Snx3 (sorting nexin 3) - Rat Genome Database

Name: Snx3
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Snx3 (sorting nexin 3) Rattus norvegicus

Analyze

Symbol:

Snx3

Name:

sorting nexin 3

RGD ID:

1595151

Description:

Predicted to enable phosphatidylinositol phosphate binding activity; protein phosphatase binding activity; and retromer complex binding activity. Predicted to be involved in several processes, including endosomal transport; intralumenal vesicle formation; and negative regulation of transport. Predicted to act upstream of or within several processes, including hemoglobin biosynthetic process; regulation of intracellular protein transport; and transferrin transport. Predicted to be located in cytoplasmic vesicle and cytosol. Predicted to be part of retromer complex. Predicted to be active in early endosome membrane. Human ortholog(s) of this gene implicated in syndromic microphthalmia 8. Orthologous to human SNX3 (sorting nexin 3); PARTICIPATES IN retromer-mediated pathway; INTERACTS WITH bisphenol A; caffeine; finasteride.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

LOC684097; similar to sorting nexin 3; sorting nexin-3

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

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):	SNX3 (sorting nexin 3)	RGD	RGD
Mus musculus (house mouse):	Snx3 (sorting nexin 3)	RGD	RGD
Chinchilla lanigera (long-tailed chinchilla):	Snx3 (sorting nexin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	SNX3 (sorting nexin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	SNX3 (sorting nexin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Snx3 (sorting nexin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	SNX3 (sorting nexin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	SNX3 (sorting nexin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Snx3 (sorting nexin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	SNX12 (sorting nexin 12)	HGNC	OrthoDB
Alliance orthologs ³
Homo sapiens (human):	SNX3 (sorting nexin 3)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Mus musculus (house mouse):	Snx3 (sorting nexin 3)	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	Snx3	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Saccharomyces cerevisiae (baker's yeast):	SNX3	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Caenorhabditis elegans (roundworm):	snx-3	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	20	45,992,446 - 46,025,361 (+)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	20	45,992,720 - 46,025,379 (+)	Ensembl
Rnor_6.0	20	47,225,382 - 47,263,390 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	20	47,225,619 - 47,263,390 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	20	48,923,090 - 48,932,814 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
Celera	20	53,947,195 - 53,979,808 (-)	NCBI		Celera
Cytogenetic Map	20	q13	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

COVID-19 (ISO)

syndromic microphthalmia 8 (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (ISO)

2,3',4,4',5-Pentachlorobiphenyl (ISO)

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

acrolein (ISO)

acrylamide (ISO)

alpha-pinene (ISO)

arsenite(3-) (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

cadmium dichloride (ISO)

caffeine (EXP)

carbon nanotube (ISO)

chlordecone (ISO)

chloropicrin (ISO)

cisplatin (ISO)

cobalt dichloride (ISO)

copper(II) sulfate (ISO)

dexamethasone (ISO)

ethanol (ISO)

finasteride (EXP)

folic acid (ISO)

fumonisin B1 (ISO)

ivermectin (ISO)

methoxyacetic acid (EXP)

methylmercury chloride (EXP)

Monobutylphthalate (EXP)

ozone (ISO)

perfluorooctanoic acid (ISO)

pirinixic acid (ISO)

resveratrol (ISO)

tetrachloromethane (ISO)

titanium dioxide (ISO)

triptonide (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

biological_process (ND)

endocytic recycling (IBA)

hemoglobin biosynthetic process (ISO)

intralumenal vesicle formation (ISO)

late endosome to Golgi transport (IBA)

membrane invagination (ISO)

negative regulation of early endosome to late endosome transport (ISO)

negative regulation of phagocytosis (ISO,ISS)

negative regulation of protein catabolic process (ISO)

negative regulation of protein transport (ISO)

negative regulation of viral entry into host cell (ISO)

positive regulation of neuron projection development (ISO,ISS)

protein to membrane docking (ISO,ISS)

regulation of cellular protein metabolic process (ISO)

regulation of intracellular protein transport (ISO)

regulation of Wnt signaling pathway (ISO,ISS)

response to bacterium (ISO)

transferrin transport (ISO)

