397 (-)Ensembl
Rnor_6.0712,663,965 - 12,673,723 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl712,663,965 - 12,673,718 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0712,833,687 - 12,843,445 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4711,355,538 - 11,365,188 (-)NCBIRGSC3.4rn4RGSC3.4
Celera78,017,276 - 8,027,027 (-)NCBICelera
Cytogenetic Map7q11NCBI
PTBP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl19797,075 - 812,327 (+)EnsemblGRCh38hg38GRCh38
GRCh3819797,452 - 812,316 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3719797,452 - 812,312 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3619748,411 - 763,327 (+)NCBINCBI36hg18NCBI36
Build 3419748,410 - 763,327NCBI
Celera193,882 - 18,816 (-)NCBI
Cytogenetic Map19p13.3NCBI
HuRef19566,615 - 581,055 (+)NCBIHuRef
CHM1_119796,984 - 811,921 (+)NCBICHM1_1
Ptbp1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391079,690,266 - 79,700,269 (+)NCBIGRCm39mm39
GRCm39 Ensembl1079,690,261 - 79,700,605 (+)Ensembl
GRCm381079,854,432 - 79,864,435 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1079,854,427 - 79,864,771 (+)EnsemblGRCm38mm10GRCm38
MGSCv371079,317,350 - 79,327,178 (+)NCBIGRCm37mm9NCBIm37
MGSCv361079,257,809 - 79,267,900 (+)NCBImm8
Celera1080,869,418 - 80,879,246 (+)NCBICelera
Cytogenetic Map10C1NCBI
cM Map1039.72NCBI
Ptbp1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554956,987,182 - 7,002,492 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554956,990,565 - 7,002,492 (-)NCBIChiLan1.0ChiLan1.0
PTBP1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.119766,372 - 781,888 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v019319,953 - 334,945 (-)NCBIMhudiblu_PPA_v0panPan3
PTBP1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12057,806,450 - 57,818,435 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2057,807,826 - 57,818,359 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2057,608,475 - 57,620,432 (-)NCBI
ROS_Cfam_1.02058,548,741 - 58,560,735 (-)NCBI
UMICH_Zoey_3.12057,603,413 - 57,615,372 (-)NCBI
UNSW_CanFamBas_1.02058,083,168 - 58,095,128 (-)NCBI
UU_Cfam_GSD_1.02058,286,193 - 58,298,155 (-)NCBI
Ptbp1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118217,507,888 - 217,518,465 (-)NCBI
SpeTri2.0NW_004936588316,348 - 326,895 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PTBP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl277,551,563 - 77,563,107 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1277,551,562 - 77,563,153 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2278,360,161 - 78,371,916 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PTBP1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.16546,010 - 560,086 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl6545,964 - 562,630 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660818,365,736 - 8,379,517 (-)NCBIVero_WHO_p1.0
Ptbp1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248287,750,419 - 7,762,645 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH128371  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21149,050,008 - 49,050,188 (+)MAPPERmRatBN7.2
mRatBN7.279,842,584 - 9,842,764 (+)MAPPERmRatBN7.2
Rnor_6.0712,663,976 - 12,664,155NCBIRnor6.0
Rnor_6.01151,494,714 - 51,494,893NCBIRnor6.0
Rnor_5.01154,674,121 - 54,674,300UniSTSRnor5.0
Rnor_5.0712,833,698 - 12,833,877UniSTSRnor5.0
RGSC_v3.41150,177,629 - 50,177,808UniSTSRGSC3.4
RGSC_v3.4711,355,477 - 11,355,656UniSTSRGSC3.4
Celera78,017,287 - 8,017,466UniSTS
Celera1148,716,420 - 48,716,599UniSTS
Cytogenetic Map7q11UniSTS
RH129173  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map7q11UniSTS
Ptb  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21149,050,033 - 49,050,190 (+)MAPPERmRatBN7.2
mRatBN7.279,842,609 - 9,842,766 (+)MAPPERmRatBN7.2
Rnor_6.01151,494,739 - 51,494,895NCBIRnor6.0
Rnor_6.0712,664,001 - 12,664,157NCBIRnor6.0
Rnor_5.01154,674,146 - 54,674,302UniSTSRnor5.0
Rnor_5.0712,833,723 - 12,833,879UniSTSRnor5.0
RGSC_v3.41150,177,654 - 50,177,810UniSTSRGSC3.4
RGSC_v3.4711,355,502 - 11,355,658UniSTSRGSC3.4
Celera78,017,312 - 8,017,468UniSTS
Celera1148,716,445 - 48,716,601UniSTS
