Prpf39 (pre-mRNA processing factor 39)

Gene: Prpf39 (pre-mRNA processing factor 39) Rattus norvegicus

Analyze

Symbol:

Prpf39

Name:

pre-mRNA processing factor 39

RGD ID:

1308702

Description:

Predicted to contribute to pre-mRNA 5'-splice site binding activity. Predicted to be involved in mRNA 5'-splice site recognition. Predicted to be part of U1 snRNP; U2-type prespliceosome; and commitment complex. Orthologous to human PRPF39 (pre-mRNA processing factor 39); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; acrylamide.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

LOC314171; pre-mRNA-processing factor 39; PRP39 pre-mRNA processing factor 39 homolog; PRP39 pre-mRNA processing factor 39 homolog (S. cerevisiae); PRP39 pre-mRNA processing factor 39 homolog (yeast)

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):	PRPF39 (pre-mRNA processing factor 39)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, Panther, Treefam
Mus musculus (house mouse):	Prpf39 (pre-mRNA processing factor 39)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Prpf39 (pre-mRNA processing factor 39)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	PRPF39 (pre-mRNA processing factor 39)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	PRPF39 (pre-mRNA processing factor 39)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Prpf39 (pre-mRNA processing factor 39)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	PRPF39 (pre-mRNA processing factor 39)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	PRPF39 (pre-mRNA processing factor 39)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Prpf39 (pre-mRNA processing factor 39)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	PRPF39 (pre-mRNA processing factor 39)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Prpf39 (pre-mRNA processing factor 39)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	prpf39 (PRP39 pre-mRNA processing factor 39 homolog (yeast))	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	CG1646	Alliance	DIOPT (InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	F25B4.5	Alliance	DIOPT (InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	PRP39	Alliance	DIOPT (OrthoFinder\|OrthoInspector\|PANTHER)
Saccharomyces cerevisiae (baker's yeast):	PRP42	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OrthoFinder\|PANTHER)
Xenopus tropicalis (tropical clawed frog):	prpf39.1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

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
GRCr8	6	88,825,227 - 88,851,342 (+)	NCBI		GRCr8
mRatBN7.2	6	83,088,981 - 83,113,826 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	6	83,088,986 - 83,113,825 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	6	83,448,548 - 83,473,385 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	6	83,747,910 - 83,772,747 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	6	83,189,628 - 83,214,483 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	6	86,785,793 - 86,810,806 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	6	86,785,771 - 86,810,316 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	6	96,274,772 - 96,299,877 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	6	86,385,975 - 86,412,072 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	6	86,395,686 - 86,413,568 (+)	NCBI
Celera	6	81,656,963 - 81,681,773 (+)	NCBI		Celera
Cytogenetic Map	6	q24	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Brain-Lung-Thyroid Syndrome (ISO)

Fanconi anemia (ISO)

genetic disease (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

17beta-estradiol (EXP)

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

2,4,6-tribromophenol (ISO)

2-hydroxypropanoic acid (ISO)

3,4-methylenedioxymethamphetamine (ISO)

4,4'-diaminodiphenylmethane (ISO)

4-hydroxyphenyl retinamide (ISO)

acrolein (ISO)

acrylamide (EXP)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

alpha-pinene (ISO)

azoxystrobin (EXP)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

carbon nanotube (ISO)

chlorpyrifos (EXP)

crocidolite asbestos (ISO)

cyclosporin A (ISO)

dicrotophos (ISO)

diquat (ISO)

folic acid (ISO)

gentamycin (EXP)

glyphosate (EXP)

imidacloprid (EXP)

methylphenidate (ISO)

nickel atom (ISO)

ozone (ISO)

paracetamol (ISO)

phenobarbital (ISO)

rac-lactic acid (ISO)

silicon dioxide (ISO)

sodium arsenate (ISO)

sodium arsenite (ISO)

succimer (ISO)

sunitinib (ISO)

tetrachloromethane (EXP)

tetraphene (ISO)

thiabendazole (EXP)

thioacetamide (EXP)

trichloroethene (EXP)

trichostatin A (ISO)

tris(2-butoxyethyl) phosphate (ISO)

troglitazone (ISO)

trovafloxacin (ISO)

tungsten (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

mRNA 5'-splice site recognition (IBA)

Cellular Component

commitment complex (IBA)

U1 snRNP (IBA)

U2-type prespliceosome (IBA)

Molecular Function

pre-mRNA 5'-splice site binding (IBA)

protein binding (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

Additional References at PubMed

PMID:8889548	PMID:12477932

Genomics

Comparative Map Data

Prpf39
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	6	88,825,227 - 88,851,342 (+)	NCBI		GRCr8
mRatBN7.2	6	83,088,981 - 83,113,826 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	6	83,088,986 - 83,113,825 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	6	83,448,548 - 83,473,385 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	6	83,747,910 - 83,772,747 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	6	83,189,628 - 83,214,483 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	6	86,785,793 - 86,810,806 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	6	86,785,771 - 86,810,316 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	6	96,274,772 - 96,299,877 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	6	86,385,975 - 86,412,072 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	6	86,395,686 - 86,413,568 (+)	NCBI
Celera	6	81,656,963 - 81,681,773 (+)	NCBI		Celera
Cytogenetic Map	6	q24	NCBI

PRPF39
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	14	45,084,116 - 45,116,282 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	14	45,084,107 - 45,116,282 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	14	45,553,319 - 45,585,485 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	14	44,623,052 - 44,654,554 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	14	44,623,073 - 44,654,552	NCBI
Celera	14	25,414,556 - 25,446,057 (+)	NCBI		Celera
Cytogenetic Map	14	q21.2	NCBI
HuRef	14	25,663,974 - 25,695,536 (+)	NCBI		HuRef
CHM1_1	14	45,491,468 - 45,522,951 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	14	39,276,128 - 39,308,293 (+)	NCBI		T2T-CHM13v2.0

Prpf39
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	12	65,083,094 - 65,110,160 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	12	65,083,107 - 65,110,160 (+)	Ensembl		GRCm39 Ensembl
GRCm38	12	65,036,334 - 65,063,386 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	12	65,036,333 - 65,063,386 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	12	66,137,321 - 66,164,373 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	12	65,972,667 - 65,981,991 (+)	NCBI		MGSCv36	mm8
Celera	12	66,166,020 - 66,193,073 (+)	NCBI		Celera
Cytogenetic Map	12	C1	NCBI
cM Map	12	27.21	NCBI

