Polr1f (RNA polymerase I subunit F)

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Gene: Polr1f (RNA polymerase I subunit F) Rattus norvegicus

Analyze

Symbol:

Polr1f

Name:

RNA polymerase I subunit F

RGD ID:

1307824

Description:

Predicted to enable DNA binding activity. Predicted to be involved in DNA-templated transcription initiation. Predicted to act upstream of or within cellular response to leukemia inhibitory factor. Predicted to be part of RNA polymerase I complex. Orthologous to human POLR1F (RNA polymerase I subunit F); PARTICIPATES IN RNA polymerase I transcription pathway; INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

DNA-directed RNA polymerase I subunit RPA43; LOC362728; TWIST neighbor; Twistnb

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):	POLR1F (RNA polymerase I subunit F)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Polr1f (RNA polymerase I subunit F)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Polr1f (RNA polymerase I subunit F)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	POLR1F (RNA polymerase I subunit F)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	POLR1F (RNA polymerase I subunit F)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Polr1f (RNA polymerase I subunit F)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	POLR1F (RNA polymerase I subunit F)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	POLR1F (RNA polymerase I subunit F)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Polr1f (RNA polymerase I subunit F)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	AIG1 (androgen induced 1)	HGNC	OMA
Alliance orthologs ³
Homo sapiens (human):	POLR1F (RNA polymerase I subunit F)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Polr1f (RNA polymerase I subunit F)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	twistnb (TWIST neighbor)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	CG13773	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Saccharomyces cerevisiae (baker's yeast):	RPA43	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Xenopus tropicalis (tropical clawed frog):	polr1f	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER\|PhylomeDB)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	6	50,053,289 - 50,070,514 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	6	50,053,289 - 50,070,514 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	6	50,357,723 - 50,374,910 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	6	50,672,665 - 50,689,853 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	6	50,111,709 - 50,129,462 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	6	52,751,106 - 52,768,574 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	6	52,751,106 - 52,768,574 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	6	62,372,118 - 62,389,586 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	6	51,789,847 - 51,807,076 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	6	51,789,616 - 51,807,711 (+)	NCBI
Celera	6	49,243,164 - 49,260,395 (+)	NCBI		Celera
Cytogenetic Map	6	q16	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

genetic disease (ISO)

pleomorphic xanthoastrocytoma (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-schisandrin B (EXP)

(-)-epigallocatechin 3-gallate (ISO)

1,2-dichloroethane (ISO)

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (ISO)

17beta-estradiol (ISO)

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

2,4-dinitrotoluene (EXP)

2-hydroxypropanoic acid (ISO)

4,4'-sulfonyldiphenol (ISO)

6-propyl-2-thiouracil (EXP)

acrylamide (EXP)

aflatoxin B1 (ISO)

aflatoxin M1 (ISO)

all-trans-retinoic acid (ISO)

antirheumatic drug (ISO)

arsenite(3-) (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP)

caffeine (ISO)

CGP 52608 (ISO)

chlorpyrifos (ISO)

clofibrate (ISO)

coumarin (ISO)

cylindrospermopsin (ISO)

dicrotophos (ISO)

disodium selenite (ISO)

doxorubicin (ISO)

flutamide (EXP)

gentamycin (EXP)

indole-3-methanol (EXP)

lipopolysaccharide (ISO)

methyl methanesulfonate (ISO)

nefazodone (EXP)

paraquat (EXP)

pentachlorophenol (ISO)

pirinixic acid (ISO)

potassium chromate (ISO)

pyrogallol (ISO)

quercetin (ISO)

rac-lactic acid (ISO)

S-(1,2-dichlorovinyl)-L-cysteine (ISO)

sodium arsenite (ISO)

sodium dichromate (EXP)

testosterone (ISO)

tetrachloromethane (EXP,ISO)

thioacetamide (EXP)

titanium dioxide (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

biological_process (ND)

cellular response to leukemia inhibitory factor (ISO)

DNA-templated transcription initiation (IEA)

Cellular Component

RNA polymerase I complex (IBA)

Molecular Function

DNA binding (IEA)

Molecular Pathway Annotations Click to see Annotation Detail View

RNA polymerase I 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.	GOA pipeline	RGD automated data pipeline
3.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
4.	Comprehensive gene review and curation	RGD comprehensive gene curation
5.	RNA polymerase I activity is regulated at multiple steps in the transcription cycle: recent insights into factors that influence transcription elongation.	Schneider DA Gene. 2012 Feb 10;493(2):176-84. doi: 10.1016/j.gene.2011.08.006. Epub 2011 Aug 26.
6.	Conservation between the RNA polymerase I, II, and III transcription initiation machineries.	Vannini A and Cramer P, Mol Cell. 2012 Feb 24;45(4):439-46. doi: 10.1016/j.molcel.2012.01.023.