Cellular Component

cellular_component (ND)

clathrin-coated vesicle (ISO,ISS)

cytoplasm (ISO)

cytosol (ISO)

early endosome (ISO,ISS)

early endosome membrane (IBA,ISO)

early phagosome (ISO,ISS)

endosome membrane (ISO,ISS)

retromer complex (IBA,ISO)

Molecular Function

molecular_function (ND)

phosphatidylinositol-3,5-bisphosphate binding (ISO,ISS)

phosphatidylinositol-3-phosphate binding (IBA,ISO,ISS)

phosphatidylinositol-4-phosphate binding (ISO,ISS)

phosphatidylinositol-5-phosphate binding (ISO,ISS)

protein binding (ISO)

protein phosphatase binding (ISO)

retromer complex binding (ISO,ISS)

Molecular Pathway Annotations Click to see Annotation Detail View

retromer-mediated pathway (ISO)

References

References - curated


1.	Gallon M and Cullen PJ, Biochem Soc Trans. 2015 Feb;43(1):33-47. doi: 10.1042/BST20140290.
2.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3.	RGD automated data pipeline
4.	RGD automated import pipeline for gene-chemical interactions
5.	RGD comprehensive gene curation

Additional References at PubMed

PMID:9819414	PMID:11279102	PMID:11433298	PMID:12477932	PMID:15673616	PMID:17622474	PMID:18767904	PMID:19056867	PMID:19576982	PMID:20482551	PMID:21725319	PMID:22719997
PMID:22871113	PMID:23237080	PMID:23376485	PMID:23416069	PMID:24344282

Genomics

Comparative Map Data

Snx3
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	20	45,992,446 - 46,025,361 (+)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	20	45,992,720 - 46,025,379 (+)	Ensembl
Rnor_6.0	20	47,225,382 - 47,263,390 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	20	47,225,619 - 47,263,390 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	20	48,923,090 - 48,932,814 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
Celera	20	53,947,195 - 53,979,808 (-)	NCBI		Celera
Cytogenetic Map	20	q13	NCBI

SNX3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	6	108,211,222 - 108,261,040 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p13 Ensembl	6	108,211,222 - 108,261,246 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	6	108,532,426 - 108,582,244 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	6	108,639,410 - 108,689,156 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	6	108,639,410 - 108,689,156	NCBI
Celera	6	109,279,209 - 109,328,955 (-)	NCBI
Cytogenetic Map	6	q21	NCBI
HuRef	6	106,100,989 - 106,150,564 (-)	NCBI		HuRef
CHM1_1	6	108,795,674 - 108,845,435 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	6	109,388,338 - 109,438,159 (-)	NCBI

Snx3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	10	42,378,050 - 42,411,365 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	10	42,378,026 - 42,411,377 (+)	Ensembl
GRCm38	10	42,502,054 - 42,535,369 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	10	42,502,030 - 42,535,381 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	10	42,221,860 - 42,255,175 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	10	42,190,444 - 42,223,782 (+)	NCBI			mm8
Celera	10	43,369,479 - 43,403,088 (+)	NCBI		Celera
Cytogenetic Map	10	B2	NCBI
cM Map	10	22.89	NCBI

Snx3
(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_004955411	33,340,274 - 33,345,500 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955411	33,339,974 - 33,344,563 (-)	NCBI	ChiLan1.0	ChiLan1.0

SNX3
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	6	109,874,095 - 109,924,185 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	6	109,874,105 - 109,924,185 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	6	106,010,633 - 106,063,331 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

SNX3
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	12	65,252,175 - 65,294,620 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	12	65,252,175 - 65,294,611 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	12	65,067,774 - 65,110,209 (-)	NCBI
ROS_Cfam_1.0	12	66,127,936 - 66,170,477 (-)	NCBI
ROS_Cfam_1.0 Ensembl	12	66,127,942 - 66,170,467 (-)	Ensembl
UMICH_Zoey_3.1	12	65,483,130 - 65,525,574 (-)	NCBI
UNSW_CanFamBas_1.0	12	65,329,591 - 65,371,812 (-)	NCBI
UU_Cfam_GSD_1.0	12	65,602,544 - 65,644,998 (-)	NCBI

Snx3
(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_024404946	100,197,614 - 100,245,855 (-)	NCBI
SpeTri2.0	NW_004936564	4,472,171 - 4,520,732 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SNX3
(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	74,306,453 - 74,349,335 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	1	74,306,450 - 74,349,735 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	1	83,576,787 - 83,585,208 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

SNX3
(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	13	65,590,413 - 65,640,368 (+)	NCBI	ChlSab1.1		chlSab2
ChlSab1.1 Ensembl	13	65,589,801 - 65,640,876 (+)	Ensembl	ChlSab1.1		chlSab2
Vero_WHO_p1.0	NW_023666040	37,916,042 - 37,966,796 (+)	NCBI	Vero_WHO_p1.0

Snx3
(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_004624780	14,043,003 - 14,080,380 (+)	Ensembl	HetGla_female_1.0		hetGla2
HetGla 1.0	NW_004624780	14,043,002 - 14,080,380 (+)	NCBI	HetGla_female_1.0		hetGla2

Position Markers

REN49968

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	20	46,013,127 - 46,013,385 (+)	MAPPER	mRatBN7.2
Rnor_6.0	20	47,251,161 - 47,251,418	NCBI	Rnor6.0
Rnor_5.0	20	48,920,585 - 48,920,842	UniSTS	Rnor5.0
Celera	20	53,959,169 - 53,959,426	UniSTS

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
2305926	Iddm37	Insulin dependent diabetes mellitus QTL 37	6		blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	20	1527842	46527842	Rat
1641915	Colcr9	Colorectal carcinoma resistance QTL 9	2.97	0.0024	intestine integrity trait (VT:0010554)	benign colorectal tumor number (CMO:0001795)	20	1530655	46530655	Rat
1598816	Memor12	Memory QTL 12	2.4		exploratory behavior trait (VT:0010471)	average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)	20	2606836	47606836	Rat
7411652	Foco24	Food consumption QTL 24		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	20	11757515	54435887	Rat
9590092	Insglur9	Insulin/glucose ratio QTL 9	18.38	0.001	blood insulin amount (VT:0001560)	calculated plasma insulin level (CMO:0002170)	20	11757515	54435887	Rat
4889610	Pancm3	Pancreatic morphology QTL 3	3.75	0.001	pancreas mass (VT:0010144)	pancreas wet weight (CMO:0000626)	20	17617832	47606836	Rat
2317880	Alcrsp25	Alcohol response QTL 25	2.3		response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	20	17697550	54435887	Rat
2303626	Vencon10	Ventilatory control QTL 10		0.001	respiration trait (VT:0001943)	respiration rate (CMO:0000289)	20	19190721	54435887	Rat
2303578	Gluco50	Glucose level QTL 50	2		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	20	25106722	54435887	Rat
2303587	Bw93	Body weight QTL 93	13		body mass (VT:0001259)	body weight (CMO:0000012)	20	25106722	54435887	Rat
2300188	Bmd68	Bone mineral density QTL 68	6.4	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	20	25106722	54435887	Rat
1331747	Hrtrt16	Heart rate QTL 16	3.163		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	20	25209734	54435887	Rat
1598869	Memor6	Memory QTL 6	3.1		exploratory behavior trait (VT:0010471)	total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)	20	29244388	54435887	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	375
Count of miRNA genes:	211
Interacting mature miRNAs:	248
Transcripts:	ENSRNOT00000074532
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.

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	43	57	41	19	41	8	11	74	35	41	11	8
Low
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001044283	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039099063	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039099064	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC086341	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC107918	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC158608	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474025	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ211490	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ231492	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ234595	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000330	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000074532

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	20	45,992,965 - 46,025,361 (+)	Ensembl
Rnor_6.0 Ensembl	20	47,225,619 - 47,263,389 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000075924

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	20	45,992,720 - 46,025,379 (+)	Ensembl
Rnor_6.0 Ensembl	20	47,253,664 - 47,263,390 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000103931 ⟹ ENSRNOP00000082616

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	20	45,993,047 - 46,025,361 (+)	Ensembl

RefSeq Acc Id:

NM_001044283 ⟹ NP_001037748

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	20	45,992,721 - 46,025,361 (+)	NCBI
Rnor_6.0	20	47,225,382 - 47,263,390 (+)	NCBI
Rnor_5.0	20	48,923,090 - 48,932,814 (+)	NCBI
Celera	20	53,947,195 - 53,979,808 (-)	RGD

Sequence:

show sequence

GTCTCCCGGTATCCTTGGCGCCCACCGTTCCGTGACGCCGCCGCCCCTCAGCCCCACCCCGCAG
TGTCCCTCCGGGGCCGCCGCGGGGCCTGCGAACCGGGCGCGGCGTTCAGGCCAGTCAGCTGTTT
CTCCTTGGGCAAAGGGCGGAAGCCCGAGCAGCCTGGGGCGGAGCTTCGCGTAGAGCGAACGCCC
ACCCGTCCTACGTGCTCGTTCGCCTCTGTTCGCTGCGCGCGAGCCGGGAGTCCCCCGCGGCGGG
CGGCGGCGGCGGCGTTGGCGGAAGGAGGCGGCGGTGGAGAGAAGCCCGCGGCTGCCGCGGCGAT
AGCGAAATGGCGGAGACCGTAGCGGACACCCGGCGGCTCATCACCAAGCCGCAGAACCTGAATG
ACGCCTACGGGCCGCCCAGCAACTTCCTCGAGATCGACGTGAGCAATCCGCAGACTGTGGGGGT
CGGCCGGGGCCGCTTCACCACCTACGAGATCAGGGTCAAGACCAATCTTCCTATCTTCAAGCTG
AAGGAATCTACTGTTAGAAGAAGATACAGTGACTTTGAGTGGCTTCGAAGTGAACTAGAGAGAG
AGAGCAAGGTTGTCGTTCCCCCACTCCCGGGGAAAGCATTTTTGCGGCAGCTTCCTTTTAGAGG
AGACGATGGAATATTTGACGATAATTTCATCGAGGAAAGGAAGCAAGGGCTGGAACAGTTCATA
AACAAGGTCGCTGGTCATCCTCTGGCCCAGAATGAACGTTGTCTTCACATGTTTTTACAGGATG
AAATCATAGATAAAAGCTATACTCCATCTAAAATAAGACATGCCTGAGTTTGGCAAGAAGAGGC
AAACCCCAAGACCATGAATGATTCGTCCGTACCAATGAAGACGTTGTAACTAACTTAGCATGCT
GCAGACACTGCTGTAACAAACGCGCACGCCCTGGATGTACTAACACTCACGCTCCCTTTCATTC
TGTCTGTTTGGCAAGACGTTCATTTGCTTTAGTGGAAACTCCCTCACTTCTCCAGCCTTTCTAA
GTAGCCCTTCCCACCGTGTCCCTCCGTGTGCACTGTAGCCTCAGCCCTGTAGACCTGCAGTGTT
CTGACTAAAGCTGCCGACTTGCTCGAATTTGCAGTTTCTGTGTCGTGTGCTTCTTGAATCTGAT
TGACTAGGATATTTCTCCCCACCCCTGATGTGTGATGTCACCACTTGGTCCTAATTTATGTGCA
GGAGCACGACACCATTTGTCTCCAGTGCCACACATACGAGGTGTACTTTGTGTGCAGAATGTGT
CTTCCTTCTGGCCTGTAATCCCCTTCACATGAGAGATTAATGAGGGAAATCTTTATATTCTGTA
TAAAACAAAATCAAATTTATATACTAAAATCATTTGTCTAAAATTTAAGTTGTTTTCAAATAAA
AGTTGAAATGCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_039099063 ⟹ XP_038954991

