Polrmt (RNA polymerase mitochondrial) - Rat Genome Database

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Gene: Polrmt (RNA polymerase mitochondrial) Rattus norvegicus
Analyze
Symbol: Polrmt
Name: RNA polymerase mitochondrial
RGD ID: 1304599
Description: Predicted to enable 3'-5'-RNA exonuclease activity; DNA-directed RNA polymerase activity; and mitochondrial promoter sequence-specific DNA binding activity. Predicted to be involved in transcription initiation at mitochondrial promoter. Predicted to be located in mitochondrial nucleoid. Predicted to be part of mitochondrial DNA-directed RNA polymerase complex. Human ortholog(s) of this gene implicated in combined oxidative phosphorylation deficiency 55. Orthologous to human POLRMT (RNA polymerase mitochondrial); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; amitrole.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: DNA-directed RNA polymerase, mitochondrial; LOC299604; polymerase (RNA) mitochondrial; polymerase (RNA) mitochondrial (DNA directed)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8710,610,149 - 10,620,411 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl710,610,198 - 10,621,205 (+)EnsemblGRCr8
mRatBN7.279,959,532 - 9,969,791 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl79,959,576 - 9,969,791 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx712,840,510 - 12,850,716 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0714,718,591 - 14,728,797 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0712,577,950 - 12,588,159 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0712,840,907 - 12,851,153 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl712,840,938 - 12,851,153 (+)Ensemblrn6Rnor6.0
Rnor_5.0713,011,127 - 13,021,357 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4711,474,465 - 11,484,680 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera78,133,096 - 8,143,311 (+)NCBICelera
RGSC_v3.1711,474,487 - 11,484,570 (+)NCBI
Cytogenetic Map7q11NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:14651853   PMID:17337445   PMID:18063578   PMID:18614015   PMID:21278163   PMID:22658674   PMID:22681889   PMID:23283301   PMID:29445193  


Genomics

Comparative Map Data
Polrmt
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8710,610,149 - 10,620,411 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl710,610,198 - 10,621,205 (+)EnsemblGRCr8
mRatBN7.279,959,532 - 9,969,791 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl79,959,576 - 9,969,791 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx712,840,510 - 12,850,716 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0714,718,591 - 14,728,797 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0712,577,950 - 12,588,159 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0712,840,907 - 12,851,153 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl712,840,938 - 12,851,153 (+)Ensemblrn6Rnor6.0
Rnor_5.0713,011,127 - 13,021,357 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4711,474,465 - 11,484,680 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera78,133,096 - 8,143,311 (+)NCBICelera
RGSC_v3.1711,474,487 - 11,484,570 (+)NCBI
Cytogenetic Map7q11NCBI
POLRMT
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3819617,221 - 633,537 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl19617,168 - 633,572 (-)Ensemblhg38GRCh38
GRCh3719617,221 - 633,537 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3619568,223 - 584,568 (-)NCBIBuild 36Build 36hg18NCBI36
Build 3419568,224 - 584,530NCBI
Celera19184,054 - 200,399 (+)NCBICelera
Cytogenetic Map19p13.3NCBI
HuRef19387,094 - 403,439 (-)NCBIHuRef
CHM1_119616,639 - 633,229 (-)NCBICHM1_1
T2T-CHM13v2.019571,527 - 587,843 (-)NCBIT2T-CHM13v2.0
Polrmt
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391079,571,951 - 79,582,436 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1079,571,957 - 79,582,415 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381079,736,125 - 79,746,604 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1079,736,123 - 79,746,581 (-)Ensemblmm10GRCm38
MGSCv371079,198,870 - 79,209,326 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361079,139,259 - 79,149,702 (-)NCBIMGSCv36mm8
Celera1080,750,719 - 80,761,175 (-)NCBICelera
Cytogenetic Map10C1NCBI
cM Map1039.72NCBI
Polrmt
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554957,111,260 - 7,124,291 (+)Ensembl
ChiLan1.0NW_0049554957,111,271 - 7,124,005 (+)NCBIChiLan1.0ChiLan1.0
POLRMT
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2204,942,597 - 4,962,796 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1194,180,930 - 4,198,380 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v019504,823 - 521,281 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.119584,178 - 599,874 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl19584,219 - 599,783 (-)EnsemblpanPan2panpan1.1
SHC2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12058,001,442 - 58,023,201 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2057,804,227 - 57,825,834 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02058,744,465 - 58,766,097 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2058,743,210 - 58,766,090 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12057,798,377 - 57,819,985 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02058,278,093 - 58,299,887 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02058,481,722 - 58,503,345 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Polrmt
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118217,612,891 - 217,625,063 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936588209,610 - 221,905 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936588209,720 - 221,847 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
POLRMT
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl277,694,266 - 77,708,096 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1277,694,271 - 77,708,099 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
POLRMT
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.16358,865 - 377,007 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl6358,917 - 377,089 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660818,607,264 - 8,626,573 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Polrmt
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248287,876,739 - 7,888,923 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248287,876,682 - 7,888,990 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Polrmt
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11155,127,089 - 155,137,444 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Polrmt
80 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:31
Count of miRNA genes:24
Interacting mature miRNAs:30
Transcripts:ENSRNOT00000039232
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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7166965846669658Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)7123748937Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7721609752216097Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)71051708662346019Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)71011291699900612Rat
2290372Gluco33Glucose level QTL 332.71blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)7131777942Rat
1300149Cm6Cardiac mass QTL 64.09heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)71104117804Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7170952746709527Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)71509236116977875Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7132612984Rat
1582260Bw72Body weight QTL 723.20.0043body mass (VT:0001259)body weight (CMO:0000012)7139960528Rat
1582261Bw69Body weight QTL 693.20.0048body mass (VT:0001259)body weight (CMO:0000012)7139960528Rat
1582262Bw75Body weight QTL 7530.0038body mass (VT:0001259)body weight (CMO:0000012)7139960528Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)71011291660150541Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7946087754460877Rat
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7129716167Rat
1300138Hrtrt9Heart rate QTL 94.72heart pumping trait (VT:2000009)heart rate (CMO:0000002)71049882055498820Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134650782Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7132612984Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 162 91 90 59 92 59 6 356 192 11 141 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000039232   ⟹   ENSRNOP00000032448
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl710,610,199 - 10,620,364 (+)Ensembl
mRatBN7.2 Ensembl79,959,576 - 9,969,791 (+)Ensembl
Rnor_6.0 Ensembl712,840,938 - 12,851,153 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000118094   ⟹   ENSRNOP00000078121
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl710,610,198 - 10,621,205 (+)Ensembl
mRatBN7.2 Ensembl79,959,576 - 9,969,791 (+)Ensembl
RefSeq Acc Id: NM_001106766   ⟹   NP_001100236
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8710,610,196 - 10,620,411 (+)NCBI
mRatBN7.279,959,576 - 9,969,791 (+)NCBI
Rnor_6.0712,840,938 - 12,851,153 (+)NCBI
Rnor_5.0713,011,127 - 13,021,357 (+)NCBI
RGSC_v3.4711,474,465 - 11,484,680 (+)RGD
Celera78,133,096 - 8,143,311 (+)RGD
Sequence:
RefSeq Acc Id: XM_006240859   ⟹   XP_006240921
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8710,610,149 - 10,620,364 (+)NCBI
mRatBN7.279,959,532 - 9,969,744 (+)NCBI
Rnor_6.0712,840,907 - 12,851,106 (+)NCBI
Rnor_5.0713,011,127 - 13,021,357 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001100236 (Get FASTA)   NCBI Sequence Viewer  
  XP_006240921 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL89399 (Get FASTA)   NCBI Sequence Viewer  
  EDL89400 (Get FASTA)   NCBI Sequence Viewer  
  EDL89401 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000032448
  ENSRNOP00000032448.7
  ENSRNOP00000078121.2
RefSeq Acc Id: NP_001100236   ⟸   NM_001106766
- UniProtKB: D3ZYB6 (UniProtKB/TrEMBL),   A6K8X9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006240921   ⟸   XM_006240859
- Peptide Label: isoform X1
- UniProtKB: D3ZYB6 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000032448   ⟸   ENSRNOT00000039232
Ensembl Acc Id: ENSRNOP00000078121   ⟸   ENSRNOT00000118094
Protein Domains
DNA-directed RNA polymerase N-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZYB6-F1-model_v2 AlphaFold D3ZYB6 1-1203 view protein structure

