Nipsnap3b (nipsnap homolog 3B) - Rat Genome Database

Name: Nipsnap3b
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: Nipsnap3b (nipsnap homolog 3B) Rattus norvegicus

Analyze

Symbol:

Nipsnap3b (Ensembl: Nipsnap3a)

Name:

nipsnap homolog 3B (Ensembl:nipsnap homolog 3A (C. elegans))

RGD ID:

1359688

Description:

Predicted to be active in mitochondrion. Orthologous to several human genes including NIPSNAP3A (nipsnap homolog 3A); INTERACTS WITH (+)-schisandrin B; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

MGC105691; nipsnap homolog 3A; nipsnap homolog 3A (C. elegans); nipsnap homolog 3B (C. elegans); NIPSNAP-related protein; Nipsnap3a

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):	NIPSNAP3A (nipsnap homolog 3A)	HGNC	Ensembl, HomoloGene, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Nipsnap3b (nipsnap homolog 3B)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	LOC100972219 (protein NipSnap homolog 3A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	LOC474791 (protein NipSnap homolog 3A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	LOC100739365 (protein NipSnap homolog 3A-like)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	NIPSNAP3A (nipsnap homolog 3A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Nipsnap3a (nipsnap homolog 3A)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	NIPSNAP3B (nipsnap homolog 3B)	HGNC	Inparanoid, OrthoDB, Panther, PhylomeDB, Treefam
Alliance orthologs ³
Homo sapiens (human):	NIPSNAP3B (nipsnap homolog 3B)	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Homo sapiens (human):	NIPSNAP3A (nipsnap homolog 3A)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Nipsnap3b (nipsnap homolog 3B)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	nipsnap3a (nipsnap homolog 3A (C. elegans))	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	nipsnap3a	Alliance	DIOPT (Ensembl Compara\|OMA\|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
GRCr8	5	72,446,945 - 72,465,090 (+)	NCBI		GRCr8
mRatBN7.2	5	67,637,644 - 67,669,698 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	5	67,614,036 - 67,669,700 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	5	69,544,132 - 69,554,837 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	5	71,352,498 - 71,369,689 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	5	71,332,968 - 71,343,673 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	5	69,833,200 - 69,849,116 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	5	69,833,225 - 69,849,112 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	5	73,997,156 - 74,012,019 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	70,448,727 - 70,481,754 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	5	70,453,839 - 70,486,868 (+)	NCBI
Celera	5	66,521,615 - 66,564,163 (+)	NCBI		Celera
Cytogenetic Map	5	q23	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)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-schisandrin B (EXP)

17alpha-ethynylestradiol (EXP)

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

2-methoxyethanol (EXP)

4,4'-sulfonyldiphenol (ISO)

6-propyl-2-thiouracil (EXP)

aflatoxin B1 (EXP,ISO)

amitrole (EXP)

amphetamine (EXP)

aristolochic acid A (ISO)

azoxystrobin (ISO)

benzo[a]pyrene (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP)

cadmium dichloride (ISO)

cefaloridine (EXP)

cisplatin (ISO)

clofibric acid (EXP)

clotrimazole (EXP)

cobalt dichloride (ISO)

copper(II) sulfate (ISO)

dibutyl phthalate (EXP)

dicrotophos (ISO)

epoxiconazole (ISO)

gentamycin (EXP)

hydrogen peroxide (ISO)

ivermectin (ISO)

methimazole (EXP)

methylmercury chloride (ISO)

methylparaben (ISO)

N-nitrosodiethylamine (EXP)

naphthalene (EXP)

nefazodone (EXP)

p-toluidine (EXP)

paracetamol (ISO)

paraquat (EXP)

perfluorooctanoic acid (ISO)

phenobarbital (ISO)

quercetin (ISO)

rotenone (ISO)

sulforaphane (ISO)

tetrachloromethane (EXP)

thioacetamide (EXP)

titanium dioxide (EXP)

urethane (ISO)

valproic acid (ISO)

vancomycin (ISO)

vinclozolin (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Cellular Component

mitochondrion (IBA)

Molecular Function

protein binding (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Expression pattern and raft association of NIPSNAP3 and NIPSNAP4, highly homologous proteins encoded by genes in close proximity to the ATP-binding cassette transporter A1.	Buechler C, etal., Genomics 2004 Jun;83(6):1116-24.
2.	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.
3.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
4.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
5.	Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.	Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.

