Snrnp40 (small nuclear ribonucleoprotein U5 subunit 40)

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Gene: Snrnp40 (small nuclear ribonucleoprotein U5 subunit 40) Rattus norvegicus

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Symbol:

Snrnp40

Name:

small nuclear ribonucleoprotein U5 subunit 40

RGD ID:

1309198

Description:

Predicted to be located in cytosol and nuclear speck. Predicted to be part of U2-type catalytic step 2 spliceosome and U4/U6 x U5 tri-snRNP complex. Orthologous to human SNRNP40 (small nuclear ribonucleoprotein U5 subunit 40); PARTICIPATES IN spliceosome pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acrylamide; bisphenol A.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

hypothetical protein LOC313056; LOC313056; RGD1309198; similar to U5 snRNP-specific protein (Prp8-binding); small nuclear ribonucleoprotein 40 (U5); U5 small nuclear ribonucleoprotein 40 kDa protein

RGD Orthologs

Alliance Orthologs

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):	SNRNP40 (small nuclear ribonucleoprotein U5 subunit 40)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, Panther, Treefam
Mus musculus (house mouse):	Snrnp40 (small nuclear ribonucleoprotein 40 (U5))	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Snrnp40 (small nuclear ribonucleoprotein U5 subunit 40)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	SNRNP40 (small nuclear ribonucleoprotein U5 subunit 40)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	SNRNP40 (small nuclear ribonucleoprotein U5 subunit 40)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Snrnp40 (small nuclear ribonucleoprotein U5 subunit 40)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	SNRNP40 (small nuclear ribonucleoprotein U5 subunit 40)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	SNRNP40 (small nuclear ribonucleoprotein U5 subunit 40)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Snrnp40 (small nuclear ribonucleoprotein U5 subunit 40)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Mus musculus (house mouse):	Snrnp40 (small nuclear ribonucleoprotein 40 (U5))	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Homo sapiens (human):	SNRNP40 (small nuclear ribonucleoprotein U5 subunit 40)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	snrnp40 (small nuclear ribonucleoprotein 40 (U5))	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	CG3436	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	snrp-40.1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	snrp-40.2	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	snrnp40	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	5	147,984,758 - 148,017,932 (+)	NCBI		GRCr8
mRatBN7.2	5	142,700,632 - 142,733,776 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	5	142,700,534 - 142,733,776 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	5	145,399,899 - 145,433,055 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	5	147,169,704 - 147,202,862 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	5	147,166,681 - 147,199,678 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	5	148,577,498 - 148,610,658 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	5	148,577,332 - 148,610,639 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	5	152,294,724 - 152,327,111 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	149,388,592 - 149,422,973 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	5	149,398,415 - 149,425,950 (+)	NCBI
Celera	5	141,166,979 - 141,199,871 (+)	NCBI		Celera
Cytogenetic Map	5	q36	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(-)-epigallocatechin 3-gallate (ISO)

1,2-dimethylhydrazine (ISO)

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

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

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

2,4,6-tribromophenol (ISO)

3,3',5,5'-tetrabromobisphenol A (ISO)

3-isobutyl-1-methyl-7H-xanthine (ISO)

4,4'-sulfonyldiphenol (ISO)

acrylamide (EXP)

benzo[a]pyrene (ISO)

benzo[a]pyrene diol epoxide I (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

caffeine (ISO)

captan (ISO)

CGP 52608 (ISO)

cisplatin (ISO)

clobetasol (ISO)

copper(II) sulfate (ISO)

DDE (ISO)

decabromodiphenyl ether (ISO)

dexamethasone (ISO)

Dibutyl phosphate (ISO)

dibutyl phthalate (ISO)

folic acid (ISO)

fulvestrant (ISO)

indometacin (ISO)

ivermectin (ISO)

methapyrilene (EXP)

N-methyl-4-phenylpyridinium (ISO)

nickel atom (ISO)

paracetamol (EXP)

piroxicam (ISO)

potassium chromate (ISO)

sodium arsenite (ISO)

sodium dichromate (ISO)

temozolomide (ISO)

testosterone (ISO)

tetrachloromethane (ISO)

triptonide (ISO)

tungsten (ISO)

urethane (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Cellular Component

catalytic step 2 spliceosome (IBA,ISO)

cytosol (IEA,ISO)

nuclear speck (IEA,ISO)

U2-type catalytic step 2 spliceosome (ISO)

U4/U6 x U5 tri-snRNP complex (ISO)

Molecular Function

protein binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

spliceosome pathway (IEA)

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.	KEGG Annotation Import Pipeline	Pipeline to import KEGG annotations from KEGG into RGD
3.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:11991638	PMID:22658674	PMID:28076346	PMID:31505169

Genomics

Comparative Map Data

Snrnp40
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	5	147,984,758 - 148,017,932 (+)	NCBI		GRCr8
mRatBN7.2	5	142,700,632 - 142,733,776 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	5	142,700,534 - 142,733,776 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	5	145,399,899 - 145,433,055 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	5	147,169,704 - 147,202,862 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	5	147,166,681 - 147,199,678 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	5	148,577,498 - 148,610,658 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	5	148,577,332 - 148,610,639 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	5	152,294,724 - 152,327,111 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	149,388,592 - 149,422,973 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	5	149,398,415 - 149,425,950 (+)	NCBI
Celera	5	141,166,979 - 141,199,871 (+)	NCBI		Celera
Cytogenetic Map	5	q36	NCBI

SNRNP40
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	1	31,259,568 - 31,296,788 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	1	31,259,568 - 31,296,788 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	1	31,732,415 - 31,769,635 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	1	31,505,002 - 31,542,231 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Celera	1	29,988,910 - 30,026,143 (-)	NCBI		Celera
Cytogenetic Map	1	p35.2	NCBI
HuRef	1	29,838,837 - 29,876,344 (-)	NCBI		HuRef
CHM1_1	1	31,848,319 - 31,885,550 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	1	31,111,784 - 31,149,010 (-)	NCBI		T2T-CHM13v2.0

Snrnp40
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	4	130,253,925 - 130,283,826 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	4	130,253,925 - 130,283,819 (+)	Ensembl		GRCm39 Ensembl
GRCm38	4	130,360,132 - 130,390,033 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	4	130,360,132 - 130,390,026 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	4	130,037,379 - 130,067,281 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	4	130,037,379 - 130,067,281 (+)	NCBI		MGSCv36	mm8
Celera	4	128,693,024 - 128,724,145 (+)	NCBI		Celera
Cytogenetic Map	4	D2.2	NCBI
cM Map	4	63.43	NCBI

Snrnp40
(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_004955452	9,759,452 - 9,793,105 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955452	9,759,452 - 9,793,105 (-)	NCBI	ChiLan1.0	ChiLan1.0

SNRNP40
(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	1	195,536,864 - 195,574,025 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	1	194,655,594 - 194,692,819 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	1	30,539,536 - 30,576,753 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	1	31,559,860 - 31,597,076 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	1	31,559,860 - 31,597,076 (-)	Ensembl	panpan1.1		panPan2

SNRNP40
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	2	69,721,065 - 69,761,306 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	2	69,721,087 - 69,804,165 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	2	66,299,527 - 66,339,486 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	2	70,285,409 - 70,325,441 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	2	70,285,431 - 70,325,441 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	2	67,121,212 - 67,161,195 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	2	68,117,918 - 68,157,891 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	2	69,117,581 - 69,157,599 (+)	NCBI		UU_Cfam_GSD_1.0

Snrnp40
(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_024405058	48,664,879 - 48,700,078 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936474	14,488,327 - 14,524,883 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936474	14,489,657 - 14,524,858 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SNRNP40
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	6	87,839,337 - 87,879,570 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	6	87,838,894 - 87,879,623 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	6	81,545,687 - 81,586,288 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

SNRNP40
(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	20	101,540,827 - 101,580,298 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	20	101,540,948 - 101,580,542 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666033	15,081,984 - 15,133,462 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Snrnp40
(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_004624764	14,621,002 - 14,649,695 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624764	14,620,494 - 14,649,768 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Snrnp40
247 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	41
Count of miRNA genes:	41
Interacting mature miRNAs:	41
Transcripts:	ENSRNOT00000016325
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
1331796	Thshl2	Thyroid stimulating hormone level QTL 2	2.3		blood thyroid-stimulating hormone amount (VT:0005119)	serum thyroid stimulating hormone level (CMO:0001248)	5	97059760	147465714	Rat
10053720	Scort26	Serum corticosterone level QTL 26	2.06	0.0147	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	5	124965598	166875058	Rat
1549845	Scl44	Serum cholesterol level QTL 44	6		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	5	40128307	148607290	Rat
8552960	Pigfal15	Plasma insulin-like growth factor 1 level QTL 15			blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	5	111416838	156416838	Rat
631562	Apr2	Acute phase response QTL 2	3.7		blood murinoglobulin 1 amount (VT:0010597)	plasma murinoglobulin 1 level (CMO:0001931)	5	135927956	166875058	Rat
61444	Strs2	Sensitivity to stroke QTL 2	4.7		cerebrum integrity trait (VT:0010549)	post-insult time to onset of cerebrovascular lesion (CMO:0002343)	5	135929696	166875058	Rat
61452	Ciaa5	CIA Autoantibody QTL 5	3.5		blood autoantibody amount (VT:0003725)	calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)	5	94858972	143070159	Rat
70156	Niddm30	Non-insulin dependent diabetes mellitus QTL 30	3.98		blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	5	129132447	151006154	Rat
8552908	Pigfal4	Plasma insulin-like growth factor 1 level QTL 4	6.6		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	5	128506074	166875058	Rat
1331803	Rf32	Renal function QTL 32	2.798		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal vascular resistance (CMO:0001900)	5	129132428	143070159	Rat
61393	Bp7	Blood pressure QTL 7	4.5	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	60293434	161481680	Rat
7794791	Mcs33	Mammary carcinoma susceptibility QTL 33	1.93		mammary gland integrity trait (VT:0010552)	mammary tumor incidence/prevalence measurement (CMO:0000946)	5	131345754	166875058	Rat
7207486	Bss109	Bone structure and strength QTL 109			femur strength trait (VT:0010010)	femur total energy absorbed before break (CMO:0001677)	5	106906205	151906205	Rat
7207481	Bss106	Bone structure and strength QTL 106	7.9		femur strength trait (VT:0010010)	femur ultimate force (CMO:0001675)	5	106906205	151906205	Rat
1302790	Scl20	Serum cholesterol level QTL 20	6.4	0.0001	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	82394392	166664054	Rat
1598861	Cm64	Cardiac mass QTL 64	2.9		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	5	127798274	166875058	Rat
1578766	Tcas11	Tongue tumor susceptibility QTL 11	4.12		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	5	46711509	161317411	Rat
631505	Bp103	Blood pressure QTL 103	3.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	132717196	165560427	Rat
1549838	Bss4	Bone structure and strength QTL 4	9.2		femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	5	106906205	151906205	Rat
1641920	Colcs1	Colorectal carcinoma susceptibility QTL 1	2.99	0.0055	intestine integrity trait (VT:0010554)	benign colorectal tumor surface area measurement (CMO:0001799)	5	121846814	166846814	Rat
8694169	Bw148	Body weight QTL 148	5	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	5	128506074	166875058	Rat
8657050	Bw146	Body weight QTL 146	19.84	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	5	108938288	153938288	Rat
1581510	Cm54	Cardiac mass QTL 54	3.4	0.05	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	5	120740824	143608494	Rat
1576314	Eutr1	Estrogen induced uterine response QTL 1			uterus integrity trait (VT:0010575)	pyometritis severity score (CMO:0002009)	5	2138965	166875058	Rat
2317056	Wbc3	White blood cell count QTL 3	2.51	0.01	leukocyte quantity (VT:0000217)	white blood cell count (CMO:0000027)	5	105999803	150999803	Rat
634349	Bp139	Blood pressure QTL 139		0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	128924607	166875058	Rat
724525	Bp147	Blood pressure QTL 147	4.3	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	126424772	166875058	Rat
1598847	Cm62	Cardiac mass QTL 62	3.4		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	5	108845856	153845856	Rat
2293642	Bss37	Bone structure and strength QTL 37	4.64	0.0001	femur strength trait (VT:0010010)	femur ultimate force (CMO:0001675)	5	120740824	151018848	Rat
1578673	Bmd13	Bone mineral density QTL 13	4.9		femur mineral mass (VT:0010011)	trabecular volumetric bone mineral density (CMO:0001729)	5	103689353	148689353	Rat
738018	Anxrr4	Anxiety related response QTL 4	5.1		exploratory behavior trait (VT:0010471)	percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)	5	130130159	166875058	Rat
7207488	Bss110	Bone structure and strength QTL 1	8.4		femur strength trait (VT:0010010)	femur stiffness (CMO:0001674)	5	106906205	151906205	Rat
8694441	Bw169	Body weight QTL 169	17.61	0.001	retroperitoneal fat pad mass (VT:0010430)	retroperitoneal fat pad weight to body weight ratio (CMO:0000635)	5	111416838	156416838	Rat
7207491	Bss112	Bone structure and strength QTL 112	7		femur morphology trait (VT:0000559)	femur midshaft cortical cross-sectional area (CMO:0001663)	5	106906205	151906205	Rat
8694389	Bw160	Body weight QTL 160	6.17	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	5	111416838	156416838	Rat
61426	Scl2	Serum cholesterol level QTL 2	7.3	0.001	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	5	59793399	143070159	Rat
1354598	Srn6	Serum renin concentration QTL 6	3.8		blood renin amount (VT:0003349)	plasma renin activity level (CMO:0000116)	5	69540295	151018848	Rat
8694198	Abfw3	Abdominal fat weight QTL 3	16.13	0.001	visceral adipose mass (VT:0010063)	abdominal fat pad weight to body weight ratio (CMO:0000095)	5	111416838	156416838	Rat
1298089	Scl14	Serum cholesterol level QTL 14	5.8	0.0004	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	108845856	153845856	Rat
1598819	Bp292	Blood pressure QTL 292	4.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	127798274	166875058	Rat
1358187	Emca1	Estrogen-induced mammary cancer QTL 1	4.4		mammary gland integrity trait (VT:0010552)	post-insult time to mammary tumor formation (CMO:0000345)	5	99216724	148607142	Rat

Markers in Region

RH128769

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	5	142,733,525 - 142,733,723 (+)	MAPPER	mRatBN7.2
Rnor_6.0	5	148,610,408 - 148,610,605	NCBI	Rnor6.0
Rnor_5.0	5	152,326,861 - 152,327,058	UniSTS	Rnor5.0
RGSC_v3.4	5	149,422,723 - 149,422,920	UniSTS	RGSC3.4
Celera	5	141,199,621 - 141,199,818	UniSTS
Cytogenetic Map	5	q36	UniSTS

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Download All Expressed Objects for this Gene

alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	nervous system	renal system	reproductive system	respiratory system
9	11	49	113	91	90	59	25	59	6	218	97	93	45	60	31

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001134556	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039109799	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_063287574	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH473968	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000005	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000016325 ⟹ ENSRNOP00000016325

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	5	142,700,534 - 142,733,776 (+)	Ensembl
Rnor_6.0 Ensembl	5	148,577,332 - 148,610,639 (+)	Ensembl

RefSeq Acc Id:

NM_001134556 ⟹ NP_001128028

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	5	147,984,790 - 148,017,932 (+)	NCBI
mRatBN7.2	5	142,700,632 - 142,733,776 (+)	NCBI
Rnor_6.0	5	148,577,498 - 148,610,658 (+)	NCBI
Rnor_5.0	5	152,294,724 - 152,327,111 (+)	NCBI
RGSC_v3.4	5	149,388,592 - 149,422,973 (+)	RGD
Celera	5	141,166,979 - 141,199,871 (+)	RGD

Sequence:

show sequence

GCGCGGTTACTGGCGGCGCCGAGGGTAGTGGTTGCCGCCATGATCGAGCAGCAGAAACGCAAGG
GCCCAGAGCTACCCCTGGTTCCCGTCAAGCGGCCGCGACATGAGTTGCTGTTGGGAGCCGCAGG
ATCCGGCCCCGGAGCCGGGCAACAGCAGGCGACTCCGGGGGCATTGCTGCAGACGGGACCGCCA
AGGTGTTCGTCCCTTCAAGCCCCCATCATGCTGCTCTCAGGACACGAAGGGGAAGTGTATTGCT
GCAAGTTTCACCCCAATGGATCTACCCTGGCTTCTGCAGGATTTGACCGACTCATACTACTGTG
GAGCGTCTATGGAGACTGTGACAACTATGCTACGTTGAAGGGACACAGCGGAGCAGTAATGGAG
CTGCACTACAACACAGACGGCAGCATGCTCTTCTCAGCATCAACAGATAAAACTGTGGCAGTGT
GGGATAGTGAAACAGGAGAGAGAGTTAAAAGGCTAAAAGGGCATACTTCCTTTGTGAACTCCTG
TTATCCAGCCAGGCGGGGGCCCCAGCTTGTCTGCACAGGCAGCGACGATGGCACAGTTAAGCTT
TGGGACATCCGGAAGAAAGCAGCCATCCAGACATTTCAGAACACATACCAGGTGTTAGCCGTCA
CCTTCAATGACACGAGCGATCAGATCATCTCTGGCGGAATAGACAATGACATCAAGGTTTGGGA
CCTACGCCAAAACAAGTTAACCTACACCATGAGAGGCCATGCCGACTCTGTAACTGGCTTGAGC
TTGAGTTCTGAAGGATCTTATCTCTTGTCCAATGCAATGGACAACACAGTGCGTGTCTGGGATG
TCCGGCCATTTGCTCCCAAAGAGAGATGTGTGAAGATATTTCAAGGAAATGTCCACAACTTTGA
AAAGAACCTCCTGAGGTGTTCCTGGTCACCAGACGGAAGCAAGATAGCAGCTGGCTCAGCAGAC
AGGTTTGTGTACGTGTGGGACACCACAAGCAGAAGGATCCTGTATAAGCTTCCTGGTCATGCTG
GCTCCATCAATGAGGTGGCCTTCCATCCCGATGAGCCCATCATCCTCTCAGCATCCAGTGACAA
GAGGCTGTACATGGGTGAGATCCAGTGAAAATGTGGAATGGAAGGCCCCGTGACCCGAGGCTCA
GACTACGCCATTGGCCAGAGTCAGATGGTGTCTGGGCTGACCTGCCTTCAGATGACCATCGTTA
GCAAGCAGCTGGACCTGATGGCCATATTCCAGCAACCTCTTGTACCCCATTTACCAGAACCACT
GTGGCCTCTGGTACCACCCGCCAGATTCAGGGATTGGTTTCTTCTCTTTAAAAATAAGATTTCT
TCAGAAAGACAAACGTTGGTTTGATATTTCCTGTTTTTAATCTAGGCTGGAGACAGGGAGTGGC
AATTTGAAATTTGTTAGTTGCATTTATTTTTGTTTTATTTTTAAATTGAATAACTAGCTTGTAT
GATATTTGTTTCTGTGTTTGAGTCATTTTGTATTAAAAATCCAAACAGATACCTTTTTACAAGA
ACCTTGTGGCTTGG

hide sequence

RefSeq Acc Id:

XM_039109799 ⟹ XP_038965727

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	5	147,993,261 - 148,017,919 (+)	NCBI
mRatBN7.2	5	142,712,639 - 142,733,763 (+)	NCBI

RefSeq Acc Id:

XM_063287574 ⟹ XP_063143644

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	5	147,984,758 - 148,007,402 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_001128028	(Get FASTA)	NCBI Sequence Viewer
	XP_038965727	(Get FASTA)	NCBI Sequence Viewer
	XP_063143644	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDL80592	(Get FASTA)	NCBI Sequence Viewer
	EDL80593	(Get FASTA)	NCBI Sequence Viewer
	EDL80594	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000016325.6

RefSeq Acc Id:

NP_001128028 ⟸ NM_001134556

- UniProtKB:

