Polr2j (polymerase (RNA) II (DNA directed) polypeptide J) - Rat Genome Database

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Gene: Polr2j (polymerase (RNA) II (DNA directed) polypeptide J) Mus musculus
Analyze
Symbol: Polr2j
Name: polymerase (RNA) II (DNA directed) polypeptide J
RGD ID: 1320958
MGI Page MGI
Description: Predicted to enable LRR domain binding activity. Predicted to contribute to RNA polymerase II activity. Predicted to be involved in transcription by RNA polymerase II. Located in nucleus. Part of RNA polymerase II, core complex. Is expressed in several structures, including alimentary system; branchial arch; integumental system; limb; and nervous system. Orthologous to several human genes including POLR2J (RNA polymerase II subunit J).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 14.5kD; 14.5kDa; DNA-directed RNA polymerase II 13.3 kDa polypeptide; DNA-directed RNA polymerase II subunit J; DNA-directed RNA polymerase II subunit RPB11; Polr2i; polymerase (RNA) II (DNA directed) polypeptide I; RNA polymerase II 13.3 kDa subunit; RNA polymerase II 4 (14 kDa subunit); RNA polymerase II subunit B11; RNA polymerase II subunit RPB14; Rpb; Rpb11a; RPB14; Rpo; Rpo2-4
RGD Orthologs
Human
Rat
Chinchilla
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395136,145,545 - 136,151,801 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl5136,145,485 - 136,151,801 (+)EnsemblGRCm39 Ensembl
GRCm385136,116,691 - 136,122,947 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5136,116,631 - 136,122,947 (+)EnsemblGRCm38mm10GRCm38
MGSCv375136,592,561 - 136,598,817 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv365136,401,364 - 136,407,566 (+)NCBIMGSCv36mm8
Celera5133,137,045 - 133,143,301 (+)NCBICelera
Cytogenetic Map5G2NCBI
cM Map575.8NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. TFIIB-related factors in RNA polymerase I transcription. Knutson BA and Hahn S, Biochim Biophys Acta. 2013 Mar-Apr;1829(3-4):265-73. doi: 10.1016/j.bbagrm.2012.08.003. Epub 2012 Aug 30.
2. MGDs mouse GO annotations MGD data from the GO Consortium
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:9034305   PMID:9099876   PMID:10349636   PMID:10512203   PMID:10922068   PMID:11042159   PMID:11076861   PMID:11217851   PMID:11747469   PMID:11752298   PMID:12466851   PMID:12477932  
PMID:12520002   PMID:14610273   PMID:14681479   PMID:15226435   PMID:15840001   PMID:16141072   PMID:16141073   PMID:16141233   PMID:16602821   PMID:17967808   PMID:18799693   PMID:20059953  
PMID:20211142   PMID:21267068   PMID:21677750   PMID:21873635   PMID:22544055   PMID:28794184   PMID:31598710  


Genomics

Comparative Map Data
Polr2j
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395136,145,545 - 136,151,801 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl5136,145,485 - 136,151,801 (+)EnsemblGRCm39 Ensembl
GRCm385136,116,691 - 136,122,947 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5136,116,631 - 136,122,947 (+)EnsemblGRCm38mm10GRCm38
MGSCv375136,592,561 - 136,598,817 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv365136,401,364 - 136,407,566 (+)NCBIMGSCv36mm8
Celera5133,137,045 - 133,143,301 (+)NCBICelera
Cytogenetic Map5G2NCBI
cM Map575.8NCBI
POLR2J
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh387102,473,128 - 102,478,922 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl7102,473,128 - 102,478,922 (-)EnsemblGRCh38hg38GRCh38
GRCh377102,113,575 - 102,119,369 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 367101,900,552 - 101,906,386 (-)NCBINCBI36Build 36hg18NCBI36
Build 347101,707,623 - 101,713,077NCBI
Celera797,125,817 - 97,127,251 (-)NCBICelera
Cytogenetic Map7q22.1NCBI
HuRef796,703,776 - 96,705,210 (-)NCBIHuRef
CHM1_17102,043,567 - 102,049,407 (-)NCBICHM1_1
T2T-CHM13v2.07103,790,727 - 103,796,555 (-)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v27101,473,848 - 101,479,682 (-)NCBI
Polr2j
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81226,179,649 - 26,185,201 (-)NCBIGRCr8
mRatBN7.21220,543,038 - 20,548,590 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1220,543,038 - 20,548,594 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1221,683,016 - 21,688,571 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01222,295,721 - 22,301,276 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01221,361,193 - 21,366,748 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01223,587,222 - 23,592,774 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1223,587,222 - 23,592,774 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01225,587,572 - 25,593,124 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41221,658,406 - 21,663,958 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11221,649,381 - 21,654,560 (-)NCBI
Celera1222,311,433 - 22,316,972 (-)NCBICelera
Cytogenetic Map12q12NCBI
Polr2j
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545615,146,713 - 15,151,311 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495545615,146,713 - 15,151,320 (+)NCBIChiLan1.0ChiLan1.0
POLR2J
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.167,707,426 - 7,710,882 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha69,402,443 - 9,405,898 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.067,527,599 - 7,531,054 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl67,527,645 - 7,531,266 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.167,496,109 - 7,499,564 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.067,459,175 - 7,462,631 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.067,622,887 - 7,626,343 (+)NCBIUU_Cfam_GSD_1.0
Polr2j
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344132,136,578 - 132,140,703 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365431,895,828 - 1,899,904 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365431,895,827 - 1,899,918 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
POLR2J
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl39,812,441 - 9,816,656 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.139,812,746 - 9,816,657 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.239,695,498 - 9,699,407 (+)NCBISscrofa10.2Sscrofa10.2susScr3
POLR2J
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12810,742,636 - 10,748,084 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2810,742,570 - 10,749,382 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660705,660,475 - 5,666,066 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Polr2j
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474015,169,459 - 15,173,805 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474015,169,414 - 15,174,212 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Polr2j
118 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:604
Count of miRNA genes:330
Interacting mature miRNAs:369
Transcripts:ENSMUST00000041366, ENSMUST00000111127, ENSMUST00000111129
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
11341716Rvfs3_mRift Valley fever susceptibility 3 (mouse)526441234138455402Mouse
27226719Tibw6_mtibia width 6, proximal, 16 week (mouse)572857343139985755Mouse
1301362Prnr1_mprion resistance 1 (mouse)Not determined589418876146787935Mouse
14746986Manh58_mmandible shape 58 (mouse)5102446283136446283Mouse
11532736Sluc33b_msusceptibility to lung cancer 33b (mouse)5102945037136945196Mouse
10412202Bbaa26_mB.burgdorferi-associated arthritis 26 (mouse)Not determined5104583688138555455Mouse
10412239Alpq7_malcohol preference QTL 7 (mouse)Not determined5104705939138705939Mouse
10043890Trigq4_mtriglyceride QTL 4 (mouse)Not determined5107906299141906412Mouse
4142473Chlq11_mcirculating hormone level QTL 11 (mouse)Not determined5107906299141906412Mouse
13464243Ahl20_mage related hearing loss, early onset 20 (mouse)5107906299141906412Mouse
10412197Bbaa25_mB.burgdorferi-associated arthritis 25 (mouse)Not determined5109167240143167381Mouse
13464251Ahl21_mage related hearing loss, early onset 21 (mouse)5109167240143167381Mouse
1301543Hypch_mhypercholesterolemia (mouse)Not determined5109238624139118905Mouse
1300913Bwefm_mbody weight females and males day 10 (mouse)Not determined5109439348143439459Mouse
1301102Cia14_mcollagen induced arthritis 14 (mouse)Not determined5113320385138555455Mouse
1301226Bbaa2_mB.burgdorferi-associated arthritis 2 (mouse)Not determined5115156883149157015Mouse
1300827Cora1_mcorrelation in cytokine production 1 (mouse)Not determined5115156883149157015Mouse
1301857Bglq14_mbody growth late QTL 14 (mouse)Not determined5118948964151758149Mouse
10412191Bbaa24_mB.burgdorferi-associated arthritis 24 (mouse)Not determined5119945037141700466Mouse
4141081Nidd7k_mNidd7 on KK-A (mouse)Not determined119945037149347326Mouse
11528552Scram1_mspinal cord resistance to astrocytoma modifier 1 (mouse)5121455402151758149Mouse
1301986Bpq4_mblood pressure QTL 4 (mouse)Not determined5121555236151758149Mouse
1302079Lbw3_mlupus NZB x NZW 3 (mouse)Not determined5124700335151758149Mouse
1301363Pbwg13_mpostnatal body weight growth 13 (mouse)Not determined5125133457151758149Mouse
1301715Elmaz2_melevated maze behavior 2 (mouse)Not determined5125178229141700466Mouse
4141218Ath24_matherosclerosis 24 (mouse)Not determined129520084151758149Mouse
12880406Jcdq2_mjoint cartilage degeneration QTL 2 (mouse)5129787831151758149Mouse
13464143Bbaa2b_mB.burgdorferi-associated arthritis 2b (mouse)5133052969140709801Mouse
11049557Lmr26_mleishmaniasis resistance 26 (mouse)5133925558151758149Mouse
14700793Mencq4_mmeniscus calcification QTL 4 (mouse)5135895854136218854Mouse