Prpf39
(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_004955409	16,824,638 - 16,845,778 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955409	16,824,638 - 16,845,778 (-)	NCBI	ChiLan1.0	ChiLan1.0

PRPF39
(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	15	46,256,678 - 46,288,112 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	14	45,473,188 - 45,504,622 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	14	25,700,636 - 25,732,012 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	14	44,027,452 - 44,059,865 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	14	44,027,452 - 44,059,865 (+)	Ensembl	panpan1.1		panPan2

PRPF39
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	8	22,510,816 - 22,549,481 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	8	22,511,329 - 22,549,226 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	8	22,329,071 - 22,367,476 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	8	22,670,271 - 22,708,705 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	8	22,670,294 - 22,708,701 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	8	22,332,687 - 22,371,098 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	8	22,399,191 - 22,437,601 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	8	22,735,047 - 22,773,473 (+)	NCBI		UU_Cfam_GSD_1.0

Prpf39
(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_024408640	54,494,288 - 54,526,534 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936583	4,161,945 - 4,194,699 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936583	4,162,381 - 4,194,615 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

PRPF39
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	1	175,285,270 - 175,317,298 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	1	175,285,219 - 175,317,245 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	1	195,153,563 - 195,185,567 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

PRPF39
(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	24	22,204,010 - 22,235,740 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	24	22,216,451 - 22,239,051 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666116	306,474 - 338,254 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Prpf39
(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_004624731	23,409,610 - 23,450,772 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624731	23,409,610 - 23,450,286 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Prpf39
69 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	210
Count of miRNA genes:	89
Interacting mature miRNAs:	105
Transcripts:	ENSRNOT00000065090, ENSRNOT00000066702
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
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
1576309	Emca7	Estrogen-induced mammary cancer QTL 7	4		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	6	15107216	107351382	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
4889848	Pur25	Proteinuria QTL 25	14	0.003	urine total protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	6	56728562	90198260	Rat
6893332	Cm74	Cardiac mass QTL 74	0.4	0.64	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	6	57730540	104085867	Rat
1558641	Cm47	Cardiac mass QTL 47	2.9	0.001	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	6	57730540	104085867	Rat
70176	Mcsm1	Mammary carcinoma susceptibility modifier QTL 1			mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	6	58632962	103632962	Rat
12801471	Schws9	Schwannoma susceptibility QTL 9			nervous system integrity trait (VT:0010566)	percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)	6	61747639	106747639	Rat
731173	Uae22	Urinary albumin excretion QTL 22	10.1		urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	6	65531555	140994061	Rat
2290393	Uae37	Urinary albumin excretion QTL 37		0.0001	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	6	65531555	140994061	Rat
1641904	Alcrsp4	Alcohol response QTL 4			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	6	67262953	112262953	Rat
1300075	Glom7	Glomerulus QTL 7	5.6	0.0000002	kidney glomerulus morphology trait (VT:0005325)	count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)	6	71201409	116201409	Rat
1331789	Rf37	Renal function QTL 37	3.224		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal vascular resistance (CMO:0001900)	6	72202632	115200186	Rat
70196	BpQTLcluster7	Blood pressure QTL cluster 7	6.82		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	6	72202632	117202632	Rat
724536	Uae7	Urinary albumin excretion QTL 7	3.5		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	6	72202632	130729475	Rat
1331799	Bp211	Blood pressure QTL 211	3.66407		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	6	72202632	130919985	Rat
1581550	Pur8	Proteinuria QTL 8			urine total protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	6	72227641	130729205	Rat
1581563	Uae33	Urinary albumin excretion QTL 33			urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	6	72227641	130729205	Rat
724524	Uae2	Urinary albumin excretion QTL 2	2.7	0.0005	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	6	73463459	109394713	Rat
2293837	Kiddil1	Kidney dilation QTL 1	3.7		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	6	81132889	104393926	Rat
2293842	Kiddil3	Kidney dilation QTL 3	4.3		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	6	81132889	104393926	Rat
737827	Hcar11	Hepatocarcinoma resistance QTL 11	4.4		liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	6	82523650	110548006	Rat

Markers in Region

D6Got105

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	6	83,099,031 - 83,099,256 (+)	MAPPER	mRatBN7.2
Rnor_6.0	6	86,796,011 - 86,796,235	NCBI	Rnor6.0
Rnor_5.0	6	96,284,990 - 96,285,214	UniSTS	Rnor5.0
RGSC_v3.4	6	86,396,004 - 86,396,229	RGD	RGSC3.4
RGSC_v3.4	6	86,396,005 - 86,396,229	UniSTS	RGSC3.4
RGSC_v3.1	6	86,399,461 - 86,399,685	RGD
Celera	6	81,666,988 - 81,667,212	UniSTS
RH 3.4 Map	6	549.19	UniSTS
RH 3.4 Map	6	549.19	RGD
RH 2.0 Map	6	802.0	RGD
Cytogenetic Map	6	q24	UniSTS

RH131276

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	6	83,114,912 - 83,115,062 (+)	MAPPER	mRatBN7.2
Rnor_6.0	6	86,811,893 - 86,812,042	NCBI	Rnor6.0
Rnor_5.0	6	96,300,872 - 96,301,021	UniSTS	Rnor5.0
RGSC_v3.4	6	86,411,887 - 86,412,036	UniSTS	RGSC3.4
Celera	6	81,682,860 - 81,683,009	UniSTS
RH 3.4 Map	6	564.8	UniSTS
Cytogenetic Map	6	q24	UniSTS

RH137341

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	6	83,113,518 - 83,113,706 (+)	MAPPER	mRatBN7.2
Rnor_6.0	6	86,810,499 - 86,810,686	NCBI	Rnor6.0
Rnor_5.0	6	96,299,478 - 96,299,665	UniSTS	Rnor5.0
RGSC_v3.4	6	86,410,493 - 86,410,680	UniSTS	RGSC3.4
Celera	6	81,681,466 - 81,681,653	UniSTS
RH 3.4 Map	6	564.7	UniSTS
Cytogenetic Map	6	q24	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	40	52	36	19	36	8	8	74	35	37	11	8
Low		3	5	5		5		3			4
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001108026	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_003750171	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_003754180	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006225783	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006225784	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006225785	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006225786	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006225787	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006240140	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006240141	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006240142	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006240143	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006240144	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039112247	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_063261917	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC166472	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BQ782205	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473947	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000006	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSRNOT00000066702 ⟹ ENSRNOP00000061487