A6ISP1 (UniProtKB/TrEMBL), D4A944 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MIEQQKRKGPELPLVPVKRPRHELLLGAAGSGPGAGQQQATPGALLQTGPPRCSSLQAPIMLLS
GHEGEVYCCKFHPNGSTLASAGFDRLILLWSVYGDCDNYATLKGHSGAVMELHYNTDGSMLFSA
STDKTVAVWDSETGERVKRLKGHTSFVNSCYPARRGPQLVCTGSDDGTVKLWDIRKKAAIQTFQ
NTYQVLAVTFNDTSDQIISGGIDNDIKVWDLRQNKLTYTMRGHADSVTGLSLSSEGSYLLSNAM
DNTVRVWDVRPFAPKERCVKIFQGNVHNFEKNLLRCSWSPDGSKIAAGSADRFVYVWDTTSRRI
LYKLPGHAGSINEVAFHPDEPIILSASSDKRLYMGEIQ

hide sequence

Ensembl Acc Id:

ENSRNOP00000016325 ⟸ ENSRNOT00000016325

RefSeq Acc Id:	XP_038965727 ⟸ XM_039109799
- Peptide Label:	isoform X2

RefSeq Acc Id:	XP_063143644 ⟸ XM_063287574
- Peptide Label:	isoform X1

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-D4A944-F1-model_v2	AlphaFold	D4A944	1-400	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:1309198	AgrOrtholog
BioCyc Gene	G2FUF-39747	BioCyc
Ensembl Genes	ENSRNOG00000012219	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000016325.8	UniProtKB/TrEMBL
Gene3D-CATH	2.130.10.10	UniProtKB/TrEMBL
InterPro	G-protein_beta_WD-40_rep	UniProtKB/TrEMBL
	U5_snRNP_Component	UniProtKB/TrEMBL
	WD40/YVTN_repeat-like_dom_sf	UniProtKB/TrEMBL
	WD40_repeat	UniProtKB/TrEMBL
	WD40_repeat_CS	UniProtKB/TrEMBL
	WD40_repeat_dom_sf	UniProtKB/TrEMBL
KEGG Report	rno:313056	UniProtKB/TrEMBL
NCBI Gene	313056	ENTREZGENE
PANTHER	U5 SMALL NUCLEAR RIBONUCLEOPROTEIN 40 KDA PROTEIN	UniProtKB/TrEMBL
	U5 SMALL NUCLEAR RIBONUCLEOPROTEIN 40 KDA PROTEIN	UniProtKB/TrEMBL
Pfam	WD40	UniProtKB/TrEMBL
PhenoGen	Snrnp40	PhenoGen
PRINTS	GPROTEINBRPT	UniProtKB/TrEMBL
PROSITE	WD_REPEATS_1	UniProtKB/TrEMBL
	WD_REPEATS_2	UniProtKB/TrEMBL
	WD_REPEATS_REGION	UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000012219	RatGTEx
SMART	WD40	UniProtKB/TrEMBL
Superfamily-SCOP	WD40_like	UniProtKB/TrEMBL
UniProt	A6ISP1	ENTREZGENE, UniProtKB/TrEMBL
	D4A944	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-03-16	Snrnp40	small nuclear ribonucleoprotein U5 subunit 40	Snrnp40	small nuclear ribonucleoprotein 40 (U5)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2010-04-23	Snrnp40	small nuclear ribonucleoprotein 40 (U5)	RGD1309198	similar to U5 snRNP-specific protein (Prp8-binding)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-04-30	RGD1309198	similar to U5 snRNP-specific protein (Prp8-binding)	RGD1309198_predicted	similar to U5 snRNP-specific protein (Prp8-binding) (predicted)	'predicted' is removed	2292626	APPROVED
2005-01-20	RGD1309198_predicted	similar to U5 snRNP-specific protein (Prp8-binding) (predicted)	LOC313056_predicted		Symbol and Name status set to approved	1331353	APPROVED
2005-01-12	LOC313056_predicted	similar to U5 snRNP-specific protein (Prp8-binding) (predicted)			Symbol and Name status set to provisional	70820	PROVISIONAL

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 Annotations - KEGG (archival)