Pnpt1 (polyribonucleotide nucleotidyltransferase 1) - Rat Genome Database

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Gene: Pnpt1 (polyribonucleotide nucleotidyltransferase 1) Rattus norvegicus
Analyze
Symbol: Pnpt1
Name: polyribonucleotide nucleotidyltransferase 1
RGD ID: 1307987
Description: Exhibits polyribonucleotide nucleotidyltransferase activity. Involved in several processes, including liver regeneration; response to cAMP; and response to growth hormone. Localizes to endoplasmic reticulum membrane; nucleus; and polysomal ribosome. Human ortholog(s) of this gene implicated in autosomal recessive nonsyndromic deafness 70 and combined oxidative phosphorylation deficiency 13. Orthologous to human PNPT1 (polyribonucleotide nucleotidyltransferase 1); PARTICIPATES IN purine metabolic pathway; pyrimidine metabolic pathway; RNA degradation pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; finasteride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC360992; polyribonucleotide nucleotidyltransferase 1, mitochondrial
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
mRatBN7.214102,877,553 - 102,908,696 (+)NCBI
Rnor_6.0 Ensembl14113,530,470 - 113,561,645 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.014113,530,470 - 113,561,645 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.014113,205,574 - 113,236,749 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.414110,130,417 - 110,161,762 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.114110,156,766 - 110,187,382 (+)NCBI
Celera14101,762,647 - 101,794,453 (+)NCBICelera
Cytogenetic Map14q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:12477932   PMID:12721301   PMID:16055741   PMID:16410805   PMID:16934922   PMID:16966381   PMID:18083836   PMID:18083837   PMID:18501193   PMID:18614015   PMID:19509288   PMID:19864255  
PMID:20547861   PMID:20691904   PMID:22681889   PMID:29967381  


Genomics

Comparative Map Data
Pnpt1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.214102,877,553 - 102,908,696 (+)NCBI
Rnor_6.0 Ensembl14113,530,470 - 113,561,645 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.014113,530,470 - 113,561,645 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.014113,205,574 - 113,236,749 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.414110,130,417 - 110,161,762 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.114110,156,766 - 110,187,382 (+)NCBI
Celera14101,762,647 - 101,794,453 (+)NCBICelera
Cytogenetic Map14q22NCBI
PNPT1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl255,634,061 - 55,693,863 (-)EnsemblGRCh38hg38GRCh38
GRCh38255,634,061 - 55,693,853 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37255,861,196 - 55,920,979 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36255,715,956 - 55,774,463 (-)NCBINCBI36hg18NCBI36
Build 34255,774,117 - 55,832,610NCBI
Celera255,701,589 - 55,761,360 (-)NCBI
Cytogenetic Map2p16.1NCBI
HuRef255,596,276 - 55,655,947 (-)NCBIHuRef
CHM1_1255,791,555 - 55,851,305 (-)NCBICHM1_1
Pnpt1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391129,080,236 - 29,112,010 (+)NCBIGRCm39mm39
GRCm39 Ensembl1129,080,744 - 29,111,828 (+)Ensembl
GRCm381129,130,129 - 29,161,827 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1129,130,744 - 29,161,828 (+)EnsemblGRCm38mm10GRCm38
MGSCv371129,030,751 - 29,061,828 (+)NCBIGRCm37mm9NCBIm37
MGSCv361129,030,751 - 29,061,828 (+)NCBImm8
Celera1131,494,148 - 31,527,000 (+)NCBICelera
Cytogenetic Map11A3.3NCBI
Pnpt1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542427,407,489 - 27,448,992 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542427,407,451 - 27,449,830 (+)NCBIChiLan1.0ChiLan1.0
PNPT1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A56,931,110 - 56,986,408 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A56,931,365 - 56,986,326 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A55,792,412 - 55,848,242 (-)NCBIMhudiblu_PPA_v0panPan3
PNPT1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11056,478,771 - 56,520,992 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1056,478,680 - 56,520,967 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1056,435,176 - 56,478,020 (-)NCBI
ROS_Cfam_1.01057,482,766 - 57,525,822 (-)NCBI
UMICH_Zoey_3.11057,184,232 - 57,226,744 (-)NCBI
UNSW_CanFamBas_1.01057,463,411 - 57,505,932 (-)NCBI
UU_Cfam_GSD_1.01057,754,350 - 57,797,122 (-)NCBI
Pnpt1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629226,538,923 - 26,583,394 (+)NCBI
SpeTri2.0NW_0049364911,989,429 - 2,032,430 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PNPT1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl385,595,392 - 85,639,690 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1385,595,356 - 85,639,665 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2390,333,302 - 90,422,937 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PNPT1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11451,211,385 - 51,267,706 (+)NCBI
ChlSab1.1 Ensembl1451,211,118 - 51,267,098 (+)Ensembl
Pnpt1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248335,883,300 - 5,923,758 (+)NCBI