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	6	83,088,986 - 83,113,825 (+)	Ensembl
Rnor_6.0 Ensembl	6	86,785,771 - 86,810,316 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000110268 ⟹ ENSRNOP00000077104

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	6	83,088,991 - 83,113,821 (+)	Ensembl

RefSeq Acc Id:

NM_001108026 ⟹ NP_001101496

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	6	88,825,240 - 88,850,078 (+)	NCBI
mRatBN7.2	6	83,088,986 - 83,113,826 (+)	NCBI

RefSeq Acc Id:

XM_006240140 ⟹ XP_006240202

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	6	88,831,786 - 88,851,342 (+)	NCBI
mRatBN7.2	6	83,089,012 - 83,113,826 (+)	NCBI
Rnor_6.0	6	86,785,800 - 86,810,806 (+)	NCBI
Rnor_5.0	6	96,274,772 - 96,299,877 (+)	NCBI

Sequence:

show sequence

GCGGTGGCAGCGGCGCTTGTGGTGGTGGCTGCGGTAGCTGAGTGAACTGAGGCATTGGCAGGCT
CATCTTTGGCGATCTTGGCCCTGGCTTCGGCTCATGGCACCGAGAAGCATCCATCGTAAGATCA
TTAACTGAAGACCAAATAAATAGCTATGCAAAATTCCCACATGGATGAGTACAGGAACTCTGAT
AATGGCAGCACAGGCAACAGTTCAGAGGTAGTGATAGAGCATCCAGATTTTAGTACTGAGATTA
TGAACGTTACGGAGATGGAGCAGTCGCCTGATGCCTCTCCCAGCGTACGTGTATCTACAGAAGA
AAACGAAATGGCAAATGCTGTGGACCTTCCAGTGACAGAAACAGAAGGAAACTTCCCTCCAGAG
TTTGAAAAATTTTGGAAAACAGTAGAAACGAATCCTCAGGATTTTACAGGATGGGTATATTTGC
TTCAGTATGTAGAACAGGAGAATCACTTGATGGCTGCCAGAAAAGCATTTGACAAATTTTTCAT
ACATTACCCGTATTGCTATGGTTACTGGAAAAAGTATGCAGACCTTGAAAAGCGACATGACAAC
ATTAAACAATCAGATGAGGTGCGTATATCAATGAATACAGTTTTCTCTGTTAGGTACTGTAAGC
CAATTAATAACAAAACAGACTTTCTTTTTCTGGCTGGCAGTACCTACCATTTATGGTCAAACTT
TTTTTATAGGGTATTTTATTTGCATTTGTCACTATTGTGGCATTTGTAGCTAATATTTTCTCTC
TTTGTTGGCAGGTGCGTTAAACTTCTACAGTTTGTCAAGCTTTGCAGTGCAAGCCTCTGTATTA
CACTGCAGCTTAACAAGTAGGGCAGGGCTTTTCTCTCACTTACATTTATTTCTCATTTTCCAAA
CAATATAGTTGGTTTGCTAGTCACATTTGCTACGTCTTATTGCATTTTTGGTCAGACGCTGTCA
TTGATGCTCTAATGGGTCTGTGCCCTATGGTCTGTAACCCAAAGCCTGCCCACACAACCCGGTC
AGAATGCAGGGACTGCTGCGCTTTGAAGATCAAGACTCTGCACGTGGGGATCAGAACATTGCCA
TGTTCTATCCAACCTCCACCCAAATGGTTTATCGACGGGGGCTTCAGGCAATACCTCTTAGTGT
TGATCTTTGGATACATTATATAAACTTCTTAAAAGAAACATTGGACCCTGGTGATCCTGAGACA
AACAGTACAATAAGAGGAACTTTTGAGCATGCTGTTCTAGCTGCAGGAACGGATTTTCGATCTG
ACAAATTATGGGAAATGTATATAAACTGGGAGAATGAACAGGGAAATCTGAGAGAAGTTACAGC
TGTATACGATCGTATTCTTGGTATTCCAACCCAGCTGTACAGTCATCATTTTCAGAGATTTAAA
GAACATGTGCAAAATAACTTGCCTAGAGATCTTTTAACTGGTGAACAGTTTATTCAGTTGAGAA
GGGAATTAGCTTCTGTAAATGGACACAATGGTGATGACGGACCTCCTGGTGATGACCTTCCATC
AGGAATTGAAGACATAACTGATCCAGCAAAGCTAATTACTGAAATAGAAAACATGAGACATAGA
ATCATTGAAATTCATCAAGAAATGTTTAATTATAATGAGCATGAAGTTAGTAAGAGGTGGACAT
TTGAAGAAGGTATTAAAAGACCTTATTTTCATGTGAAACCACTGGAAAAGGCTCAGCTAAAAAA
CTGGAAAGAATACTTAGAATTTGAAATTGAAAATGGGACTCATGAAAGAGTCGTGGTTCTCTTT
GAAAGATGTGTCATATCTTGTGCCCTCTATGAGGAGTTTTGGATTAAGTATGCCAAGTACATGG
AAAACCACAGCATTGAAGGAGTGAGGCATGTCTTCAGCAGAGCCTGTACTGTTCATCTCCCAAA
GAAGCCCATGGCGCACATGCTGTGGGCAGCTTTTGAGGAACAACAGGGGAATATTAATGAAGCC
AGGATTATCTTGAGAACGTTTGAAGAATGTGTTCTAGGATTGGCAATGGTTCGATTGCGAAGAG
TTAGTTTAGAACGACGGCATGGAAATATGGAAGAAGCTGAACATTTGCTTCAAGACGCTATAAG
GAATGCCAAATCAAATAATGAGTCATCATTTTATGCTATCAAACTAGCCCGACATCTTTTCAAA
ATACAGAAAAACCTTCCAAAATCAAGAAAGGTACTTTTGGAAGCAATCGAAAAAGATAAGGAAA
ACACAAAGTTATACCTCAATTTACTTGAAATGGAATACAGTTGTGACCTCAAGCAAAATGAAGA
AAATATCCTCAATTGCTTTGACAAAGCCATACATGGTTCGTTGCCTATTAAAATGAGAATTACG
TTTTCTCAAAGAAAAGTGGAATTCCTTGAAGATTTTGGCTCAGATGTTAATAAGCTTCTGAATG
CATATGATGAACATCAAACACTTCTAAAAGAACAGGACACTTTAAAAAGGAAAGCTGAAAATGG
CTCAGAAGAACCAGAAGAAAAGAAAGCACACACAGAAGATGTATCATCAGCACAGATCATTGAT
GGGGATTTACAGGCAAATCAAGCTGCATATAATTACAGTGCCTGGTATCAGTACAATTATCAGA
ATCCCTGGAATTACGGACAGTATTACCCTCCACCTCCAACCTGAAGGGAACACGTAAATTTCAG
ATGGCTTATATAAGACAATGTGGAACTATTTTTTTTGAAGGATGTAAAACATAGTATAAGCTTG
TTGTATTTGATAATTTGTCTTCCCAGTTTCTGTGTAACATTTATTTTATTTAGTTAATAGCAGG
AAATGTCAATTAATAGTGTATCATAGAAATTTTCCTACCATTTTTAAAATTTACTTTTTATTGA
AGAACTATTTTTTTTATTTTTATTTTTTATTTTATCGTATCTTTTTGCATTAAATGGTCTAGAA
TTCTTTTGCAGCTCATGCAGGAGATTTGTAGCCTTAACTGTAGGGGGAAAACTGACTGTAAATC
ATGTCAGTTAAAAAAGATTTTTTTGGGGAAAAAAAAGGGCTGGTTAGTGAGAATCTTGCCTCCT
ATAAAAACAGACTTTTAAAAAATTGACTTTTAACCTTAAACCCCAAAGTTATGTATATGTTTTG
ATTATACTGGGGAATTTGGTTCTAACTGCAGGATAGATGAACTGTTGACATGCACTGCCTTTGA
CTAGATAATAATGGAGAAAGTGTAATGTCAGCTTCCCCTTAAGAAATGAAATATCAAAGTATGT
TTTAGAGTTTGTATCTAGAATATTCATGTAAAACGCAAGCTTTCATTTTGATCAAATTTACCAT
TTTTGTAATAAAAATTAAGACTCACGCA