Additional References at PubMed

PMID:20439489

Genomics

Comparative Map Data

Polr1f
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	6	50,053,289 - 50,070,514 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	6	50,053,289 - 50,070,514 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	6	50,357,723 - 50,374,910 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	6	50,672,665 - 50,689,853 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	6	50,111,709 - 50,129,462 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	6	52,751,106 - 52,768,574 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	6	52,751,106 - 52,768,574 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	6	62,372,118 - 62,389,586 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	6	51,789,847 - 51,807,076 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	6	51,789,616 - 51,807,711 (+)	NCBI
Celera	6	49,243,164 - 49,260,395 (+)	NCBI		Celera
Cytogenetic Map	6	q16	NCBI

POLR1F
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	7	19,695,461 - 19,709,037 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	7	19,695,461 - 19,709,037 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	7	19,735,084 - 19,748,660 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	7	19,701,610 - 19,715,185 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	7	19,508,324 - 19,521,900	NCBI
Celera	7	19,719,385 - 19,732,961 (-)	NCBI		Celera
Cytogenetic Map	7	p21.1	NCBI
HuRef	7	19,624,238 - 19,637,814 (-)	NCBI		HuRef
CHM1_1	7	19,735,885 - 19,749,461 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	7	19,829,933 - 19,843,507 (-)	NCBI		T2T-CHM13v2.0
CRA_TCAGchr7v2	7	19,786,489 - 19,800,065 (-)	NCBI

Polr1f
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	12	33,479,593 - 33,491,434 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	12	33,479,634 - 33,491,391 (+)	Ensembl		GRCm39 Ensembl
GRCm38	12	33,429,624 - 33,439,380 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	12	33,429,635 - 33,441,392 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	12	34,114,489 - 34,124,245 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	12	34,014,871 - 34,024,627 (+)	NCBI		MGSCv36	mm8
Celera	12	34,873,998 - 34,883,760 (+)	NCBI		Celera
Cytogenetic Map	12	A3	NCBI
cM Map	12	14.38	NCBI

Polr1f
(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_004955410	22,434,704 - 22,442,862 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955410	22,435,136 - 22,442,839 (-)	NCBI	ChiLan1.0	ChiLan1.0

POLR1F
(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	7	72,873,225 - 72,886,815 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	7	20,369,819 - 20,383,414 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	7	19,689,786 - 19,703,403 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	7	19,692,639 - 19,703,338 (-)	Ensembl	panpan1.1		panPan2

POLR1F
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	14	33,845,768 - 33,865,686 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	14	33,845,995 - 33,865,720 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	14	33,381,992 - 33,401,977 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	14	33,766,758 - 33,786,754 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	14	33,767,041 - 33,786,724 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	14	33,876,784 - 33,896,768 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	14	33,584,529 - 33,604,502 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	14	33,895,186 - 33,915,178 (-)	NCBI		UU_Cfam_GSD_1.0

Polr1f
(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_024405118	78,051,132 - 78,071,391 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936546	5,731,825 - 5,746,569 (-)	Ensembl	SpeTri2.0
SpeTri2.0	NW_004936546	5,732,413 - 5,746,481 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

POLR1F
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	9	88,760,398 - 88,785,802 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	9	88,760,394 - 88,785,802 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	9	97,982,186 - 98,006,808 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

