Pabpc1 (poly(A) binding protein, cytoplasmic 1) - Rat Genome Database

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Gene: Pabpc1 (poly(A) binding protein, cytoplasmic 1) Rattus norvegicus
Analyze
Symbol: Pabpc1
Name: poly(A) binding protein, cytoplasmic 1
RGD ID: 619838
Description: Exhibits mRNA binding activity. Predicted to be involved in gene silencing by RNA; positive regulation of viral genome replication; and regulation of mRNA catabolic process. Localizes to dendrite and messenger ribonucleoprotein complex. Orthologous to several human genes including PABPC1 (poly(A) binding protein cytoplasmic 1); PARTICIPATES IN microRNA pathway; translation initiation pathway; mRNA decay pathway; INTERACTS WITH 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane; 17alpha-ethynylestradiol; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: MGC91496; Pabp; PABP 1; PABP-1; Pabp1; poly(A)-binding protein 1; polyadenylate-binding protein 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: Pabpc1-ps1  
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2767,777,438 - 67,789,731 (-)NCBI
Rnor_6.0 Ensembl775,409,581 - 75,422,268 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0775,409,581 - 75,421,874 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0775,557,634 - 75,569,927 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4772,116,140 - 72,128,433 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1772,136,510 - 72,149,407 (-)NCBI
Celera764,857,404 - 64,869,695 (-)NCBICelera
Cytogenetic Map7q22NCBI
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
(-)-epigallocatechin 3-gallate  (ISO)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP,ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-hydroxy-17-methylestra-4,9,11-trien-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-dinitrotoluene  (EXP)
3,4-methylenedioxymethamphetamine  (EXP,ISO)
3-chloropropane-1,2-diol  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-vinylcyclohexene dioxide  (ISO)
7,12-dimethyltetraphene  (EXP,ISO)
aconitine  (EXP)
acrolein  (ISO)
alpha-pinene  (ISO)
amino acid  (ISO)
aristolochic acid  (EXP)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bleomycin A2  (EXP)
carbon nanotube  (ISO)
chloropicrin  (ISO)
chloroprene  (ISO)
choline  (ISO)
cisplatin  (ISO)
clobetasol  (ISO)
clofibric acid  (EXP)
cocaine  (EXP)
cyclosporin A  (ISO)
dexamethasone  (ISO)
dibutyl phthalate  (EXP,ISO)
disodium selenite  (ISO)
doxorubicin  (ISO)
enzyme inhibitor  (ISO)
ethanol  (ISO)
etoposide  (ISO)
flavonoids  (EXP)
folic acid  (ISO)
gentamycin  (EXP)
indometacin  (ISO)
isoflavones  (EXP)
L-methionine  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
menadione  (ISO)
methoxychlor  (ISO)
N-nitrosodiethylamine  (EXP)
ozone  (ISO)
paracetamol  (ISO)
perfluorooctanoic acid  (ISO)
potassium chromate  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
silicon dioxide  (ISO)
sirolimus  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
Soman  (EXP)
sunitinib  (ISO)
tetrachloromethane  (ISO)
torin 1  (ISO)
tungsten  (ISO)
valproic acid  (ISO)
vitamin E  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:11991638   PMID:12477932   PMID:15121898   PMID:15303970   PMID:15489334   PMID:15663938   PMID:16126846   PMID:16452087   PMID:16554297   PMID:16778019   PMID:16804161   PMID:17289661  
PMID:18447585   PMID:18625844   PMID:19716330   PMID:19946888   PMID:21423176   PMID:21700703   PMID:21883093   PMID:21940797   PMID:21984414   PMID:22658674   PMID:22681889   PMID:22871113  
PMID:23533145   PMID:24625528   PMID:25225333   PMID:26627310   PMID:26735137   PMID:28252024   PMID:28259758   PMID:28733330   PMID:28755400   PMID:29476059   PMID:30053369   PMID:31743794  