hide sequence

RefSeq Acc Id:

XM_006240141 ⟹ XP_006240203

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	6	88,831,786 - 88,851,342 (+)	NCBI
mRatBN7.2	6	83,089,012 - 83,113,826 (+)	NCBI
Rnor_6.0	6	86,785,800 - 86,810,806 (+)	NCBI
Rnor_5.0	6	96,274,772 - 96,299,877 (+)	NCBI

Sequence:

show sequence

GCGGTGGCAGCGGCGCTTGTGGTGGTGGCTGCGGTAGCTGAGTGAACTGAGGCATTGGCAGGCT
CATCTTTGGCGATCTTGGCCCTGGCTTCGGCTCATGGCACCGAGAAGCATCCATCGTAAGATCA
TTAACTGAAGACCAAATAAATAGCTATGCAAAATTCCCACATGGATGAGTACAGGAACTCTGAT
AATGGCAGCACAGGCAACAGTTCAGAGGTAGTGATAGAGCATCCAGATTTTAGTACTGAGATTA
TGAACGTTACGGAGATGGAGCAGTCGCCTGATGCCTCTCCCAGCGTACGTGTATCTACAGAAGA
AAACGAAATGGCAAATGCTGTGGACCTTCCAGTGACAGAAACAGAAGGAAACTTCCCTCCAGAG
TTTGAAAAATTTTGGAAAACAGTAGAAACGAATCCTCAGGATTTTACAGGATGGGTATATTTGC
TTCAGTATGTAGAACAGGAGAATCACTTGATGGCTGCCAGAAAAGCATTTGACAAATTTTTCAT
ACATTACCCGTATTGCTATGGTTACTGGAAAAAGTATGCAGACCTTGAAAAGCGACATGACAAC
ATTAAACAATCAGATGAGGTGCGTATATCAATGAATACAGTTTTCTCTGTTAGGTACTGTAAGC
CAATTAATAACAAAACAGACTTTCTTTTTCTGGCTGGCAGTACCTACCATTTATGGTCAAACTT
TTTTTATAGGGTATTTTATTTGCATTTGTCACTATTGTGGCATTTGTAGCTAATATTTTCTCTC
TTTGTTGGCAGGTGCGTTAAACTTCTACAGTTTGTCAAGCTTTGCAGTGCAAGCCTCTGTATTA
CACTGCAGCTTAACAAACGCTGTCATTGATGCTCTAATGGGTCTGTGCCCTATGGTCTGTAACC
CAAAGCCTGCCCACACAACCCGGTCAGAATGCAGGGACTGCTGCGCTTTGAAGATCAAGACTCT
GCACGTGGGGATCAGAACATTGCCATGTTCTATCCAACCTCCACCCAAATGGTTTATCGACGGG
GGCTTCAGGCAATACCTCTTAGTGTTGATCTTTGGATACATTATATAAACTTCTTAAAAGAAAC
ATTGGACCCTGGTGATCCTGAGACAAACAGTACAATAAGAGGAACTTTTGAGCATGCTGTTCTA
GCTGCAGGAACGGATTTTCGATCTGACAAATTATGGGAAATGTATATAAACTGGGAGAATGAAC
AGGGAAATCTGAGAGAAGTTACAGCTGTATACGATCGTATTCTTGGTATTCCAACCCAGCTGTA
CAGTCATCATTTTCAGAGATTTAAAGAACATGTGCAAAATAACTTGCCTAGAGATCTTTTAACT
GGTGAACAGTTTATTCAGTTGAGAAGGGAATTAGCTTCTGTAAATGGACACAATGGTGATGACG
GACCTCCTGGTGATGACCTTCCATCAGGAATTGAAGACATAACTGATCCAGCAAAGCTAATTAC
TGAAATAGAAAACATGAGACATAGAATCATTGAAATTCATCAAGAAATGTTTAATTATAATGAG
CATGAAGTTAGTAAGAGGTGGACATTTGAAGAAGGTATTAAAAGACCTTATTTTCATGTGAAAC
CACTGGAAAAGGCTCAGCTAAAAAACTGGAAAGAATACTTAGAATTTGAAATTGAAAATGGGAC
TCATGAAAGAGTCGTGGTTCTCTTTGAAAGATGTGTCATATCTTGTGCCCTCTATGAGGAGTTT
TGGATTAAGTATGCCAAGTACATGGAAAACCACAGCATTGAAGGAGTGAGGCATGTCTTCAGCA
GAGCCTGTACTGTTCATCTCCCAAAGAAGCCCATGGCGCACATGCTGTGGGCAGCTTTTGAGGA
ACAACAGGGGAATATTAATGAAGCCAGGATTATCTTGAGAACGTTTGAAGAATGTGTTCTAGGA
TTGGCAATGGTTCGATTGCGAAGAGTTAGTTTAGAACGACGGCATGGAAATATGGAAGAAGCTG
AACATTTGCTTCAAGACGCTATAAGGAATGCCAAATCAAATAATGAGTCATCATTTTATGCTAT
CAAACTAGCCCGACATCTTTTCAAAATACAGAAAAACCTTCCAAAATCAAGAAAGGTACTTTTG
GAAGCAATCGAAAAAGATAAGGAAAACACAAAGTTATACCTCAATTTACTTGAAATGGAATACA
GTTGTGACCTCAAGCAAAATGAAGAAAATATCCTCAATTGCTTTGACAAAGCCATACATGGTTC
GTTGCCTATTAAAATGAGAATTACGTTTTCTCAAAGAAAAGTGGAATTCCTTGAAGATTTTGGC
TCAGATGTTAATAAGCTTCTGAATGCATATGATGAACATCAAACACTTCTAAAAGAACAGGACA
CTTTAAAAAGGAAAGCTGAAAATGGCTCAGAAGAACCAGAAGAAAAGAAAGCACACACAGAAGA
TGTATCATCAGCACAGATCATTGATGGGGATTTACAGGCAAATCAAGCTGCATATAATTACAGT
GCCTGGTATCAGTACAATTATCAGAATCCCTGGAATTACGGACAGTATTACCCTCCACCTCCAA
CCTGAAGGGAACACGTAAATTTCAGATGGCTTATATAAGACAATGTGGAACTATTTTTTTTGAA
GGATGTAAAACATAGTATAAGCTTGTTGTATTTGATAATTTGTCTTCCCAGTTTCTGTGTAACA
TTTATTTTATTTAGTTAATAGCAGGAAATGTCAATTAATAGTGTATCATAGAAATTTTCCTACC
ATTTTTAAAATTTACTTTTTATTGAAGAACTATTTTTTTTATTTTTATTTTTTATTTTATCGTA
TCTTTTTGCATTAAATGGTCTAGAATTCTTTTGCAGCTCATGCAGGAGATTTGTAGCCTTAACT
GTAGGGGGAAAACTGACTGTAAATCATGTCAGTTAAAAAAGATTTTTTTGGGGAAAAAAAAGGG
CTGGTTAGTGAGAATCTTGCCTCCTATAAAAACAGACTTTTAAAAAATTGACTTTTAACCTTAA
ACCCCAAAGTTATGTATATGTTTTGATTATACTGGGGAATTTGGTTCTAACTGCAGGATAGATG
AACTGTTGACATGCACTGCCTTTGACTAGATAATAATGGAGAAAGTGTAATGTCAGCTTCCCCT
TAAGAAATGAAATATCAAAGTATGTTTTAGAGTTTGTATCTAGAATATTCATGTAAAACGCAAG
CTTTCATTTTGATCAAATTTACCATTTTTGTAATAAAAATTAAGACTCACGCA

