Polr2d (RNA polymerase II subunit D)

Gene: Polr2d (RNA polymerase II subunit D) Rattus norvegicus

Analyze

Symbol:

Polr2d

Name:

RNA polymerase II subunit D

RGD ID:

1308565

Description:

Predicted to enable translation initiation factor binding activity. Predicted to be involved in recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex and transcription initiation at RNA polymerase II promoter. Predicted to be located in cytosol and nuclear speck. Predicted to be part of RNA polymerase II, core complex. Orthologous to human POLR2D (RNA polymerase II subunit D); PARTICIPATES IN RNA polymerase II transcription pathway; Huntington's disease pathway; purine metabolic pathway; INTERACTS WITH 2,4-dinitrotoluene; 6-propyl-2-thiouracil; bisphenol A.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

DNA-directed RNA polymerase II subunit RPB4; LOC364834; polymerase (RNA) II (DNA directed) polypeptide D; polymerase (RNA) II subunit D

RGD Orthologs

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	POLR2D (RNA polymerase II subunit D)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Polr2d (polymerase (RNA) II (DNA directed) polypeptide D)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Polr2d (RNA polymerase II subunit D)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	LOC100992899 (DNA-directed RNA polymerase II subunit RPB4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	POLR2D (RNA polymerase II subunit D)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Polr2d (RNA polymerase II subunit D)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	POLR2D (RNA polymerase II subunit D)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	POLR2D (RNA polymerase II subunit D)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Polr2d (RNA polymerase II subunit D)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	RPS29 (ribosomal protein S29)	HGNC	OMA
Alliance orthologs ³
Homo sapiens (human):	POLR2D (RNA polymerase II subunit D)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Polr2d (polymerase (RNA) II (DNA directed) polypeptide D)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	polr2d (polymerase (RNA) II (DNA directed) polypeptide D)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	rpb-4	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	RPB4	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	Rpb4	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	polr2d	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

NCBI Annotation Information:

Annotation category: suggests misassembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	18	23,692,578 - 23,699,709 (+)	NCBI		GRCr8
mRatBN7.2	18	23,418,097 - 23,425,228 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	18	23,418,097 - 23,425,228 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	18	23,546,442 - 23,553,573 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	18	24,295,466 - 24,302,598 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	18	23,641,409 - 23,648,541 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	18	24,570,762 - 24,577,894 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	18	24,570,762 - 24,577,894 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	18	24,287,960 - 24,295,092 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	18	24,205,326 - 24,212,458 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	18	24,232,026 - 24,239,027 (+)	NCBI
Celera	18	23,170,705 - 23,177,837 (+)	NCBI		Celera
Cytogenetic Map	18	p12	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

autosomal dominant thrombophilia due to protein C deficiency (ISO)

genetic disease (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (ISO)

2,2',4,4'-Tetrabromodiphenyl ether (ISO)

2,3,7,8-tetrachlorodibenzodioxine (ISO)

2,4-dinitrotoluene (EXP)

6-propyl-2-thiouracil (EXP)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

arsenite(3-) (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

carbon nanotube (ISO)

CGP 52608 (ISO)

chlorpyrifos (ISO)

copper(II) sulfate (ISO)

coumestrol (ISO)

cylindrospermopsin (ISO)

dibutyl phthalate (ISO)

fluoranthene (ISO)

folic acid (ISO)

gentamycin (EXP)

methapyrilene (EXP)

methimazole (EXP)

N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine (ISO)

nickel atom (ISO)

ozone (ISO)

paracetamol (EXP,ISO)

propiconazole (EXP)

resveratrol (ISO)

rotenone (ISO)

sulfadimethoxine (EXP)

tetrachloromethane (ISO)

thioacetamide (EXP)

titanium dioxide (ISO)

trovafloxacin (ISO)

valproic acid (ISO)

vinclozolin (EXP)

zoledronic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

biological_process (ND)

obsolete recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex (IBA)

transcription by RNA polymerase II (ISO)

transcription initiation at RNA polymerase II promoter (IBA)

Cellular Component

cytosol (IEA,ISO)

nuclear speck (IEA,ISO)

nucleoplasm (ISO)

nucleus (ISO)

RNA polymerase II, core complex (IBA,ISO)

Molecular Function

nucleotide binding (IEA)

protein binding (ISO)

translation initiation factor binding (IBA)