Transcriptome

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

Promoters
RGD ID:13695054
Promoter ID:EPDNEW_R5578
Type:multiple initiation site
Name:Polrmt_1
Description:RNA polymerase mitochondrial
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_6.0712,840,940 - 12,841,000EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1304599 AgrOrtholog
BioCyc Gene G2FUF-34885 BioCyc
Ensembl Genes ENSRNOG00000024879 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000039232 ENTREZGENE
  ENSRNOT00000039232.7 UniProtKB/TrEMBL
  ENSRNOT00000118094.2 UniProtKB/TrEMBL
Gene3D-CATH 1.10.1320.10 UniProtKB/TrEMBL
  1.10.287.280 UniProtKB/TrEMBL
  1.25.40.10 UniProtKB/TrEMBL
  5' to 3' exonuclease, C-terminal subdomain UniProtKB/TrEMBL
InterPro DNA-dir_RNA_pol_phage UniProtKB/TrEMBL
  DNA-dir_Rpol_C_phage-type UniProtKB/TrEMBL
  DNA/RNA_pol_sf UniProtKB/TrEMBL
  RNA_POL_N_sf UniProtKB/TrEMBL
  RPOL_N UniProtKB/TrEMBL
  TPR-like_helical_dom_sf UniProtKB/TrEMBL
KEGG Report rno:299604 UniProtKB/TrEMBL
NCBI Gene 299604 ENTREZGENE
PANTHER DNA-DIRECTED RNA POLYMERASE, MITOCHONDRIAL UniProtKB/TrEMBL
  RNA_pol_phage UniProtKB/TrEMBL
Pfam RNA_pol UniProtKB/TrEMBL
  RPOL_N UniProtKB/TrEMBL
PhenoGen Polrmt PhenoGen
PROSITE RNA_POL_PHAGE_1 UniProtKB/TrEMBL
  RNA_POL_PHAGE_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000024879 RatGTEx
SMART RPOL_N UniProtKB/TrEMBL
Superfamily-SCOP SSF56672 UniProtKB/TrEMBL
UniProt A0A8I5Y8F7_RAT UniProtKB/TrEMBL
  A6K8X9 ENTREZGENE, UniProtKB/TrEMBL
  D3ZYB6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-21 Polrmt  RNA polymerase mitochondrial  Polrmt  polymerase (RNA) mitochondrial  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-03-08 Polrmt  polymerase (RNA) mitochondrial  Polrmt  polymerase (RNA) mitochondrial (DNA directed)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Polrmt  polymerase (RNA) mitochondrial (DNA directed)   Polrmt_predicted  polymerase (RNA) mitochondrial (DNA directed) (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Polrmt_predicted  polymerase (RNA) mitochondrial (DNA directed) (predicted)      Symbol and Name status set to approved 70820 APPROVED