hide sequence

RefSeq Acc Id:

XM_006240143 ⟹ XP_006240205

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	6	88,832,244 - 88,851,342 (+)	NCBI
mRatBN7.2	6	83,095,992 - 83,113,826 (+)	NCBI
Rnor_6.0	6	86,793,012 - 86,810,806 (+)	NCBI
Rnor_5.0	6	96,274,772 - 96,299,877 (+)	NCBI

Sequence:

show sequence

TTCATACATTACCCGTATTGCTATGGTTACTGGAAAAAGTATGCAGACCTTGAAAAGCGACATG
ACAACATTAAACAATCAGATGAGGTGCGTTAAACTTCTACAGTTTGTCAAGCTTTGCAGTGCAA
GCCTCTGTATTACACTGCAGCTTAACAAACGCTGTCATTGATGCTCTAATGGGTCTGTGCCCTA
TGGTCTGTAACCCAAAGCCTGCCCACACAACCCGGTCAGAATGCAGGGACTGCTGCGCTTTGAA
GATCAAGACTCTGCACGTGGGGATCAGAACATTGCCATGTTCTATCCAACCTCCACCCAAATGG
TTTATCGACGGGGGCTTCAGGCAATACCTCTTAGTGTTGATCTTTGGATACATTATATAAACTT
CTTAAAAGAAACATTGGACCCTGGTGATCCTGAGACAAACAGTACAATAAGAGGAACTTTTGAG
CATGCTGTTCTAGCTGCAGGAACGGATTTTCGATCTGACAAATTATGGGAAATGTATATAAACT
GGGAGAATGAACAGGGAAATCTGAGAGAAGTTACAGCTGTATACGATCGTATTCTTGGTATTCC
AACCCAGCTGTACAGTCATCATTTTCAGAGATTTAAAGAACATGTGCAAAATAACTTGCCTAGA
GATCTTTTAACTGGTGAACAGTTTATTCAGTTGAGAAGGGAATTAGCTTCTGTAAATGGACACA
ATGGTGATGACGGACCTCCTGGTGATGACCTTCCATCAGGAATTGAAGACATAACTGATCCAGC
AAAGCTAATTACTGAAATAGAAAACATGAGACATAGAATCATTGAAATTCATCAAGAAATGTTT
AATTATAATGAGCATGAAGTTAGTAAGAGGTGGACATTTGAAGAAGGTATTAAAAGACCTTATT
TTCATGTGAAACCACTGGAAAAGGCTCAGCTAAAAAACTGGAAAGAATACTTAGAATTTGAAAT
TGAAAATGGGACTCATGAAAGAGTCGTGGTTCTCTTTGAAAGATGTGTCATATCTTGTGCCCTC
TATGAGGAGTTTTGGATTAAGTATGCCAAGTACATGGAAAACCACAGCATTGAAGGAGTGAGGC
ATGTCTTCAGCAGAGCCTGTACTGTTCATCTCCCAAAGAAGCCCATGGCGCACATGCTGTGGGC
AGCTTTTGAGGAACAACAGGGGAATATTAATGAAGCCAGGATTATCTTGAGAACGTTTGAAGAA
TGTGTTCTAGGATTGGCAATGGTTCGATTGCGAAGAGTTAGTTTAGAACGACGGCATGGAAATA
TGGAAGAAGCTGAACATTTGCTTCAAGACGCTATAAGGAATGCCAAATCAAATAATGAGTCATC
ATTTTATGCTATCAAACTAGCCCGACATCTTTTCAAAATACAGAAAAACCTTCCAAAATCAAGA
AAGGTACTTTTGGAAGCAATCGAAAAAGATAAGGAAAACACAAAGTTATACCTCAATTTACTTG
AAATGGAATACAGTTGTGACCTCAAGCAAAATGAAGAAAATATCCTCAATTGCTTTGACAAAGC
CATACATGGTTCGTTGCCTATTAAAATGAGAATTACGTTTTCTCAAAGAAAAGTGGAATTCCTT
GAAGATTTTGGCTCAGATGTTAATAAGCTTCTGAATGCATATGATGAACATCAAACACTTCTAA
AAGAACAGGACACTTTAAAAAGGAAAGCTGAAAATGGCTCAGAAGAACCAGAAGAAAAGAAAGC
ACACACAGAAGATGTATCATCAGCACAGATCATTGATGGGGATTTACAGGCAAATCAAGCTGCA
TATAATTACAGTGCCTGGTATCAGTACAATTATCAGAATCCCTGGAATTACGGACAGTATTACC
CTCCACCTCCAACCTGAAGGGAACACGTAAATTTCAGATGGCTTATATAAGACAATGTGGAACT
ATTTTTTTTGAAGGATGTAAAACATAGTATAAGCTTGTTGTATTTGATAATTTGTCTTCCCAGT
TTCTGTGTAACATTTATTTTATTTAGTTAATAGCAGGAAATGTCAATTAATAGTGTATCATAGA
AATTTTCCTACCATTTTTAAAATTTACTTTTTATTGAAGAACTATTTTTTTTATTTTTATTTTT
TATTTTATCGTATCTTTTTGCATTAAATGGTCTAGAATTCTTTTGCAGCTCATGCAGGAGATTT
GTAGCCTTAACTGTAGGGGGAAAACTGACTGTAAATCATGTCAGTTAAAAAAGATTTTTTTGGG
GAAAAAAAAGGGCTGGTTAGTGAGAATCTTGCCTCCTATAAAAACAGACTTTTAAAAAATTGAC
TTTTAACCTTAAACCCCAAAGTTATGTATATGTTTTGATTATACTGGGGAATTTGGTTCTAACT
GCAGGATAGATGAACTGTTGACATGCACTGCCTTTGACTAGATAATAATGGAGAAAGTGTAATG
TCAGCTTCCCCTTAAGAAATGAAATATCAAAGTATGTTTTAGAGTTTGTATCTAGAATATTCAT
GTAAAACGCAAGCTTTCATTTTGATCAAATTTACCATTTTTGTAATAAAAATTAAGACTCACGC
A

hide sequence

RefSeq Acc Id:

XM_006240144 ⟹ XP_006240206

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	6	88,832,246 - 88,851,342 (+)	NCBI
mRatBN7.2	6	83,095,990 - 83,113,826 (+)	NCBI
Rnor_6.0	6	86,793,007 - 86,810,806 (+)	NCBI
Rnor_5.0	6	96,274,772 - 96,299,877 (+)	NCBI

Sequence:

show sequence

AATTTTTCATACATTACCCGTATTGCTATGGTTACTGGAAAAAGTATGCAGACCTTGAAAAGCG
ACATGACAACATTAAACAATCAGATGAGACGCTGTCATTGATGCTCTAATGGGTCTGTGCCCTA
TGGTCTGTAACCCAAAGCCTGCCCACACAACCCGGTCAGAATGCAGGGACTGCTGCGCTTTGAA
GATCAAGACTCTGCACGTGGGGATCAGAACATTGCCATGTTCTATCCAACCTCCACCCAAATGG
TTTATCGACGGGGGCTTCAGGCAATACCTCTTAGTGTTGATCTTTGGATACATTATATAAACTT
CTTAAAAGAAACATTGGACCCTGGTGATCCTGAGACAAACAGTACAATAAGAGGAACTTTTGAG
CATGCTGTTCTAGCTGCAGGAACGGATTTTCGATCTGACAAATTATGGGAAATGTATATAAACT
GGGAGAATGAACAGGGAAATCTGAGAGAAGTTACAGCTGTATACGATCGTATTCTTGGTATTCC
AACCCAGCTGTACAGTCATCATTTTCAGAGATTTAAAGAACATGTGCAAAATAACTTGCCTAGA
GATCTTTTAACTGGTGAACAGTTTATTCAGTTGAGAAGGGAATTAGCTTCTGTAAATGGACACA
ATGGTGATGACGGACCTCCTGGTGATGACCTTCCATCAGGAATTGAAGACATAACTGATCCAGC
AAAGCTAATTACTGAAATAGAAAACATGAGACATAGAATCATTGAAATTCATCAAGAAATGTTT
AATTATAATGAGCATGAAGTTAGTAAGAGGTGGACATTTGAAGAAGGTATTAAAAGACCTTATT
TTCATGTGAAACCACTGGAAAAGGCTCAGCTAAAAAACTGGAAAGAATACTTAGAATTTGAAAT
TGAAAATGGGACTCATGAAAGAGTCGTGGTTCTCTTTGAAAGATGTGTCATATCTTGTGCCCTC
TATGAGGAGTTTTGGATTAAGTATGCCAAGTACATGGAAAACCACAGCATTGAAGGAGTGAGGC
ATGTCTTCAGCAGAGCCTGTACTGTTCATCTCCCAAAGAAGCCCATGGCGCACATGCTGTGGGC
AGCTTTTGAGGAACAACAGGGGAATATTAATGAAGCCAGGATTATCTTGAGAACGTTTGAAGAA
TGTGTTCTAGGATTGGCAATGGTTCGATTGCGAAGAGTTAGTTTAGAACGACGGCATGGAAATA
TGGAAGAAGCTGAACATTTGCTTCAAGACGCTATAAGGAATGCCAAATCAAATAATGAGTCATC
ATTTTATGCTATCAAACTAGCCCGACATCTTTTCAAAATACAGAAAAACCTTCCAAAATCAAGA
AAGGTACTTTTGGAAGCAATCGAAAAAGATAAGGAAAACACAAAGTTATACCTCAATTTACTTG
AAATGGAATACAGTTGTGACCTCAAGCAAAATGAAGAAAATATCCTCAATTGCTTTGACAAAGC
CATACATGGTTCGTTGCCTATTAAAATGAGAATTACGTTTTCTCAAAGAAAAGTGGAATTCCTT
GAAGATTTTGGCTCAGATGTTAATAAGCTTCTGAATGCATATGATGAACATCAAACACTTCTAA
AAGAACAGGACACTTTAAAAAGGAAAGCTGAAAATGGCTCAGAAGAACCAGAAGAAAAGAAAGC
ACACACAGAAGATGTATCATCAGCACAGATCATTGATGGGGATTTACAGGCAAATCAAGCTGCA
TATAATTACAGTGCCTGGTATCAGTACAATTATCAGAATCCCTGGAATTACGGACAGTATTACC
CTCCACCTCCAACCTGAAGGGAACACGTAAATTTCAGATGGCTTATATAAGACAATGTGGAACT
ATTTTTTTTGAAGGATGTAAAACATAGTATAAGCTTGTTGTATTTGATAATTTGTCTTCCCAGT
TTCTGTGTAACATTTATTTTATTTAGTTAATAGCAGGAAATGTCAATTAATAGTGTATCATAGA
AATTTTCCTACCATTTTTAAAATTTACTTTTTATTGAAGAACTATTTTTTTTATTTTTATTTTT
TATTTTATCGTATCTTTTTGCATTAAATGGTCTAGAATTCTTTTGCAGCTCATGCAGGAGATTT
GTAGCCTTAACTGTAGGGGGAAAACTGACTGTAAATCATGTCAGTTAAAAAAGATTTTTTTGGG
GAAAAAAAAGGGCTGGTTAGTGAGAATCTTGCCTCCTATAAAAACAGACTTTTAAAAAATTGAC
TTTTAACCTTAAACCCCAAAGTTATGTATATGTTTTGATTATACTGGGGAATTTGGTTCTAACT
GCAGGATAGATGAACTGTTGACATGCACTGCCTTTGACTAGATAATAATGGAGAAAGTGTAATG