Additional References at PubMed

PMID:14651853	PMID:18614015	PMID:21630459

Genomics

Comparative Map Data

Nipsnap3b
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	5	72,446,945 - 72,465,090 (+)	NCBI		GRCr8
mRatBN7.2	5	67,637,644 - 67,669,698 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	5	67,614,036 - 67,669,700 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	5	69,544,132 - 69,554,837 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	5	71,352,498 - 71,369,689 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	5	71,332,968 - 71,343,673 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	5	69,833,200 - 69,849,116 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	5	69,833,225 - 69,849,112 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	5	73,997,156 - 74,012,019 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	70,448,727 - 70,481,754 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	5	70,453,839 - 70,486,868 (+)	NCBI
Celera	5	66,521,615 - 66,564,163 (+)	NCBI		Celera
Cytogenetic Map	5	q23	NCBI

NIPSNAP3A
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	9	104,747,683 - 104,760,120 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	9	104,747,683 - 104,760,120 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	9	107,509,964 - 107,522,401 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	9	106,549,790 - 106,562,226 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	9	104,589,523 - 104,601,958	NCBI
Celera	9	78,015,286 - 78,027,720 (+)	NCBI		Celera
Cytogenetic Map	9	q31.1	NCBI
HuRef	9	77,112,138 - 77,124,575 (+)	NCBI		HuRef
CHM1_1	9	107,656,885 - 107,669,288 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	9	116,922,473 - 116,934,903 (+)	NCBI		T2T-CHM13v2.0

Nipsnap3b
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	4	53,011,932 - 53,022,060 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	4	53,011,880 - 53,022,060 (+)	Ensembl		GRCm39 Ensembl
GRCm38	4	53,011,880 - 53,022,060 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	4	53,011,880 - 53,022,060 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	4	53,024,796 - 53,034,931 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	4	53,033,024 - 53,043,159 (+)	NCBI		MGSCv36	mm8
Celera	4	52,988,904 - 53,000,857 (+)	NCBI		Celera
Cytogenetic Map	4	B2	NCBI
cM Map	4	28.57	NCBI

LOC100972219
(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	11	34,631,600 - 34,652,935 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	9	34,633,970 - 34,652,314 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	9	75,915,507 - 75,927,937 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	9	104,043,118 - 104,055,632 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	9	104,043,139 - 104,055,634 (+)	Ensembl	panpan1.1		panPan2

LOC474791
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	11	60,715,223 - 60,729,186 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	11	60,715,165 - 60,757,351 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	11	59,176,647 - 59,190,609 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	11	61,848,473 - 61,862,437 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	11	61,848,528 - 61,890,843 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	11	60,370,123 - 60,384,086 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	11	60,384,005 - 60,397,995 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	11	61,079,066 - 61,093,049 (+)	NCBI		UU_Cfam_GSD_1.0

LOC100739365
(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	246,105,250 - 246,140,397 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	1	246,129,422 - 246,140,407 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	1	275,511,781 - 275,522,727 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