POLR1F
(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	21	38,488,802 - 38,501,106 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	21	38,488,825 - 38,501,158 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666042	66,064,323 - 66,076,619 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Polr1f
(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_004624739	10,904,932 - 10,917,075 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624739	10,905,010 - 10,916,141 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Polr1f
139 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	224
Count of miRNA genes:	160
Interacting mature miRNAs:	185
Transcripts:	ENSRNOT00000014373
Prediction methods:	Miranda, Rnahybrid
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
2301972	Bp325	Blood pressure QTL 325	4.8		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	6	1	72227641	Rat
1300164	Rf15	Renal function QTL 15	3.12		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	6	5074497	54641141	Rat
4145119	Mcs25	Mammary carcinoma susceptibility QTL 25		0.0001	mammary gland integrity trait (VT:0010552)	ratio of deaths to total study population during a period of time (CMO:0001023)	6	10894415	110548006	Rat
1578665	Bss16	Bone structure and strength QTL 16	4.4		femur morphology trait (VT:0000559)	bone trabecular cross-sectional area (CMO:0002311)	6	11735669	72593685	Rat
1578668	Bmd14	Bone mineral density QTL 14	3.8		femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	6	11735669	72593685	Rat
10401812	Kidm54	Kidney mass QTL 54			kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	6	14368788	59368788	Rat
10401800	Kidm49	Kidney mass QTL 49			kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	6	14368788	59368788	Rat
1576309	Emca7	Estrogen-induced mammary cancer QTL 7	4		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	6	15107216	107351382	Rat
2292589	Emca10	Estrogen-induced mammary cancer QTL 10		0.048	mammary gland integrity trait (VT:0010552)	post-insult time to mammary tumor formation (CMO:0000345)	6	16536140	61536140	Rat
1354664	Slep2	Serum leptin concentration QTL 2	4.49		blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	6	16536140	71636405	Rat
1641898	Colcr4	Colorectal carcinoma resistance QTL4	3.71	0.0007	intestine integrity trait (VT:0010554)	well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)	6	20338777	62613667	Rat
2293839	Kiddil2	Kidney dilation QTL 2	4.8		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	6	20866422	81133036	Rat
2293841	Kiddil4	Kidney dilation QTL 4	4.4		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	6	20866422	81133036	Rat
1331779	Rf38	Renal function QTL 38	2.876		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal vascular resistance (CMO:0001900)	6	32074428	72227641	Rat
634318	Bw118	Body weight QTL 118	3.55		abdominal fat pad mass (VT:1000711)	abdominal fat pad weight (CMO:0000088)	6	33309549	57730294	Rat
6893340	Cm77	Cardiac mass QTL 77	0.26	0.57	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	6	33309549	81132889	Rat
1300143	Rf14	Renal function QTL 14	2.92		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	6	34434137	77102317	Rat
1354632	Scl29	Serum cholesterol level QTL 29	3.74		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	6	35098709	71636405	Rat
634307	Bp141	Blood pressure QTL 141	4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	6	35230417	80230417	Rat
70199	Coreg1	Compensatory renal growth QTL 1	11.8		kidney mass (VT:0002707)	compensatory renal growth score (CMO:0001894)	6	35691618	57730540	Rat
9590290	Uminl2	Urine mineral level QTL 2	3.96	0.001	urine mineral amount (VT:0015086)	urine electrolyte level (CMO:0000593)	6	38783989	83783989	Rat
9590306	Scort18	Serum corticosterone level QTL 18	2.88	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	6	38783989	83783989	Rat
9590140	Scort4	Serum corticosterone level QTL 4	14.49	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	6	38783989	83783989	Rat
634330	Pia16	Pristane induced arthritis QTL 16	3.9		joint integrity trait (VT:0010548)	arthritic paw count (CMO:0001460)	6	45790088	104200226	Rat

Markers in Region

RH130274

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	6	50,069,085 - 50,069,293 (+)	MAPPER	mRatBN7.2
Rnor_6.0	6	52,767,146 - 52,767,353	NCBI	Rnor6.0
Rnor_5.0	6	62,388,158 - 62,388,365	UniSTS	Rnor5.0
RGSC_v3.4	6	51,805,648 - 51,805,855	UniSTS	RGSC3.4
Celera	6	49,258,967 - 49,259,174	UniSTS
RH 3.4 Map	6	332.1	UniSTS
Cytogenetic Map	6	q16	UniSTS