TCAGCTTCCCCTTAAGAAATGAAATATCAAAGTATGTTTTAGAGTTTGTATCTAGAATATTCAT
GTAAAACGCAAGCTTTCATTTTGATCAAATTTACCATTTTTGTAATAAAAATTAAGACTCACGC
A

hide sequence

RefSeq Acc Id:

XM_039112247 ⟹ XP_038968175

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	6	88,825,227 - 88,844,019 (+)	NCBI
mRatBN7.2	6	83,088,981 - 83,107,673 (+)	NCBI

RefSeq Acc Id:

XM_063261917 ⟹ XP_063117987

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	6	88,825,227 - 88,844,019 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_001101496	(Get FASTA)	NCBI Sequence Viewer
	XP_006240202	(Get FASTA)	NCBI Sequence Viewer
	XP_006240203	(Get FASTA)	NCBI Sequence Viewer
	XP_006240205	(Get FASTA)	NCBI Sequence Viewer
	XP_006240206	(Get FASTA)	NCBI Sequence Viewer
	XP_038968175	(Get FASTA)	NCBI Sequence Viewer
	XP_063117987	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDM03483	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000061487
	ENSRNOP00000061487.1
	ENSRNOP00000077104.1

RefSeq Acc Id:	XP_006240202 ⟸ XM_006240140
- Peptide Label:	isoform X1
- UniProtKB:	A0A8I5YBM8 (UniProtKB/TrEMBL)
- Sequence:	show sequence MQGLLRFEDQDSARGDQNIAMFYPTSTQMVYRRGLQAIPLSVDLWIHYINFLKETLDPGDPETN STIRGTFEHAVLAAGTDFRSDKLWEMYINWENEQGNLREVTAVYDRILGIPTQLYSHHFQRFKE HVQNNLPRDLLTGEQFIQLRRELASVNGHNGDDGPPGDDLPSGIEDITDPAKLITEIENMRHRI IEIHQEMFNYNEHEVSKRWTFEEGIKRPYFHVKPLEKAQLKNWKEYLEFEIENGTHERVVVLFE RCVISCALYEEFWIKYAKYMENHSIEGVRHVFSRACTVHLPKKPMAHMLWAAFEEQQGNINEAR IILRTFEECVLGLAMVRLRRVSLERRHGNMEEAEHLLQDAIRNAKSNNESSFYAIKLARHLFKI QKNLPKSRKVLLEAIEKDKENTKLYLNLLEMEYSCDLKQNEENILNCFDKAIHGSLPIKMRITF SQRKVEFLEDFGSDVNKLLNAYDEHQTLLKEQDTLKRKAENGSEEPEEKKAHTEDVSSAQIIDG DLQANQAAYNYSAWYQYNYQNPWNYGQYYPPPPT hide sequence

RefSeq Acc Id:	XP_006240203 ⟸ XM_006240141
- Peptide Label:	isoform X1
- UniProtKB:	A0A8I5YBM8 (UniProtKB/TrEMBL)
- Sequence:	show sequence MQGLLRFEDQDSARGDQNIAMFYPTSTQMVYRRGLQAIPLSVDLWIHYINFLKETLDPGDPETN STIRGTFEHAVLAAGTDFRSDKLWEMYINWENEQGNLREVTAVYDRILGIPTQLYSHHFQRFKE HVQNNLPRDLLTGEQFIQLRRELASVNGHNGDDGPPGDDLPSGIEDITDPAKLITEIENMRHRI IEIHQEMFNYNEHEVSKRWTFEEGIKRPYFHVKPLEKAQLKNWKEYLEFEIENGTHERVVVLFE RCVISCALYEEFWIKYAKYMENHSIEGVRHVFSRACTVHLPKKPMAHMLWAAFEEQQGNINEAR IILRTFEECVLGLAMVRLRRVSLERRHGNMEEAEHLLQDAIRNAKSNNESSFYAIKLARHLFKI QKNLPKSRKVLLEAIEKDKENTKLYLNLLEMEYSCDLKQNEENILNCFDKAIHGSLPIKMRITF SQRKVEFLEDFGSDVNKLLNAYDEHQTLLKEQDTLKRKAENGSEEPEEKKAHTEDVSSAQIIDG DLQANQAAYNYSAWYQYNYQNPWNYGQYYPPPPT hide sequence