NIPSNAP3A
(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	12	34,761,926 - 34,774,306 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	12	34,742,810 - 34,774,968 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666035	7,848,387 - 7,860,892 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Nipsnap3a
(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_004624758	6,633,075 - 6,651,937 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624758	6,634,215 - 6,651,379 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Nipsnap3b
177 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	39
Count of miRNA genes:	36
Interacting mature miRNAs:	37
Transcripts:	ENSRNOT00000013759
Prediction methods:	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
1331756	Rf34	Renal function QTL 34	4.16275		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal blood flow rate (CMO:0001168)	5	1	90450412	Rat
70212	Niddm25	Non-insulin dependent diabetes mellitus QTL 25	3.54		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	5	1	131345958	Rat
1331771	Rf35	Renal function QTL 35	4.36965		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal blood flow rate (CMO:0001168)	5	729470	86724018	Rat
1576314	Eutr1	Estrogen induced uterine response QTL 1			uterus integrity trait (VT:0010575)	pyometritis severity score (CMO:0002009)	5	2138965	166875058	Rat
8662454	Vetf3	Vascular elastic tissue fragility QTL 3	27.4		artery integrity trait (VT:0010639)	number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)	5	2282226	69540447	Rat
7394712	Emca13	Estrogen-induced mammary cancer QTL 13			mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	9823266	99753708	Rat
634305	Mamtr1	Mammary tumor resistance QTL 1		0.0001	mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	12789751	113558310	Rat
1358353	Srcrtb2	Stress Responsive Cort Basal QTL 2	3.48	0.003	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	5	18873947	74251464	Rat
1578767	Stresp17	Stress response QTL 17	4.3	0.01	blood aldosterone amount (VT:0005346)	plasma aldosterone level (CMO:0000551)	5	27955440	72955440	Rat
1578776	Stresp18	Stress response QTL 18	2.9		thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	5	27955440	72955440	Rat
6903292	Stl28	Serum triglyceride level QTL 28	2.6	0.0073	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	5	28515489	73515489	Rat
6903306	Scl35	Serum cholesterol QTL 35	2.6	0.0073	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	28515489	73515489	Rat
2290448	Scl54	Serum cholesterol level QTL 54	2.93		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	31663789	131345958	Rat
1598807	Glom12	Glomerulus QTL 12	2.7		kidney glomerulus morphology trait (VT:0005325)	index of glomerular damage (CMO:0001135)	5	33215665	78215665	Rat
1298067	Scl15	Serum cholesterol level QTL 15	4.8	0.001	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	33215665	78215665	Rat
1302786	Kidm8	Kidney mass QTL 8	28.15		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	5	33215665	78215665	Rat
1576317	Eutr2	Estrogen induced uterine response QTL 2		0.01	uterus integrity trait (VT:0010575)	pyometritis severity score (CMO:0002009)	5	34730116	104251008	Rat
2316959	Gluco59	Glucose level QTL 59	4.7		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	5	34944474	113558310	Rat
1641922	Alcrsp8	Alcohol response QTL 8			alcohol metabolism trait (VT:0015089)	blood ethanol level (CMO:0000535)	5	35189153	68564008	Rat
1641912	Alcrsp18	Alcohol response QTL 18			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	5	35189153	141643988	Rat
1549845	Scl44	Serum cholesterol level QTL 44	6		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	5	40128307	148607290	Rat
1331773	Scl26	Serum cholesterol level QTL 26	3.065		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	5	43726656	86724018	Rat
1331801	Rf33	Renal function QTL 33	4.149		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal vascular resistance (CMO:0001900)	5	43726656	129132602	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
1300115	Hrtrt7	Heart rate QTL 7	2.76		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	5	47869062	90099692	Rat
9589025	Epfw7	Epididymal fat weight QTL 7	20.66	0.001	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	5	49463600	94463600	Rat
7411561	Bw134	Body weight QTL 134	24	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	5	49463600	94463600	Rat
1576312	Emca8	Estrogen-induced mammary cancer QTL 8	4.1		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	50328551	141643988	Rat
2303615	Vencon7	Ventilatory control QTL 7		0.001	respiration trait (VT:0001943)	respiration rate (CMO:0000289)	5	50983895	95983895	Rat
2303574	Gluco42	Glucose level QTL 42	2		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	5	53496719	98496719	Rat
61359	Eaex	Experimental allergic encephalomyelitis QTL x	3		nervous system integrity trait (VT:0010566)	post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)	5	55715622	100715622	Rat
70189	Mcs5	Mammary carcinoma susceptibility QTL 5	10.51		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	55805606	132207589	Rat
1358895	Bp254	Blood pressure QTL 254	3.6	0.0003	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	5	58829236	128034027	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
2316954	Rf57	Renal function QTL 57	0		kidney glomerulus morphology trait (VT:0005325)	index of glomerular damage (CMO:0001135)	5	59793528	90450144	Rat
2316957	Pur21	Proteinuria QTL 21	6.2		urine protein amount (VT:0005160)	urine protein level (CMO:0000591)	5	59793528	113558156	Rat
61386	Bp49	Blood pressure QTL 49	16.6		cerebrum integrity trait (VT:0010549)	brain infarction volume (CMO:0001013)	5	60293434	98603051	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
1598814	Mcs13	Mammary carcinoma susceptibility QTL 13		0.0001	mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	63190890	69927503	Rat
2290005	Mcs24	Mammary carcinoma susceptibility QTL 24			mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	64719390	109719390	Rat
2306971	Anxrr21	Anxiety related response QTL 21	9.47		fear/anxiety-related behavior trait (VT:1000241)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	5	66174080	124160948	Rat

Markers in Region

RH128667

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	5	67,669,387 - 67,669,594 (+)	MAPPER	mRatBN7.2
Rnor_6.0	5	69,848,804 - 69,849,010	NCBI	Rnor6.0
Rnor_5.0	5	74,011,709 - 74,011,915	UniSTS	Rnor5.0
RGSC_v3.4	5	70,481,446 - 70,481,652	UniSTS	RGSC3.4
Celera	5	66,563,855 - 66,564,061	UniSTS
RH 3.4 Map	5	468.1	UniSTS
Cytogenetic Map	5	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	24	55	41	17	41			69	20	34	4
Low		19	2		2		8	11	5	15	7	7	8
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001009422	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006238164	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_063287619	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC087643	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474039	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ219476	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ221422	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000005	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSRNOT00000013759 ⟹ ENSRNOP00000013759

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	5	67,637,667 - 67,669,698 (+)	Ensembl
Rnor_6.0 Ensembl	5	69,833,225 - 69,849,112 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000059828 ⟹ ENSRNOP00000056573

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	5	67,614,036 - 67,624,737 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000095903 ⟹ ENSRNOP00000088730

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	5	67,637,712 - 67,669,700 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000098020 ⟹ ENSRNOP00000086152

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	5	67,639,188 - 67,669,700 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000099213 ⟹ ENSRNOP00000081642

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	5	67,652,533 - 67,669,696 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000100514 ⟹ ENSRNOP00000085534

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	5	67,614,036 - 67,641,108 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000107397 ⟹ ENSRNOP00000081717

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	5	67,654,879 - 67,669,698 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000115539 ⟹ ENSRNOP00000087647

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	5	67,653,641 - 67,669,698 (+)	Ensembl

RefSeq Acc Id:

NM_001009422 ⟹ NP_001009422

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	5	72,447,907 - 72,465,088 (+)	NCBI
mRatBN7.2	5	67,637,706 - 67,669,696 (+)	NCBI
Rnor_6.0	5	69,833,263 - 69,849,112 (+)	NCBI
Rnor_5.0	5	73,997,156 - 74,012,019 (+)	NCBI
RGSC_v3.4	5	70,448,727 - 70,481,754 (+)	RGD
Celera	5	66,521,615 - 66,564,163 (+)	RGD

Sequence:

show sequence

GCGCGTGTCCCGCTGCTCCGCTGCGGTCTATCTGGGCAGCACCATGCTCGCGCTCCGAAGCGGC
CTGAGGACGGCGCTGGCCCCGCGGGCTCTGACGCCTCAGGTATGTTCACCTTTTGCTACAGGCC
CCAGGCAAAGCGATGGGACATTGTATGAATTCCGCACCTACTCTCTGAAGCCCTCAAAGACAAA
TGCGTTCCTGCAGAATTTTCAGAAATACGTTCACCTTCGGACAGCTCACTCTGAGATGATTGGA
TACTGGACCGTAGAATTTGGAGGCAAAATAAACAGAGTGTTCCATATTTGGAAGTATGATAATT
TTGCTCATCGAACTGCCGTCCGCAAAGCCTTGGCCAAGGATAAGGAATGGCAAGAACAATTCCT
CATTTCAAATTTGGCTTTCATGGATGAACAAGAGGTTGAGATTACCTACTTGGTACCCTGGTGT
AAAATAAGAACACCTCCCAAGGAAGGAGTCTATGAACTGGCTACCTTTCAGATGAAGCCTGGTG
GCCCAGCTCTATGGGGTGATGCATTCAAAAGGGCAATAAACGCCCATGTTGAGCTTGGCTACTC
TACACTAGTTGGTGTTTTCCACACTGAATATGGAGCCCTCAACAGAGTTCATGTCCTCTGGTGG
AACGACAGTGCCGACAGCCGAGCAGCTGGGAGACACTGGTCCCATGAGGATCCCAGAGTAGTGG
CTGCTGTTCGGGAAAGTGTCAATTACCTCGAGTCTCAGCAGAATATGTTCCTGATTCCAACCTC
ATTTTCACCATTGAAGTAGTTTCCTACCGAGCGCTGAGCATTCCCATCACGGAGGTGAGATGCG
TTTCCCCCAGACAATCGCCCTGTTCATTGTCTGAAGGAGGTGCTGAGCTACCGCACTGCCCTCT
GCATGTCTGAGACTTCATGTATCCTTTACTACCAGTCGCTCAGGAAATGTTTCTGTCCCTTTTC
ATGTCTACTGGATGTCAGAAAGTGGTGTTATTACTCCATGCCCTGGTACTTCATTGTTCTTCTG
TGGTTTTATGATTAAGTCTTGTCCTCAAAATATGATTTTGAAATTTTTTCCCTCAAAATATTTG
GAAATTAAATAAATACAATATCTGCCTTAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_063287619 ⟹ XP_063143689

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	5	72,446,945 - 72,465,090 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_001009422	(Get FASTA)	NCBI Sequence Viewer
	XP_063143689	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH87643	(Get FASTA)	NCBI Sequence Viewer
	EDL91719	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000013759.3
	ENSRNOP00000081642.1
	ENSRNOP00000081717.1
	ENSRNOP00000085534.1
	ENSRNOP00000086152.1
	ENSRNOP00000087647.1
	ENSRNOP00000088730
	ENSRNOP00000088730.1

RefSeq Acc Id:

NP_001009422 ⟸ NM_001009422

- UniProtKB:

Q5M949 (UniProtKB/TrEMBL), A0A8I6G695 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MLALRSGLRTALAPRALTPQVCSPFATGPRQSDGTLYEFRTYSLKPSKTNAFLQNFQKYVHLRT
AHSEMIGYWTVEFGGKINRVFHIWKYDNFAHRTAVRKALAKDKEWQEQFLISNLAFMDEQEVEI
TYLVPWCKIRTPPKEGVYELATFQMKPGGPALWGDAFKRAINAHVELGYSTLVGVFHTEYGALN
RVHVLWWNDSADSRAAGRHWSHEDPRVVAAVRESVNYLESQQNMFLIPTSFSPLK

hide sequence

RefSeq Acc Id:

ENSRNOP00000013759 ⟸ ENSRNOT00000013759

RefSeq Acc Id:

ENSRNOP00000087647 ⟸ ENSRNOT00000115539

RefSeq Acc Id:

ENSRNOP00000081717 ⟸ ENSRNOT00000107397

RefSeq Acc Id:

ENSRNOP00000085534 ⟸ ENSRNOT00000100514

RefSeq Acc Id:

ENSRNOP00000056573 ⟸ ENSRNOT00000059828

RefSeq Acc Id:

ENSRNOP00000088730 ⟸ ENSRNOT00000095903

RefSeq Acc Id:

ENSRNOP00000086152 ⟸ ENSRNOT00000098020

RefSeq Acc Id:

ENSRNOP00000081642 ⟸ ENSRNOT00000099213

RefSeq Acc Id:	XP_063143689 ⟸ XM_063287619
- Peptide Label:	isoform X1

Protein Domains

NIPSNAP

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q5M949-F1-model_v2	AlphaFold	Q5M949	1-247	view protein structure

Transcriptome

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

Promoters

RGD ID:

13693740

Promoter ID:

EPDNEW_R4264

Type:

initiation region

Name:

Nipsnap3b_1

Description:

nipsnap homolog 3B

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	5	69,833,256 - 69,833,316	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1359688	AgrOrtholog
BioCyc Gene	G2FUF-41283	BioCyc
Ensembl Genes	ENSRNOG00000010332	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000013759.6	UniProtKB/TrEMBL
	ENSRNOT00000095903	ENTREZGENE
	ENSRNOT00000095903.1	UniProtKB/TrEMBL
	ENSRNOT00000098020.1	UniProtKB/TrEMBL
	ENSRNOT00000099213.1	UniProtKB/TrEMBL
	ENSRNOT00000100514.1	UniProtKB/TrEMBL
	ENSRNOT00000107397.1	UniProtKB/TrEMBL
	ENSRNOT00000115539.1	UniProtKB/TrEMBL
Gene3D-CATH	3.30.70.100	UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7307943	IMAGE-MGC_LOAD
InterPro	Dimeric_a/b-barrel	UniProtKB/TrEMBL
	NIPSNAP	UniProtKB/TrEMBL
KEGG Report	rno:313211	UniProtKB/TrEMBL
MGC_CLONE	MGC:105691	IMAGE-MGC_LOAD
NCBI Gene	313211	ENTREZGENE
PANTHER	NIPSNAP HOMOLOG 3A-RELATED	UniProtKB/TrEMBL
	NIPSNAP-RELATED	UniProtKB/TrEMBL
Pfam	NIPSNAP	UniProtKB/TrEMBL
PhenoGen	Nipsnap3b	PhenoGen
RatGTEx	ENSRNOG00000010332	RatGTEx
Superfamily-SCOP	Dimer_A_B_barrel	UniProtKB/TrEMBL
UniProt	A0A8I5ZTD2_RAT	UniProtKB/TrEMBL
	A0A8I6A0B7_RAT	UniProtKB/TrEMBL
	A0A8I6G695	ENTREZGENE, UniProtKB/TrEMBL
	A0A8I6GG78_RAT	UniProtKB/TrEMBL
	A6KDN6_RAT	UniProtKB/TrEMBL
	Q5M949	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-08-29	Nipsnap3b	nipsnap homolog 3B	Nipsnap3b	nipsnap homolog 3B (C. elegans)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2009-09-01	Nipsnap3b	nipsnap homolog 3B (C. elegans)	Nipsnap3a	nipsnap homolog 3A (C. elegans)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-03-30	Nipsnap3a	nipsnap homolog 3A (C. elegans)	MGC105691	NIPSNAP-related protein	Symbol and Name updated	1299863	APPROVED
2005-07-29	MGC105691	NIPSNAP-related protein			Symbol and Name status set to provisional	70820	PROVISIONAL

RGD Curation Notes

Note Type	Note	Reference
gene_expression	highly expressed in skeletal muscle, unlike related protein Nipsnap4	1559053

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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