RH135340

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	6	50,067,257 - 50,067,473 (+)	MAPPER	mRatBN7.2
Rnor_6.0	6	52,765,318 - 52,765,533	NCBI	Rnor6.0
Rnor_5.0	6	62,386,330 - 62,386,545	UniSTS	Rnor5.0
RGSC_v3.4	6	51,803,820 - 51,804,035	UniSTS	RGSC3.4
Celera	6	49,257,139 - 49,257,354	UniSTS
RH 3.4 Map	6	327.0	UniSTS
Cytogenetic Map	6	q16	UniSTS

AW533281

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	6	50,067,771 - 50,067,969 (+)	MAPPER	mRatBN7.2
Rnor_6.0	6	52,765,832 - 52,766,029	NCBI	Rnor6.0
Rnor_5.0	6	62,386,844 - 62,387,041	UniSTS	Rnor5.0
RGSC_v3.4	6	51,804,334 - 51,804,531	UniSTS	RGSC3.4
Celera	6	49,257,653 - 49,257,850	UniSTS
RH 3.4 Map	6	328.2	UniSTS
Cytogenetic Map	6	q16	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	18	29	20	18	20			58	22	34	11
Low		25	28	21	1	21	8	10	16	13	7		8
Below cutoff								1

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001108707	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH473947	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ230315	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ234148	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000164	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSRNOT00000014373 ⟹ ENSRNOP00000014373

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	6	50,053,289 - 50,070,514 (+)	Ensembl
Rnor_6.0 Ensembl	6	52,751,106 - 52,768,574 (+)	Ensembl

RefSeq Acc Id:

NM_001108707 ⟹ NP_001102177

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	6	50,053,289 - 50,070,514 (+)	NCBI
Rnor_6.0	6	52,751,106 - 52,768,574 (+)	NCBI
Rnor_5.0	6	62,372,118 - 62,389,586 (+)	NCBI
RGSC_v3.4	6	51,789,847 - 51,807,076 (+)	RGD
Celera	6	49,243,164 - 49,260,395 (+)	RGD

Sequence:

show sequence

GTCGCGGTCGGTCGCTTTTTGATGATGTAAGCCAAGCGTCGGAGGCGAGCGGGAATGTTTGCGT
CATTCGTGCGAGCCCCAAAGCATCCTGACAAGCCGCATGGCTGCGGGCTCTGTGGAGTCGCAGC
GGCCCAAGGCGGCCTCCGAGAGGCCGGTGGCGGGTCAGGCCGGGATTCTGCCTTGCCTGGAACT
ACCGAGCTATGCCGCGGCGTGTGCGCTGGTAAGCAGCCGCTATTCCTGCTTGGTGGCCGCCCCG
CACCGCAGGCACATCGCCTTGTCGCCCCGCTACCTGAGCAGGAAGCGCACGGGCATCCGCGAGC
AGCTGGACGCCGAACTCCTGCGCTACTCCGAGAGCCTTTTAGGTGTTCCCATTGCATATGATAA
CATCAGAGTTGTGGGTGAACTGGGAGATATTTATGATGATCAAGGACACATTCATCTTAACATT
GAAGCCGATTTTGTTATTTTCTGCCCTAAACCAGGGCAGAAACTGATGGGTACAGTTAATAAAG
TGTCTTCTAGCCATATTGGCTGTTTAGTACATGGATGTTTTAATGCTTCTATCCCTAAACCTGA
GCAGATGTCATATGAGGAGTGGCAAACATTGGAGATAAATGTAGGGGATGAACTGGAATTTGAT
GTGTTTCGCTTAGACTCAGATTCTGCTGGAGTATTCTGCATTCGAGGAAAACTAAATACCACAA
GTTTGCAGCATAAGGGCTCTGTAGTTTCTGAAGATGTAGAAGAAACTGTCATTGAAGAGGTTGT
TGAAAAAATTCCAAAGAAGAAGAAGAAGAAAGACAAAGACAGAGAAGTCTGTGCAACAGTGGAA
AGTGTTACAGAGGTAGCAGATGTTACAGATGCTGCTGCAGAGGACGAAGCAGGCCTGCCGTGTA
GTGATGATGTCAATGACTTCTTTGAGGAAGAGCCAAAGAAGAAGAAAAAGAAGAAGAAAAGGCA
CCAGGAAGATCAGGACCCCATTTTCCAAGCCAGTGACTCCAGTGGCTACCAAAGTGACCATAAA
AAGAAAAAGAAGAAAAGAAAACACAGTGAAGAGGCTAACTGAGTCACCTAAGAAGAGACAGTAA
TTGTCTTTTCTATTGTTAACATATTCAGATATACAGGTGAATAGATTTTTTGAATGGTAGGAAA
TGCTGATAGGAAATTCACAAACAAATACTTGATTGGAGGGTTTTGTACTAAAATCATACAACTG
ATTATATAAATTTTGGATAATACCAGTATTATTATAGTATTATTTTATTACAGTAAAGGGGAAA
TGTTAACAAATGTTTCTTACCTTGACTCATATTGTTAATGTTCTACGTAAAATTTTACATTCTC
AACATCTGCCAAAGAACTTTATGCTTTCAATTTTTTTCTGATAATAAATGTTGTCTTTAGCCAG
AACATTTTTTTTAAAAAGCACAATACATTTACTAAGTTTAAATTTTCCTTAAACAGTATTTCTA
TTTTATTTAAAATGTATACCTAAGGAAGATTATCTAGAACTCTTACATACCCTGTGACTGTCTG
TTGAATGTGTGGTGGGCGGAAAACTCATTGTCTCTCCCAGAGGGTGTGTGTACATGTGTTCTTG
AATTCCGAGACTGTTAGGGGAAGGGCTGTTAATTTCTACTTTGTGTTTCAGTAGTCTTTATTTT
GTTATATAGATCATGAGCAAGGTGAAGATGGGATAAATGTGGTTCTTGCTAGTTGAAAATCTCC
AGTAAGCTTTTAATGATTAGGGGTGTTCTAGACTTGTTTGAGGAGGAGCTCCACCGTCATTACT
GCTTTCACTGATAAATGTGGGATGTGTTATGCCTAACCAGAAGGTTATAATGAAGATGAGTTGG
TTGAGGTTCATAATCAACCCATAGCCAGGCACTTAATAGTTGTAATGTGTTTTATTGAGGCCAA
AGGATATAAAAATCAAGTTAATGTTCATTTCTCTGTGAAGCAAAATGGGAGAAACACTTGTGTG
CACACAGCCTAAGTGAGGAAATAAAACAGTAATTGTAAATACCATGAAGAAAACATTGATCTCC
TTAGTTAGTATCTGGAAATATACGGGCGTAGGGTTGACCTTCCGTGTCAGTCATTGCTGTTGTC
ACTGACTGGCAGACATAGTGTGAGCATCAATTTACTATTTGATAAGGAGTAACTTTTGGCAACC
ATGTTTCCTGATTTAATGTATGGTATATAGAGCATAAAGAATGCAGCAATTTAATGTGTACAGG
TAGATCTGACCAACAGAGGAAAGGTACAAACCAACATCTTTCACTCAGGATACTTGAAAATTTT
TATGTGGCTTTCAGGTCCCTTCTTAAACTGTGACTATTCCAAATTAACATGCCTTGTCTCAGTA
CAAAATATGAGATTTTAAATTAAAGATATTTTAAGAAATACAAAGAATACTGCAATACAGTTGT
CTTTCCCTCCTTTTACCTCATCCCTCCTGTTCCCATACCTACCCACTCCCGCACCCACTCTCCT
TCCTCCATCCATCCTTGATGTCTATTAAAAAATGGAGTACAGACCTAGACAGAATTCTTGGCAG
GAATCGCCAGTGGTGGAGAAGCACTTAAAGAAATGCTCAACACCCTTAGTCATCAGGGAATTGT
AAATCAGAACAACTCTGAAATTCTGTCTTACACCTATCAAAATGGCTAAGATATTAAAAAAAAC
AAAACAAAACAAAAAACCTCAAGCAACAGCTCGTGCTAACGAGGATGTGGATGTGGATCAAGGG
GAACACCCTGGTGGGGGTCCAAACTTCCAACTGCTTTGGAAGTAACTTTGGTGTTTTCTTAGAA
AACTGGGAATAGATCTACCTCAAGACACAGCTCTGGGACATATACCCAAAAGAACCACTACCAT
ATCACAAGACATTTGCTCAACTATGTTCAAAGCAGCTATTCATAATAGCCATAAACTGGAAACA
ACCCACATGTCCTTCAACTAAAGAATGCATAAAGAAAATATGGTTCATTTACACAATGGAATAG
TACTCAGCTATTGAAAACAATGACATCATTAAATTTGCAAATGGATGGAACTAGAAAAGATCCT
GAACCCAGAAAGACAAACAGTCTGTATTCACTTGTATGTGGATTTTAGTACAGGATAACTGCTA
TAAACCACAGACCCAAAGATACTAAGCATGGAAGACCCACGGGGGACACGCTCATATCTCATTG
AGAAGGGGAAATTGAAAATTTAACTTTTTGCTTAACACTTTTGCTAAGTAAAATATTAATTTTA
TCCTGTTTCCAGTTTATTTTTTCTCAGTGGTTAAGTAAGATCATAGATGAAACTCATTACATTA
CTTCAGACAATGCTCTTCAAATGAATTTGTAAATTGAAAGGGATTGTAATGTTTGTTTTGTAAG
GATTTGATGTAACATATCTAGAAAATGTTCAATAAATCCTTCATATTTTAGGAGTTGAATTTGT
GATTATATTTAGCACAGTATGGTAAGTCACATGATTCTTGCCTTCCATGAACACCAAAACAACA
TGTTAAATTTATCTATTGATAAAAAAATAGATAAGCA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001102177	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDM03293	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