Molecular Pathway Annotations Click to see Annotation Detail View

Huntington's disease pathway (IEA)

purine metabolic pathway (IEA)

pyrimidine metabolic pathway (IEA)

RNA polymerase II transcription pathway (ISO)

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.	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.
4.	KEGG Annotation Import Pipeline	Pipeline to import KEGG annotations from KEGG into RGD
5.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
6.	Comprehensive gene review and curation	RGD comprehensive gene curation

Additional References at PubMed

PMID:9268387	PMID:9528765	PMID:9852112

Genomics

Comparative Map Data

Polr2d
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	18	23,692,578 - 23,699,709 (+)	NCBI		GRCr8
mRatBN7.2	18	23,418,097 - 23,425,228 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	18	23,418,097 - 23,425,228 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	18	23,546,442 - 23,553,573 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	18	24,295,466 - 24,302,598 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	18	23,641,409 - 23,648,541 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	18	24,570,762 - 24,577,894 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	18	24,570,762 - 24,577,894 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	18	24,287,960 - 24,295,092 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	18	24,205,326 - 24,212,458 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	18	24,232,026 - 24,239,027 (+)	NCBI
Celera	18	23,170,705 - 23,177,837 (+)	NCBI		Celera
Cytogenetic Map	18	p12	NCBI

POLR2D
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	2	127,843,553 - 127,858,155 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	2	127,843,553 - 127,858,155 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	2	128,601,127 - 128,615,729 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	2	128,320,703 - 128,332,174 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	2	128,320,464 - 128,331,934	NCBI
Celera	2	121,914,770 - 121,926,680 (-)	NCBI		Celera
Cytogenetic Map	2	q14.3	NCBI
HuRef	2	120,910,124 - 120,922,025 (-)	NCBI		HuRef
CHM1_1	2	128,608,829 - 128,620,717 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	2	128,278,790 - 128,293,413 (-)	NCBI		T2T-CHM13v2.0

Polr2d
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	18	31,922,178 - 31,929,762 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	18	31,922,212 - 31,929,754 (+)	Ensembl		GRCm39 Ensembl
GRCm38	18	31,789,125 - 31,796,709 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	18	31,789,159 - 31,796,701 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	18	31,948,813 - 31,956,355 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	18	31,932,169 - 31,939,711 (+)	NCBI		MGSCv36	mm8
Celera	18	32,276,665 - 32,284,211 (+)	NCBI		Celera
Cytogenetic Map	18	B1	NCBI
cM Map	18	17.85	NCBI

Polr2d
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955459	2,686,792 - 2,696,388 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955459	2,687,005 - 2,696,388 (+)	NCBI	ChiLan1.0	ChiLan1.0

LOC100992899
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	12	15,157,425 - 15,159,052 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	2A	15,160,190 - 15,161,817 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	2A	89,092,902 - 89,093,892 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	2A	113,975,523 - 113,975,952 (+)	NCBI	panpan1.1	PanPan1.1	panPan2

POLR2D
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	19	22,754,118 - 22,774,054 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	19	22,754,141 - 22,774,231 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	19	23,001,261 - 23,021,440 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	19	24,080,704 - 24,101,101 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	19	24,080,729 - 24,100,872 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	19	22,735,537 - 22,755,756 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	19	22,979,315 - 22,999,674 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	19	24,110,885 - 24,131,035 (+)	NCBI		UU_Cfam_GSD_1.0

Polr2d
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024405303	98,122,271 - 98,135,192 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936469	43,482,507 - 43,495,441 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936469	43,482,557 - 43,495,449 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

POLR2D
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	15	59,479,510 - 59,498,132 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	15	59,479,631 - 59,495,975 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	15	66,258,471 - 66,262,027 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

POLR2D
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	10	2,361,957 - 2,372,343 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	10	2,361,992 - 2,375,474 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666061	20,389,812 - 20,400,375 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Polr2d
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624732	14,295,113 - 14,308,826 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624732	14,294,694 - 14,308,843 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Polr2d
45 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	377
Count of miRNA genes:	202
Interacting mature miRNAs:	225
Transcripts:	ENSRNOT00000021738
Prediction methods:	Microtar, Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

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

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

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
8552968	Pigfal19	Plasma insulin-like growth factor 1 level QTL 19	11.4		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	18	1	25758124	Rat
9590248	Scort10	Serum corticosterone level QTL 10	19.71	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	18	1	25758124	Rat
2312598	Bp340	Blood pressure QTL 340		0.05	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	18	1	30558703	Rat
2300180	Bmd67	Bone mineral density QTL 67	4.8	0.0001	femur mineral mass (VT:0010011)	bone mineral density (CMO:0001226)	18	1	34291613	Rat
2293661	Bss50	Bone structure and strength QTL 50	4.64	0.0003	lumbar vertebra size trait (VT:0010518)	lumbar vertebra trabecular cross-sectional area (CMO:0001692)	18	1	34291613	Rat
61388	Bp2	Blood pressure QTL 2	3.23		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	18	1	35374722	Rat
9589153	Insul31	Insulin level QTL 31	7.15	0.05	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	18	1	42547119	Rat
2299160	Iddm35	Insulin dependent diabetes mellitus QTL 35	2.79		blood glucose amount (VT:0000188)	age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)	18	4207941	60377792	Rat
2312568	Glom21	Glomerulus QTL 21	2	0.005	kidney glomerulus morphology trait (VT:0005325)	index of glomerular damage (CMO:0001135)	18	5185858	40503530	Rat
2293708	Bss46	Bone structure and strength QTL 46	8.8	0.0001	lumbar vertebra morphology trait (VT:0010494)	lumbar vertebra cortical cross-sectional area (CMO:0001690)	18	11791518	63636873	Rat
1578661	Bss20	Bone structure and strength QTL 20	3.7		femur morphology trait (VT:0000559)	femoral neck cross-sectional area (CMO:0001697)	18	11791518	83218561	Rat
1578667	Bss21	Bone structure and strength QTL 21	3.5		femur morphology trait (VT:0000559)	femoral neck cortical cross-sectional area (CMO:0001702)	18	11791518	83218561	Rat
61382	Bp46	Blood pressure QTL 46	18.8		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	18	11941791	31393320	Rat
631264	Scl22	Serum cholesterol level QTL 22	6.2		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	18	11941791	31393320	Rat
12904690	Cm129	Cardiac mass QTL 129		0.001	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	18	11944273	26548295	Rat
12904689	Cm128	Cardiac mass QTL 128		0.001	heart mass (VT:0007028)	heart wet weight to body weight ratio (CMO:0002408)	18	11944273	26548295	Rat
12904693	Am20	Aortic mass QTL 20		0.001	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	18	11944273	26548295	Rat
12904695	Kidm73	Kidney mass QTL 73		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	18	11944273	26548295	Rat
12904691	Cm130	Cardiac mass QTL 130		0.001	heart right ventricle mass (VT:0007033)	heart right ventricle weight to body weight ratio (CMO:0000914)	18	11944273	26548295	Rat
12904680	Bw189	Body weight QTL 189		0.019	body mass (VT:0001259)	body weight (CMO:0000012)	18	11944273	26548295	Rat
2301410	Bp317	Blood pressure QTL 317		0.004	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	11944273	26548295	Rat
1331781	Scl28	Serum cholesterol level QTL 28	3.995		blood HDL cholesterol amount (VT:0000184)	serum high density lipoprotein cholesterol level (CMO:0000361)	18	11944299	24797117	Rat
1331766	Bp236	Blood pressure QTL 236	3.022		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	11944299	31359530	Rat
61375	Bp41	Blood pressure QTL 41	2.4		blood pressure trait (VT:0000183)	systolic blood pressure (CMO:0000004)	18	11944299	41122201	Rat
1331753	Bp231	Blood pressure QTL 231	3.643		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	18	11944299	52293055	Rat
1358358	Sradr6	Stress Responsive Adrenal Weight QTL 6	2.49		adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	18	11944299	59330563	Rat
6903359	Bp355	Blood pressure QTL 355	3.6		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	18	11944544	59796478	Rat
2313082	Bss85	Bone structure and strength QTL 85	0.8	0.0001	long bone metaphysis morphology trait (VT:0000133)	tibia midshaft total cross-sectional area (CMO:0001715)	18	14951337	59951337	Rat
1358193	Emca2	Estrogen-induced mammary cancer QTL 2	1.6		mammary gland integrity trait (VT:0010552)	post-insult time to mammary tumor formation (CMO:0000345)	18	18007599	63571040	Rat
1331735	Rf44	Renal function QTL 44	2.981		urine total protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	18	18234564	31359530	Rat
1331775	Bp235	Blood pressure QTL 235	3.201		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	18234564	31359530	Rat
1600373	Mamtr6	Mammary tumor resistance QTL 6			mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	18	19278901	83218561	Rat
1331741	Bp232	Blood pressure QTL 232	3.59112		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	18	21372893	83213037	Rat
1641923	Colcr8	Colorectal carcinoma resistance QTL 8	3.1	0.0014	intestine integrity trait (VT:0010554)	poorly differentiated malignant colorectal tumor number (CMO:0002076)	18	22066242	52293055	Rat