Position Markers
RH126190  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.214102,888,057 - 102,888,257 (+)MAPPER
Rnor_6.014113,540,974 - 113,541,173NCBIRnor6.0
Rnor_5.014113,216,078 - 113,216,277UniSTSRnor5.0
RGSC_v3.414110,140,921 - 110,141,120UniSTSRGSC3.4
Celera14101,773,151 - 101,773,350UniSTS
Cytogenetic Map14q22UniSTS
RH139981  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.214102,886,047 - 102,886,267 (+)MAPPER
Rnor_6.014113,538,964 - 113,539,183NCBIRnor6.0
Rnor_5.014113,214,068 - 113,214,287UniSTSRnor5.0
RGSC_v3.414110,138,911 - 110,139,130UniSTSRGSC3.4
Celera14101,771,141 - 101,771,360UniSTS
Cytogenetic Map14q22UniSTS
RH144616  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.214102,882,831 - 102,882,981 (+)MAPPER
Rnor_6.014113,535,748 - 113,535,897NCBIRnor6.0
Rnor_5.014113,210,852 - 113,211,001UniSTSRnor5.0
RGSC_v3.414110,135,695 - 110,135,844UniSTSRGSC3.4
Celera14101,767,925 - 101,768,074UniSTS
Cytogenetic Map14q22UniSTS
RH141211  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.214102,907,460 - 102,907,663 (+)MAPPER
Rnor_6.014113,560,410 - 113,560,612NCBIRnor6.0
Rnor_5.014113,235,514 - 113,235,716UniSTSRnor5.0
RGSC_v3.414110,160,527 - 110,160,729UniSTSRGSC3.4
Celera14101,793,218 - 101,793,420UniSTS
Cytogenetic Map14q22UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1480049285115493446Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1480049285115493446Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:581
Count of miRNA genes:284
Interacting mature miRNAs:354
Transcripts:ENSRNOT00000004919
Prediction methods:Microtar, Miranda, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 57 41 19 41 8 8 74 35 36 11 8
Low 3 5
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000004919   ⟹   ENSRNOP00000004919
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl14113,530,470 - 113,561,645 (+)Ensembl
RefSeq Acc Id: NM_001142371   ⟹   NP_001135843
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.214102,877,553 - 102,908,696 (+)NCBI
Rnor_6.014113,530,470 - 113,561,645 (+)NCBI
Rnor_5.014113,205,574 - 113,236,749 (+)NCBI
RGSC_v3.414110,130,417 - 110,161,762 (+)RGD
Celera14101,762,647 - 101,794,453 (+)RGD
Sequence:
RefSeq Acc Id: XM_039092236   ⟹   XP_038948164
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.214102,882,051 - 102,907,822 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001135843 (Get FASTA)   NCBI Sequence Viewer  
  XP_038948164 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH92603 (Get FASTA)   NCBI Sequence Viewer  
  AAI60927 (Get FASTA)   NCBI Sequence Viewer  
  EDL98021 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001135843   ⟸   NM_001142371
- UniProtKB: G3V6G7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000004919   ⟸   ENSRNOT00000004919
RefSeq Acc Id: XP_038948164   ⟸   XM_039092236
- Peptide Label: isoform X1
Protein Domains
S1 motif

Transcriptome

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

Promoters
RGD ID:13699530
Promoter ID:EPDNEW_R10054
Type:multiple initiation site
Name:Pnpt1_1
Description:polyribonucleotide nucleotidyltransferase 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_6.014113,530,468 - 113,530,528EPDNEW

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)
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
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)
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
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
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)
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
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)
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)
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)
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)
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
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 (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
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
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
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
M520/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
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 (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
SBH/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: 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
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 (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 (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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307987 AgrOrtholog
Ensembl Genes ENSRNOG00000003600 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000004919 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000004919 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 3.30.1370.10 UniProtKB/TrEMBL
  3.30.230.70 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7305536 IMAGE-MGC_LOAD
  IMAGE:8365552 IMAGE-MGC_LOAD
InterPro ExoRNase_PH_dom1 UniProtKB/TrEMBL
  ExoRNase_PH_dom2 UniProtKB/TrEMBL
  ExoRNase_PH_dom2_sf UniProtKB/TrEMBL
  IPR004087 UniProtKB/TrEMBL
  KH_dom_type_1_sf UniProtKB/TrEMBL
  KH_type_1 UniProtKB/TrEMBL
  NA-bd_OB-fold UniProtKB/TrEMBL
  PNPase UniProtKB/TrEMBL
  PNPase/RNase_PH_dom UniProtKB/TrEMBL
  PNPase_PH_RNA-bd_bac/org-type UniProtKB/TrEMBL
  PNPase_PH_RNA-bd_sf UniProtKB/TrEMBL
  Rbsml_prot_S1_RNA-bd_dom UniProtKB/TrEMBL
  Ribosomal_S5_D2-typ_fold UniProtKB/TrEMBL
  RNA-binding_domain_S1 UniProtKB/TrEMBL
KEGG Report rno:360992 UniProtKB/TrEMBL
MGC_CLONE MGC:109192 IMAGE-MGC_LOAD
  MGC:188684 IMAGE-MGC_LOAD
NCBI Gene 360992 ENTREZGENE
PANTHER PNPase UniProtKB/TrEMBL
Pfam KH_1 UniProtKB/TrEMBL
  PF00575 UniProtKB/TrEMBL
  PNPase UniProtKB/TrEMBL
  RNase_PH UniProtKB/TrEMBL
  RNase_PH_C UniProtKB/TrEMBL
PhenoGen Pnpt1 PhenoGen
PIRSF PNPase UniProtKB/TrEMBL
PROSITE PS50126 UniProtKB/TrEMBL
SMART SM00316 UniProtKB/TrEMBL
  SM00322 UniProtKB/TrEMBL
Superfamily-SCOP 3_ExoRNase UniProtKB/TrEMBL
  3_ExoRNase UniProtKB/TrEMBL
  Nucleic_acid_OB UniProtKB/TrEMBL
  Ribosomal_S5_D2-typ_fold UniProtKB/TrEMBL
  SSF54791 UniProtKB/TrEMBL
TIGRFAMs polynuc_phos UniProtKB/TrEMBL
UniProt B1H2A4_RAT UniProtKB/TrEMBL
  G3V6G7 ENTREZGENE, UniProtKB/TrEMBL
  Q562B9_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-12-06 Pnpt1  polyribonucleotide nucleotidyltransferase 1  Pnpt1_predicted  polyribonucleotide nucleotidyltransferase 1 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Pnpt1_predicted  polyribonucleotide nucleotidyltransferase 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED