Polr2d (RNA polymerase II subunit D)

Gene: Polr2d (RNA polymerase II subunit D) Chinchilla lanigera

Analyze

Symbol:

Polr2d

Name:

RNA polymerase II subunit D

RGD ID:

8800117

Description:

INVOLVED IN transcription by RNA polymerase II (ortholog); PARTICIPATES IN RNA polymerase II transcription pathway; ASSOCIATED WITH autosomal dominant thrombophilia due to protein C deficiency (ortholog); genetic disease (ortholog); FOUND IN cytosol (ortholog); nuclear speck (ortholog); nucleoplasm (ortholog)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

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

RGD Orthologs

Alliance Genes

More Info

more info ...

Latest Assembly:

ChiLan1.0 - Chinchilla ChiLan1.0 Assembly

Position:

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

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 Ontology Annotations Click to see Annotation Detail View

Biological Process

transcription by RNA polymerase II (ISO)

Cellular Component

cytosol (ISO)

nuclear speck (ISO)

nucleoplasm (ISO)

nucleus (ISO)

RNA polymerase II, core complex (ISO)

Molecular Function

protein binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

RNA polymerase II transcription pathway (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Transitive Annotation Pipeline	Automated assignment of GO, PW and RDO ISO annotations across species

Additional References at PubMed

PMID:22301074	PMID:30032202

Genomics

Comparative Map Data

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

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
(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

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

Expression

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_005397575	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AGCD01047996	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GBCE01096350	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSCLAT00000006395 ⟹ ENSCLAP00000006291

Type:

CODING

Position:

Chinchilla Assembly	Chr	Position (strand)	Source
ChiLan1.0 Ensembl	NW_004955459	2,686,792 - 2,696,388 (+)	Ensembl

RefSeq Acc Id:

XM_005397575 ⟹ XP_005397632

Type:

CODING

Position:

Chinchilla Assembly	Chr	Position (strand)	Source
ChiLan1.0	NW_004955459	2,687,005 - 2,696,388 (+)	NCBI

Sequence:

show sequence

CCGGTGGCATCTGTGGAATTCCGCGCGGCGATGGCGGCGGGCGGCAGTGATCCGCGGGCTGGCG
ACGTAGAAGAGGACGCTTCACAACTCATCTTCCCCAAAGAGTTTGAAACAGCTGAGACACTTCT
AAATTCAGAAGTTCATATGCTTCTGGAACATCGGAAGCAACAGAACGAGAGTGCAGAGGATGAG
CAGGAGCTCTCTGGGGTCTTCATGAAAACTTTGAACTACACAGCTCGTTTCAGTCGTTTTAAAA
ACAGAGAGACCATTGCCAGTGTTCGTAGTTTGCTGCTCCAGAAAAAGCTGCATAAGTTTGAGTT
GGCCTGTTTAGCCAACCTTTGCCCAGAGACTGCTGAGGAGTCCAAGGCTCTTATCCCAAGCCTA
GAGGGGCGATTTGAAGATGAGGAGCTGCAGCAGATTCTTGATGACATACAGACAAAGCGTAGTT
TTCAGTATTAATCTCCGAACATCGCTGAGCTGCCTGGGGAGGACCACTGTGTTCTGGGTGGATC
TGCCTTGCTCAGAGGCAAGCTGGACTTCCTTGGAGGGGACAGTGCGTCTTGTGTTGGATTAGTG
CGCTGTTGAGGCGTGCCTGGAGTCCATGATCCTGTGCCTTGAGTGGCGCGGCAGTGTCTGCCGG
CTGCCACTTAAGCTTCCTGCGGAGAAGGTTGCGGGGTGATGATGTGCAGACCATGCTATCAGCT
ACCTCATACTGTGGTTTTTGGACCCCACATTATTTTTTTATTCCTAACATTTCATGTTTTAATA
TTAATGTGTTTGTAGTGTTTGAAAGTAAACAAGAACATAGGAAACTTGTACGGGGAAAAATAGT
CTTACCTAGATGCAAAAGAAAGAATTAAATCAGACCAACTTTGTATGGATTCTTGAAGGACAAG
AGTGTTGATGATGGGAATACCTGAAGCCATTGTGCCTAAGGTAAGATGGCGAGAATAAAGATGC
TAGCGAGATGCCTGTGCCCTATCCTGGGGTCATTA

hide sequence

Protein Sequences


Protein RefSeqs	XP_005397632	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSCLAP00000006291
	ENSCLAP00000006291.1

RefSeq Acc Id:	XP_005397632 ⟸ XM_005397575
- UniProtKB:	A0A8C2UYX0 (UniProtKB/TrEMBL)
- Sequence:	show sequence MAAGGSDPRAGDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSGVFMKT LNYTARFSRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGRFEDEELQ QILDDIQTKRSFQY hide sequence

RefSeq Acc Id:

ENSCLAP00000006291 ⟸ ENSCLAT00000006395

Protein Domains

RNA polymerase Rpb4/RPC9 core

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSCLAG00000004449	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSCLAT00000006395	ENTREZGENE
	ENSCLAT00000006395.1	UniProtKB/TrEMBL
Gene3D-CATH	1.20.1250.40	UniProtKB/TrEMBL
InterPro	HRDC-like_sf	UniProtKB/TrEMBL
	RNA_pol_Rpb4/RPC9_core	UniProtKB/TrEMBL
	Rpb4-like	UniProtKB/TrEMBL
	Rpb4/RPC9	UniProtKB/TrEMBL
	Rpb4/RPC9_sf	UniProtKB/TrEMBL
NCBI Gene	Polr2d	ENTREZGENE
PANTHER	DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4	UniProtKB/TrEMBL
	PTHR21297	UniProtKB/TrEMBL
Pfam	RNA_pol_Rpb4	UniProtKB/TrEMBL
SMART	RPOL4c	UniProtKB/TrEMBL
Superfamily-SCOP	SSF47819	UniProtKB/TrEMBL
UniProt	A0A8C2UYX0	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-07-26	Polr2d	RNA polymerase II subunit D		polymerase (RNA) II (DNA directed) polypeptide D	Symbol and/or name change	5135510	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)

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Imported Disease Annotations - ClinVar

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