Markers in Region

RH132660

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	18	23,424,804 - 23,424,992 (+)	MAPPER	mRatBN7.2
Rnor_6.0	18	24,577,471 - 24,577,658	NCBI	Rnor6.0
Rnor_5.0	18	24,294,669 - 24,294,856	UniSTS	Rnor5.0
RGSC_v3.4	18	24,212,035 - 24,212,222	UniSTS	RGSC3.4
Celera	18	23,177,414 - 23,177,601	UniSTS
RH 3.4 Map	18	283.3	UniSTS
Cytogenetic Map	18	p12	UniSTS

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	7	10	74	35	41	11	7
Low							1	1					1
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001108886	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH473974	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ221276	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ224930	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ228021	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ229944	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ233353	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000018	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSRNOT00000021738 ⟹ ENSRNOP00000021738

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	18	23,418,097 - 23,425,228 (+)	Ensembl
Rnor_6.0 Ensembl	18	24,570,762 - 24,577,894 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000097856 ⟹ ENSRNOP00000086996

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	18	23,418,097 - 23,424,597 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000113951 ⟹ ENSRNOP00000086092

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	18	23,418,124 - 23,425,188 (+)	Ensembl

RefSeq Acc Id:

NM_001108886 ⟹ NP_001102356

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	18	23,692,578 - 23,699,709 (+)	NCBI
mRatBN7.2	18	23,418,097 - 23,425,228 (+)	NCBI
Rnor_6.0	18	24,570,762 - 24,577,894 (+)	NCBI
Rnor_5.0	18	24,287,960 - 24,295,092 (+)	NCBI
RGSC_v3.4	18	24,205,326 - 24,212,458 (+)	RGD
Celera	18	23,170,705 - 23,177,837 (+)	RGD

Sequence:

show sequence

GAGCCCGTCCGTGCGGCTTCCGTCTCCGGCAGTGTCTGTGGCAGTGCGCAGGGCGATGGCGGCA
GGTGGAAGCGATCCTCGAGCTGGCGACGTAGAAGAAGATGCTTCCCAGCTCATCTTTCCCAAAG
AGTTCGAAACAGCTGAGACGCTCCTGAACTCTGAAGTTCACATGCTTCTGGAGCACCGAAAGCA
GCAGAATGAGAGTGCGGAGGACGAACAGGAGCTTTCAGAGGTTTTCATGAAAACCCTGAACTAT
ACAGCCCGTTTCAGCCGGTTCAAAAACAGAGAGACCATTGCCAGTGTTCGTAGCCTGCTTCTCC
AGAAGAAGTTACATAAGTTTGAATTGGCTTGTTTAGCCAATCTGTGCCCGGAGACTGCTGAGGA
GTCCAAAGCGCTGATTCCAAGCCTGGAAGGGCGTTTTGAAGATGAGGAACTGCAGCAGATTCTT
GATGATATCCAGACGAAGCGCAGCTTCCAGTACTGATCACCAGACGTCACTCTGCTCCTTGAGA
TAGCCTCCAGACCGCTCTACAGTCGGAACCCTGGGTGGGCCTCACGCAGGACTGTTGCTTCCGA
AGATACTGGGACTTCTTTAGTCATACTTTTCGCTTTACTGAGATAGAATGTCTCTCTGTACTTC
TCAAAGTTGTAACAGTCCTCCTGCCTCAGCCTCCCAAGTGCTGGGATTACAGGTGTGAGCCAAC
ACTTACAGCTTGACTTTTGGAGAAGAAACAAAGACTGGCTATTGATGCTCTAGGTGCTGTCTTC
ACCGGGACTATTAGACCATAATTACTGTGACTATTAGACCATAATTACCATCTCCTCTCATTGC
AGCCTTATAAGGGCTGCTATGGTCAAATGTGCTGCCATCCTGAACTAGGGAGGTAGACCGATGT
TAAAACATTTGGTGACTACCTCTTTCTATGTTTTTTTTTGGACCCCATGTTAATATTTTTTGTT
CTTGACATTGCAATTTTTAATGTCAATATATTTTGTAGTTTTTGAAGCTATAATGATAAATAAA
AAAATTATATGGGAGGAATGTTTTTACTTTGTTGCAAAGGGGAGAGATAAACCAGAACACTGTA
ATTATTTGATTTTTTTTTTTTTTAAGA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001102356	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDL76175	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000021738.6
	ENSRNOP00000086092
	ENSRNOP00000086092.1
	ENSRNOP00000086996.1