Genomics

Comparative Map Data
Pabpc1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2767,777,438 - 67,789,731 (-)NCBI
Rnor_6.0 Ensembl775,409,581 - 75,422,268 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0775,409,581 - 75,421,874 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0775,557,634 - 75,569,927 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4772,116,140 - 72,128,433 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1772,136,510 - 72,149,407 (-)NCBI
Celera764,857,404 - 64,869,695 (-)NCBICelera
Cytogenetic Map7q22NCBI
PABPC1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl8100,685,816 - 100,722,809 (-)EnsemblGRCh38hg38GRCh38
GRCh388100,702,916 - 100,722,088 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh378101,715,144 - 101,734,316 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 368101,784,320 - 101,803,491 (-)NCBINCBI36hg18NCBI36
Build 348101,784,319 - 101,803,491NCBI
Celera897,900,528 - 97,919,706 (-)NCBI
Cytogenetic Map8q22.3NCBI
HuRef896,913,861 - 96,933,038 (-)NCBIHuRef
CHM1_18101,755,929 - 101,775,103 (-)NCBICHM1_1
Pabpc1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391536,595,902 - 36,609,825 (-)NCBIGRCm39mm39
GRCm39 Ensembl1536,595,905 - 36,609,912 (-)Ensembl
GRCm381536,595,658 - 36,609,581 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1536,595,661 - 36,609,668 (-)EnsemblGRCm38mm10GRCm38
MGSCv371536,525,413 - 36,538,728 (-)NCBIGRCm37mm9NCBIm37
MGSCv361536,540,252 - 36,553,551 (-)NCBImm8
Celera1537,216,852 - 37,230,173 (-)NCBICelera
Cytogenetic Map15B3.1NCBI
Pabpc1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541715,868,934 - 15,885,247 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541715,872,906 - 15,885,246 (-)NCBIChiLan1.0ChiLan1.0
PABPC1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1899,518,347 - 99,534,284 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v0897,346,433 - 97,365,628 (-)NCBIMhudiblu_PPA_v0panPan3
PABPC1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1132,563,698 - 2,580,610 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl132,564,065 - 2,580,368 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha132,560,662 - 2,577,627 (-)NCBI
ROS_Cfam_1.0132,717,070 - 2,734,072 (-)NCBI
UMICH_Zoey_3.1132,561,235 - 2,578,211 (-)NCBI
UNSW_CanFamBas_1.0132,672,912 - 2,689,894 (-)NCBI
UU_Cfam_GSD_1.0132,690,335 - 2,707,304 (-)NCBI
Pabpc1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530335,202,647 - 35,244,212 (+)NCBI
SpeTri2.0NW_00493647042,628,890 - 42,670,311 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PABPC1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl436,137,639 - 36,227,690 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1436,137,644 - 36,228,075 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2439,133,409 - 39,152,542 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PABPC1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1895,560,551 - 95,578,627 (-)NCBI
ChlSab1.1 Ensembl895,561,930 - 95,578,633 (-)Ensembl
Pabpc1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247637,552,541 - 7,568,047 (-)NCBI