Cytogenetic Map7q11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7127829089Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7131962314Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7131962314Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134000259Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7135342956Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)766427026029351Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7352928048529280Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7532901950329019Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7749649952496499Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7757398552573985Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)7946224658265113Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:739
Count of miRNA genes:252
Interacting mature miRNAs:307
Transcripts:ENSRNOT00000041277, ENSRNOT00000044865
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 42 57 41 19 41 2 4 74 35 41 11 2
Low 1 6 7 6
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000041277   ⟹   ENSRNOP00000048322
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl79,842,951 - 9,852,367 (-)Ensembl
Rnor_6.0 Ensembl712,664,037 - 12,673,687 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000044865   ⟹   ENSRNOP00000043256
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl79,842,574 - 9,852,370 (-)Ensembl
Rnor_6.0 Ensembl712,663,965 - 12,673,718 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000091650   ⟹   ENSRNOP00000068856
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl79,842,951 - 9,852,367 (-)Ensembl
Rnor_6.0 Ensembl712,665,120 - 12,673,659 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000093221
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl79,842,574 - 9,852,397 (-)Ensembl
Rnor_6.0 Ensembl712,668,905 - 12,672,105 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000093324
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl712,665,894 - 12,666,538 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000093362   ⟹   ENSRNOP00000076206
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl79,842,951 - 9,852,367 (-)Ensembl
Rnor_6.0 Ensembl712,665,018 - 12,668,243 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000093388
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl712,663,965 - 12,669,181 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000093619
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl712,664,993 - 12,665,929 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000100764   ⟹   ENSRNOP00000077281
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl79,842,574 - 9,851,743 (-)Ensembl
RefSeq Acc Id: NM_001271057   ⟹   NP_001257986
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.279,842,574 - 9,852,332 (-)NCBI
Rnor_6.0712,663,965 - 12,673,723 (-)NCBI
Rnor_5.0712,833,687 - 12,843,445 (-)NCBI
Celera78,017,276 - 8,027,027 (-)NCBI
Sequence:
RefSeq Acc Id: NM_022516   ⟹   NP_071961
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.279,842,574 - 9,852,332 (-)NCBI
Rnor_6.0712,663,965 - 12,673,723 (-)NCBI
Rnor_5.0712,833,687 - 12,843,445 (-)NCBI
RGSC_v3.4711,355,538 - 11,365,188 (-)RGD
Celera78,017,276 - 8,027,027 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039078590   ⟹   XP_038934518
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.279,842,574 - 9,851,809 (-)NCBI
RefSeq Acc Id: XM_039078591   ⟹   XP_038934519
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.279,842,647 - 9,851,795 (-)NCBI
RefSeq Acc Id: XR_005486553
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.279,842,574 - 9,852,153 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_071961   ⟸   NM_022516
- Peptide Label: isoform b
- UniProtKB: D3ZB30 (UniProtKB/TrEMBL),   Q6P736 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001257986   ⟸   NM_001271057
- Peptide Label: isoform a
- UniProtKB: Q6P736 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000048322   ⟸   ENSRNOT00000041277
RefSeq Acc Id: ENSRNOP00000076206   ⟸   ENSRNOT00000093362
RefSeq Acc Id: ENSRNOP00000043256   ⟸   ENSRNOT00000044865
RefSeq Acc Id: ENSRNOP00000068856   ⟸   ENSRNOT00000091650
RefSeq Acc Id: XP_038934518   ⟸   XM_039078590
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038934519   ⟸   XM_039078591
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000077281   ⟸   ENSRNOT00000100764
Protein Domains
RRM

Transcriptome

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

Promoters
RGD ID:13695044
Promoter ID:EPDNEW_R5569
Type:initiation region
Name:Ptbp1_1