NP_001102177 ⟸ NM_001108707

- UniProtKB:

D4ADH7 (UniProtKB/TrEMBL), A6HB88 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MAAGSVESQRPKAASERPVAGQAGILPCLELPSYAAACALVSSRYSCLVAAPHRRHIALSPRYL
SRKRTGIREQLDAELLRYSESLLGVPIAYDNIRVVGELGDIYDDQGHIHLNIEADFVIFCPKPG
QKLMGTVNKVSSSHIGCLVHGCFNASIPKPEQMSYEEWQTLEINVGDELEFDVFRLDSDSAGVF
CIRGKLNTTSLQHKGSVVSEDVEETVIEEVVEKIPKKKKKKDKDREVCATVESVTEVADVTDAA
AEDEAGLPCSDDVNDFFEEEPKKKKKKKKRHQEDQDPIFQASDSSGYQSDHKKKKKKRKHSEEA
N

hide sequence

RefSeq Acc Id:

ENSRNOP00000014373 ⟸ ENSRNOT00000014373

Protein Domains

RPA43 OB

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-D4ADH7-F1-model_v2	AlphaFold	D4ADH7	1-321	view protein structure

Transcriptome

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1307824	AgrOrtholog
BioCyc Gene	G2FUF-37833	BioCyc
Ensembl Genes	ENSRNOG00000010750	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000014373	ENTREZGENE
	ENSRNOP00000014373.2	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000014373	ENTREZGENE
	ENSRNOT00000014373.4	UniProtKB/TrEMBL
Gene3D-CATH	2.40.50.1060	UniProtKB/TrEMBL
	3.30.1490.120	UniProtKB/TrEMBL
InterPro	RNA_pol_Rpb7-like_N_sf	UniProtKB/TrEMBL
	RNAP_I_Rpa43_N	UniProtKB/TrEMBL
	RPA43_OB	UniProtKB/TrEMBL
	Rpb7-like	UniProtKB/TrEMBL
KEGG Report	rno:362728	UniProtKB/TrEMBL
NCBI Gene	362728	ENTREZGENE
PANTHER	DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA43	UniProtKB/TrEMBL
	PTHR12709	UniProtKB/TrEMBL
Pfam	RPA43_OB	UniProtKB/TrEMBL
PhenoGen	Polr1f	PhenoGen
UniProt	A6HB88	ENTREZGENE, UniProtKB/TrEMBL
	D4ADH7	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2020-04-28	Polr1f	RNA polymerase I subunit F	Twistnb	TWIST neighbor	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-04-30	Twistnb	TWIST neighbor	Twistnb_predicted	TWIST neighbor (predicted)	'predicted' is removed	2292626	APPROVED
2005-01-12	Twistnb_predicted	TWIST neighbor (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

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Imported Disease Annotations - ClinVar

RGD Manual Annotations