Position Markers
Pabpc1  
Rat AssemblyChrPosition (strand)SourceJBrowse
RGSC_v3.41832,757,052 - 32,758,183UniSTSRGSC3.4
RGSC_v3.41832,757,257 - 32,757,659UniSTSRGSC3.4
RGSC_v3.4772,119,416 - 72,121,074UniSTSRGSC3.4
Celera1831,285,479 - 31,285,881UniSTS
Celera764,860,680 - 64,862,338UniSTS
Celera1831,285,274 - 31,286,405UniSTS
AW535519  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2767,777,647 - 67,777,848 (+)MAPPER
Rnor_6.0775,409,791 - 75,409,991NCBIRnor6.0
Rnor_5.0775,557,844 - 75,558,044UniSTSRnor5.0
RGSC_v3.4772,116,350 - 72,116,550UniSTSRGSC3.4
Celera764,857,614 - 64,857,814UniSTS
RH 3.4 Map7638.4UniSTS
Cytogenetic Map7q22UniSTS
Pabpc1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.0775,560,910 - 75,562,568UniSTSRnor5.0
Rnor_5.01832,642,609 - 32,643,011UniSTSRnor5.0
RGSC_v3.41832,757,257 - 32,757,659UniSTSRGSC3.4
RGSC_v3.4772,119,416 - 72,121,074UniSTSRGSC3.4
Celera1831,285,479 - 31,285,881UniSTS
Celera764,860,680 - 64,862,338UniSTS
Cytogenetic Map7q22UniSTS
Cytogenetic Map18p11UniSTS
Pabpc1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.01832,642,404 - 32,643,535UniSTSRnor5.0
RGSC_v3.41832,757,052 - 32,758,183UniSTSRGSC3.4
Celera1831,285,274 - 31,286,405UniSTS
Cytogenetic Map7q22UniSTS
Cytogenetic Map18p11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)72920071124838025Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)712328467106995532Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)72536563393155402Rat
1641885Alcrsp9Alcohol response QTL 9alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)73138152976381529Rat
1549840Bss5Bone structure and strength QTL 59.8femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)73203505377035053Rat
61439Cia8Collagen induced arthritis QTL 85.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)73257294277572942Rat
10402855Bp379Blood pressure QTL 3790.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)73586772980867729Rat
1300127Srn1Serum renin concentration QTL 13.87blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)73586772993155402Rat
10755453Coatc12Coat color QTL 120coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)73854770683547706Rat
631534Lnnr1Liver neoplastic nodule remodeling QTL 13.850.001liver integrity trait (VT:0010547)liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)74087268285872682Rat
7411605Foco14Food consumption QTL 1424.10.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)74087268285872682Rat
631513Scl7Serum cholesterol level QTL 74.1blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)74530157390301573Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)748118835128611831Rat
634326Hc3Hypercalciuria QTL 32.1urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)75025210395252103Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)750704769128085642Rat
10053722Scort27Serum corticosterone level QTL 272.410.0083blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)75079381895793818Rat
1358361Sradr5Stress Responsive Adrenal Weight QTL 55.55adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)751251919118477612Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)751251919145729302Rat
1300149Cm6Cardiac mass QTL 64.09heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)751252005111589099Rat
61428Scl3Serum cholesterol level QTL 33.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)75320034498200344Rat
738030Anxrr8Anxiety related response QTL 84.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)75425951299259512Rat
2316947Rf58Renal function QTL 587.8kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)755072862123602998Rat
2316952Pur22Proteinuria QTL 225.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)755072862123602998Rat
2316955Stl24Serum triglyceride level QTL 247.1blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)755072862123602998Rat
2300178Bmd54Bone mineral density QTL 545.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)755495689100495689Rat
2293644Bmd29Bone mineral density QTL 295.40.0001femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)755495689100495689Rat
2293667Bss42Bone structure and strength QTL 427.250.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)755495689100495689Rat
2293678Bss24Bone structure and strength QTL 246.710.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)755495689100495689Rat
2293685Bmd21Bone mineral density QTL 214.20.0003femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)755495689100495689Rat
2293696Bmd32Bone mineral density QTL 325.10.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)755495689100495689Rat
2293707Bss32Bone structure and strength QTL 327.640.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)755495689100495689Rat
1300151Bp181Blood pressure QTL 1813.36arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)761047589113228378Rat
2317035Aia16Adjuvant induced arthritis QTL 162.71joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)768518460113518460Rat
1576303Ept7Estrogen-induced pituitary tumorigenesis QTL 73.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)769399586111043530Rat
1559283Emca4Estrogen-induced mammary cancer QTL 43.7mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)769399586111043530Rat
1298528Bp169Blood pressure QTL 1690.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)770421228115421228Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)771448715145729302Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:36
Count of miRNA genes:29
Interacting mature miRNAs:34
Transcripts:ENSRNOT00000012775
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High 12 12 3 12 2 4
Medium 3 43 45 29 16 29 7 10 72 35 37 11 7
Low 1 1 1
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_134353 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AJ298278 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC083176 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473950 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ729922 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225136 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225513 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225555 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225570 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225607 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225622 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225717 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226227 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226477 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226633 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226807 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227035 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227116 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227205 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227215 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227400 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227779 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227801 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227809 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228174 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230227 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230279 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230410 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230745 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230784 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231126 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231168 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231494 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231662 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231712 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231724 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232194 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232243 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232521 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232597 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232822 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233029 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233189 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233208 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233212 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233332 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233364 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233392 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233403 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233536 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233735 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233754 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233995 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234055 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234227 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234338 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234422 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234731 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ235211 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ235339 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000185 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000012775   ⟹   ENSRNOP00000012775
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl775,409,581 - 75,421,874 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000080218   ⟹   ENSRNOP00000071159
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl775,411,311 - 75,422,268 (-)Ensembl
RefSeq Acc Id: NM_134353   ⟹   NP_599180
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2767,777,438 - 67,789,731 (-)NCBI
Rnor_6.0775,409,581 - 75,421,874 (-)NCBI
Rnor_5.0775,557,634 - 75,569,927 (-)NCBI
RGSC_v3.4772,116,140 - 72,128,433 (-)RGD
Celera764,857,404 - 64,869,695 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_599180 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH83176 (Get FASTA)   NCBI Sequence Viewer  
  CAC21554 (Get FASTA)   NCBI Sequence Viewer  
  EDM16392 (Get FASTA)   NCBI Sequence Viewer  
  Q9EPH8 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_599180   ⟸   NM_134353
- UniProtKB: Q9EPH8 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000071159   ⟸   ENSRNOT00000080218
RefSeq Acc Id: ENSRNOP00000012775   ⟸   ENSRNOT00000012775
Protein Domains
PABC   RRM

Transcriptome

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

Promoters
RGD ID:13695293
Promoter ID:EPDNEW_R5818
Type:multiple initiation site
Name:Pabpc1_1
Description:poly binding protein, cytoplasmic 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_6.0775,422,139 - 75,422,199EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 75561018 75561019 C T snv SR/JrHsd (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 72119524 72119525 C T snv SR/JrHsd (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:619838 AgrOrtholog
Ensembl Genes ENSRNOG00000008639 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000012775 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000071159 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000012775 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000080218 UniProtKB/TrEMBL
Gene3D-CATH 3.30.70.330 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7097075 IMAGE-MGC_LOAD
InterPro Nucleotide-bd_a/b_plait_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PABP-dom UniProtKB/Swiss-Prot
  PABP_1234 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PABP_HYD UniProtKB/Swiss-Prot
  RBD_domain_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RRM_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RRM_dom_euk UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:171350 UniProtKB/Swiss-Prot
MGC_CLONE MGC:91496 IMAGE-MGC_LOAD
NCBI Gene 171350 ENTREZGENE
Pfam PABP UniProtKB/Swiss-Prot
  RRM_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pabpc1 PhenoGen
PROSITE PABC UniProtKB/Swiss-Prot
  RRM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART PolyA UniProtKB/Swiss-Prot
  RRM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RRM_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF54928 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF63570 UniProtKB/Swiss-Prot
TIGRFAMs PABP-1234 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JZS2_RAT UniProtKB/TrEMBL
  PABP1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-01-20 Pabpc1  poly(A) binding protein, cytoplasmic 1      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Pabpc1  poly(A) binding protein, cytoplasmic 1      Symbol and Name status set to provisional 70820 PROVISIONAL