RefSeq Acc Id:	XP_006240206 ⟸ XM_006240144
- Peptide Label:	isoform X1
- UniProtKB:	A0A8I5YBM8 (UniProtKB/TrEMBL)
- Sequence:	show sequence MQGLLRFEDQDSARGDQNIAMFYPTSTQMVYRRGLQAIPLSVDLWIHYINFLKETLDPGDPETN STIRGTFEHAVLAAGTDFRSDKLWEMYINWENEQGNLREVTAVYDRILGIPTQLYSHHFQRFKE HVQNNLPRDLLTGEQFIQLRRELASVNGHNGDDGPPGDDLPSGIEDITDPAKLITEIENMRHRI IEIHQEMFNYNEHEVSKRWTFEEGIKRPYFHVKPLEKAQLKNWKEYLEFEIENGTHERVVVLFE RCVISCALYEEFWIKYAKYMENHSIEGVRHVFSRACTVHLPKKPMAHMLWAAFEEQQGNINEAR IILRTFEECVLGLAMVRLRRVSLERRHGNMEEAEHLLQDAIRNAKSNNESSFYAIKLARHLFKI QKNLPKSRKVLLEAIEKDKENTKLYLNLLEMEYSCDLKQNEENILNCFDKAIHGSLPIKMRITF SQRKVEFLEDFGSDVNKLLNAYDEHQTLLKEQDTLKRKAENGSEEPEEKKAHTEDVSSAQIIDG DLQANQAAYNYSAWYQYNYQNPWNYGQYYPPPPT hide sequence

RefSeq Acc Id:	XP_006240205 ⟸ XM_006240143
- Peptide Label:	isoform X1
- UniProtKB:	A0A8I5YBM8 (UniProtKB/TrEMBL)
- Sequence:	show sequence MQGLLRFEDQDSARGDQNIAMFYPTSTQMVYRRGLQAIPLSVDLWIHYINFLKETLDPGDPETN STIRGTFEHAVLAAGTDFRSDKLWEMYINWENEQGNLREVTAVYDRILGIPTQLYSHHFQRFKE HVQNNLPRDLLTGEQFIQLRRELASVNGHNGDDGPPGDDLPSGIEDITDPAKLITEIENMRHRI IEIHQEMFNYNEHEVSKRWTFEEGIKRPYFHVKPLEKAQLKNWKEYLEFEIENGTHERVVVLFE RCVISCALYEEFWIKYAKYMENHSIEGVRHVFSRACTVHLPKKPMAHMLWAAFEEQQGNINEAR IILRTFEECVLGLAMVRLRRVSLERRHGNMEEAEHLLQDAIRNAKSNNESSFYAIKLARHLFKI QKNLPKSRKVLLEAIEKDKENTKLYLNLLEMEYSCDLKQNEENILNCFDKAIHGSLPIKMRITF SQRKVEFLEDFGSDVNKLLNAYDEHQTLLKEQDTLKRKAENGSEEPEEKKAHTEDVSSAQIIDG DLQANQAAYNYSAWYQYNYQNPWNYGQYYPPPPT hide sequence

RefSeq Acc Id:

ENSRNOP00000061487 ⟸ ENSRNOT00000066702

RefSeq Acc Id:	XP_038968175 ⟸ XM_039112247
- Peptide Label:	isoform X2

RefSeq Acc Id:	NP_001101496 ⟸ NM_001108026
- UniProtKB:	D4A5S9 (UniProtKB/TrEMBL)

RefSeq Acc Id:

ENSRNOP00000077104 ⟸ ENSRNOT00000110268

RefSeq Acc Id:	XP_063117987 ⟸ XM_063261917
- Peptide Label:	isoform X2

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-D4A5S9-F1-model_v2	AlphaFold	D4A5S9	1-664	view protein structure

Transcriptome

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

Promoters

RGD ID:

13694627

Promoter ID:

EPDNEW_R5149

Type:

multiple initiation site

Name:

Prpf39_1

Description:

pre-mRNA processing factor 39

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	6	86,785,782 - 86,785,842	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1308702	AgrOrtholog
BioCyc Gene	G2FUF-37331	BioCyc
Ensembl Genes	ENSRNOG00000004521	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000066702	ENTREZGENE
	ENSRNOT00000066702.5	UniProtKB/TrEMBL
	ENSRNOT00000110268.1	UniProtKB/TrEMBL
Gene3D-CATH	1.25.40.10	UniProtKB/TrEMBL
InterPro	HAT	UniProtKB/TrEMBL
	TPR-like_helical	UniProtKB/TrEMBL
NCBI Gene	314171	ENTREZGENE
PANTHER	PRE-MRNA PROCESSING PROTEIN PRP39-RELATED	UniProtKB/TrEMBL
	PRE-MRNA-PROCESSING FACTOR 39	UniProtKB/TrEMBL
PhenoGen	Prpf39	PhenoGen
RatGTEx	ENSRNOG00000004521	RatGTEx
SMART	HAT	UniProtKB/TrEMBL
Superfamily-SCOP	SSF48452	UniProtKB/TrEMBL
UniProt	A0A8I5YBM8	ENTREZGENE, UniProtKB/TrEMBL
	D4A5S9	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2013-11-19	Prpf39	pre-mRNA processing factor 39	Prpf39	PRP39 pre-mRNA processing factor 39 homolog (S. cerevisiae)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-10-24	Prpf39	PRP39 pre-mRNA processing factor 39 homolog (S. cerevisiae)	Prpf39	PRP39 pre-mRNA processing factor 39 homolog (yeast)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-04-30	Prpf39	PRP39 pre-mRNA processing factor 39 homolog (yeast)	Prpf39_predicted	PRP39 pre-mRNA processing factor 39 homolog (yeast) (predicted)	'predicted' is removed	2292626	APPROVED
2005-01-12	Prpf39_predicted	PRP39 pre-mRNA processing factor 39 homolog (yeast) (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)

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