RefSeq Acc Id:	NP_001102356 ⟸ NM_001108886
- UniProtKB:	A6J2P3 (UniProtKB/TrEMBL), A0A8I6A2X2 (UniProtKB/TrEMBL)
- Sequence:	show sequence MAAGGSDPRAGDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKT LNYTARFSRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGRFEDEELQ QILDDIQTKRSFQY hide sequence

RefSeq Acc Id:

ENSRNOP00000021738 ⟸ ENSRNOT00000021738

RefSeq Acc Id:

ENSRNOP00000086996 ⟸ ENSRNOT00000097856

RefSeq Acc Id:

ENSRNOP00000086092 ⟸ ENSRNOT00000113951

Protein Domains

RNA polymerase Rpb4/RPC9 core

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-D4A259-F1-model_v2	AlphaFold	D4A259	1-142	view protein structure

Transcriptome

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

Promoters

RGD ID:

13700675

Promoter ID:

EPDNEW_R11199

Type:

multiple initiation site

Name:

Polr2d_1

Description:

RNA polymerase II subunit D

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	18	24,570,789 - 24,570,849	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1308565	AgrOrtholog
BioCyc Gene	G2FUF-8053	BioCyc
Ensembl Genes	ENSRNOG00000016231	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000021738.6	UniProtKB/TrEMBL
	ENSRNOT00000097856.1	UniProtKB/TrEMBL
	ENSRNOT00000113951	ENTREZGENE
	ENSRNOT00000113951.1	UniProtKB/TrEMBL
Gene3D-CATH	1.20.1250.40	UniProtKB/TrEMBL
InterPro	HRDC-like	UniProtKB/TrEMBL
	RNA_pol_II_Rpb4	UniProtKB/TrEMBL
	RNA_pol_II_Rpb4_core	UniProtKB/TrEMBL
	Rpb4-like	UniProtKB/TrEMBL
	Rpb4/RPC9_sf	UniProtKB/TrEMBL
KEGG Report	rno:364834	UniProtKB/TrEMBL
NCBI Gene	364834	ENTREZGENE
PANTHER	DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4	UniProtKB/TrEMBL
	PTHR21297	UniProtKB/TrEMBL
Pfam	RNA_pol_Rpb4	UniProtKB/TrEMBL
PhenoGen	Polr2d	PhenoGen
RatGTEx	ENSRNOG00000016231	RatGTEx
SMART	RPOL4c	UniProtKB/TrEMBL
Superfamily-SCOP	HRDC_like	UniProtKB/TrEMBL
UniProt	A0A8I6A2X2	ENTREZGENE, UniProtKB/TrEMBL
	A0A8I6GFK4_RAT	UniProtKB/TrEMBL
	A6J2P3	ENTREZGENE, UniProtKB/TrEMBL
	D4A259_RAT	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-07-21	Polr2d	RNA polymerase II subunit D	Polr2d	polymerase (RNA) II subunit D	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2016-03-09	Polr2d	polymerase (RNA) II subunit D	Polr2d	polymerase (RNA) II (DNA directed) polypeptide D	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-04-30	Polr2d	polymerase (RNA) II (DNA directed) polypeptide D	Polr2d_predicted	polymerase (RNA) II (DNA directed) polypeptide D (predicted)	'predicted' is removed	2292626	APPROVED
2005-01-12	Polr2d_predicted	polymerase (RNA) II (DNA directed) polypeptide D (predicted)			Symbol and Name status set to approved	70820	APPROVED

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

RGD Manual Annotations

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - ClinVar

RGD Manual Annotations

Imported Annotations - KEGG (archival)