Description:polypyrimidine tract binding protein 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0712,673,705 - 12,673,765EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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)
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
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
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
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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
LEW/NCrlBR (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
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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
MNS/Gib (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
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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
SBN/Ygl (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: SBN/Ygl sequenced by MCW
SBN/Ygl (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
SHR/NHsd (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
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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)
SS/JrHsdMcwi (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
WAG/Rij (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
WAG/RijCrl (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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
WKY/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 12669270 12669271 C T snv F344/NRrrc (MCW), WN/N (MCW)
7 12669292 12669293 T C snv WN/N (MCW), F344/NRrrc (MCW), M520/N (MCW), MR/N (MCW), WKY/N (MCW), BN/SsN (MCW), ACI/N (MCW), Buf/N (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 11356665 11356666 C T snv HCR/1Mco (UMich), LCR/1Mco (UMich)
7 11356697 11356698 G A snv HCR/1Mco (UMich)
7 11360771 11360772 C T snv F344/NRrrc (KNAW), WN/N (KNAW), BN/NHsdMcwi (KNAW)
7 11360793 11360794 T C snv BN/NHsdMcwi (KNAW), BUF/N (KNAW), F344/NRrrc (KNAW), LE/Stm (KNAW), M520/N (KNAW), SHRSP/Gcrc (MDC), WKY/N (KNAW), WN/N (KNAW), BN/SsN (KNAW), ACI/N (KNAW), MR/N (KNAW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:62047 AgrOrtholog
Ensembl Genes ENSRNOG00000010448 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000043256 UniProtKB/TrEMBL
  ENSRNOP00000048322 UniProtKB/TrEMBL
  ENSRNOP00000068856 UniProtKB/TrEMBL
  ENSRNOP00000076206 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000041277 UniProtKB/TrEMBL
  ENSRNOT00000044865 UniProtKB/TrEMBL
  ENSRNOT00000091650 UniProtKB/TrEMBL
  ENSRNOT00000093362 UniProtKB/TrEMBL
Gene3D-CATH 3.30.70.330 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:5598495 IMAGE-MGC_LOAD
InterPro HnRNP-L/PTB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nucleotide-bd_a/b_plait_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTBP1/2/3_RRM2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTBP1_RRM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTBP1_RRM1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTBP1_RRM3 UniProtKB/TrEMBL
  RBD_domain_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RRM_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29497 UniProtKB/TrEMBL
MGC_CLONE MGC:72282 IMAGE-MGC_LOAD
NCBI Gene 29497 ENTREZGENE
Pfam RRM_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RRM_8 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ptbp1 PhenoGen
PROSITE RRM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART RRM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF54928 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC228565
TIGRFAMs hnRNP-L_PTB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JTV1_RAT UniProtKB/TrEMBL
  A0A1W2Q6A9_RAT UniProtKB/TrEMBL
  D3ZB30 ENTREZGENE, UniProtKB/TrEMBL
  PTBP1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q6P736 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary F1LM18 UniProtKB/TrEMBL
  Q63568 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Ptbp1  polypyrimidine tract binding protein 1  Ptb  polypyrimidine tract binding protein   Symbol and Name updated 1299863 APPROVED
2002-06-10 Ptb  polypyrimidine tract binding protein       Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_domains contains four RNA-binding domains of the ribonucleoprotein fold type 633792
gene_function binds to intronic splicing repressor elements 633792
gene_function a DNA-binding protein 61718