Markers in Region
GDB:4585697  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm385136,120,001 - 136,120,084UniSTSGRCm38
MGSCv375136,595,871 - 136,595,954UniSTSGRCm37
Celera5133,140,355 - 133,140,438UniSTS
Cytogenetic Map5G1UniSTS
AU042569  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm385136,123,169 - 136,123,260UniSTSGRCm38
MGSCv375136,599,039 - 136,599,130UniSTSGRCm37
Celera5133,143,523 - 133,143,614UniSTS
Cytogenetic Map5G2UniSTS
Cytogenetic Map5G1UniSTS
Whitehead/MRC_RH51647.28UniSTS
Whitehead/MRC_RH51647.18UniSTS


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000041366   ⟹   ENSMUSP00000038505
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl5136,145,485 - 136,151,801 (+)Ensembl
GRCm38.p6 Ensembl5136,116,631 - 136,122,947 (+)Ensembl
RefSeq Acc Id: ENSMUST00000111127   ⟹   ENSMUSP00000106757
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl5136,145,485 - 136,151,577 (+)Ensembl
GRCm38.p6 Ensembl5136,116,631 - 136,122,723 (+)Ensembl
RefSeq Acc Id: ENSMUST00000111129   ⟹   ENSMUSP00000106759
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl5136,145,556 - 136,151,790 (+)Ensembl
GRCm38.p6 Ensembl5136,116,702 - 136,122,936 (+)Ensembl
RefSeq Acc Id: NM_011293   ⟹   NP_035423
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm395136,145,545 - 136,151,801 (+)NCBI
GRCm385136,116,691 - 136,122,947 (+)ENTREZGENE
MGSCv375136,592,561 - 136,598,817 (+)RGD
Celera5133,137,045 - 133,143,301 (+)RGD
cM Map5 ENTREZGENE
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_035423   ⟸   NM_011293
- UniProtKB: O08740 (UniProtKB/Swiss-Prot),   Q3TYI2 (UniProtKB/TrEMBL),   Q6PI63 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSMUSP00000106759   ⟸   ENSMUST00000111129
RefSeq Acc Id: ENSMUSP00000106757   ⟸   ENSMUST00000111127
RefSeq Acc Id: ENSMUSP00000038505   ⟸   ENSMUST00000041366
Protein Domains
DNA-directed RNA polymerase RBP11-like dimerisation

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-O08740-F1-model_v2 AlphaFold O08740 1-117 view protein structure

Promoters
RGD ID:6888358
Promoter ID:EPDNEW_M7630
Type:initiation region
Name:Polr2j_1
Description:Mus musculus polymerase II polypeptide J , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm385136,116,716 - 136,116,776EPDNEW
RGD ID:6838064
Promoter ID:MM_KWN:44402
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Liver,   Lung,   MEF_B4,   MEF_B6,   Spleen
Transcripts:ENSMUST00000111127,   ENSMUST00000111129,   OTTMUST00000062646
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv365136,591,666 - 136,592,682 (+)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:109582 AgrOrtholog
Ensembl Genes ENSMUSG00000039771 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000041366 ENTREZGENE
  ENSMUST00000041366.14 UniProtKB/TrEMBL
  ENSMUST00000111127.8 UniProtKB/TrEMBL
  ENSMUST00000111129.2 UniProtKB/TrEMBL
Gene3D-CATH 3.30.1360.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro RBP11 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RBP11-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RBP11-like_dimer UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RNA_pol_Rpb11_13-16kDa_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Rpo11-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:20022 UniProtKB/TrEMBL
MGD MGI:109582 ENTREZGENE
NCBI Gene 20022 ENTREZGENE
PANTHER DNA-DIRECTED RNA POLYMERASE I,II,III UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam RNA_pol_L_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Polr2j PhenoGen
PROSITE RNA_POL_L_13KD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF55257 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt D3YZ19_MOUSE UniProtKB/TrEMBL
  D3YZ20_MOUSE UniProtKB/TrEMBL
  O08740 ENTREZGENE
  Q3TYI2 ENTREZGENE, UniProtKB/TrEMBL
  Q6PI63 ENTREZGENE, UniProtKB/TrEMBL
  RPB11_MOUSE UniProtKB/Swiss-Prot