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	20	45,992,446 - 46,025,361 (+)	NCBI

RefSeq Acc Id:

XM_039099064 ⟹ XP_038954992

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	20	45,992,446 - 46,025,361 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_001037748	(Get FASTA)	NCBI Sequence Viewer
	XP_038954991	(Get FASTA)	NCBI Sequence Viewer
	XP_038954992	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH86341	(Get FASTA)	NCBI Sequence Viewer
	AAI07919	(Get FASTA)	NCBI Sequence Viewer
	AAI58609	(Get FASTA)	NCBI Sequence Viewer
	EDL99706	(Get FASTA)	NCBI Sequence Viewer
	Q5U211	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_001037748 ⟸ NM_001044283
- UniProtKB:	Q5U211 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MAETVADTRRLITKPQNLNDAYGPPSNFLEIDVSNPQTVGVGRGRFTTYEIRVKTNLPIFKLKE STVRRRYSDFEWLRSELERESKVVVPPLPGKAFLRQLPFRGDDGIFDDNFIEERKQGLEQFINK VAGHPLAQNERCLHMFLQDEIIDKSYTPSKIRHA hide sequence

RefSeq Acc Id:	XP_038954991 ⟸ XM_039099063
- Peptide Label:	isoform X1

RefSeq Acc Id:	XP_038954992 ⟸ XM_039099064
- Peptide Label:	isoform X2

RefSeq Acc Id:

ENSRNOP00000082616 ⟸ ENSRNOT00000103931

Protein Domains

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q5U211-F1-model_v2	AlphaFold	Q5U211	1-162	view protein structure

Transcriptome

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

Strain Variation

Strain Sequence Variants (MRatBN7.2)

ACI/EurMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

ACI/N (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN-Lx/CubMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/NHsdMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/NHsdMcwi (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/SsN (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BUF/N (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BXH2/CubMcwi (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BXH3/CubMcwi (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

DA/OlaHsd (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Envigo
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/DuCrl (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/N (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/NCrl (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/Stm (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FHH/EurMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FXLE16/Stm (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FXLE18/Stm (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

GK/FarMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB10/IpcvMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB2/IpcvMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB20/IpcvMcwi (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB31/IpcvMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB4/IpcvMcwi (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LE/Stm (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEW/Crl (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF10A/StmMcwi (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF11/Stm (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF1A/Stm (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF1C/Stm (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF2B/Stm (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF3/Stm (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF4/Stm (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LH/MavRrrcAek (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LL/MavRrrcAek (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LN/MavRrrcAek (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

M520/N (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

M520/NRrrcMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

MR/N (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

MWF/Hsd (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

PVG/Seac (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SHR/OlalpcvMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SHRSP/A3NCrl (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SR/JrHsd (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Envigo
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SS/JrHsdMcwi (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WAG/RijCrl (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WKY/N (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WKY/NCrl (2019)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

WN/N (2020)

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Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1595151	AgrOrtholog
BioCyc Gene	G2FUF-3359	BioCyc
Ensembl Genes	ENSRNOG00000046705	Ensembl, ENTREZGENE
Ensembl Protein	ENSRNOP00000087527	ENTREZGENE
	ENSRNOP00000092005	ENTREZGENE
Ensembl Transcript	ENSRNOT00000074532	ENTREZGENE
	ENSRNOT00000075924	ENTREZGENE
Gene3D-CATH	3.30.1520.10	UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:7301775	IMAGE-MGC_LOAD
	IMAGE:7301779	IMAGE-MGC_LOAD
	IMAGE:7458016	IMAGE-MGC_LOAD
InterPro	Phox	UniProtKB/Swiss-Prot
	PX_dom_sf	UniProtKB/Swiss-Prot
	PX_SNX3_Vert	UniProtKB/Swiss-Prot
KEGG Report	rno:684097	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:105945	IMAGE-MGC_LOAD
	MGC:125029	IMAGE-MGC_LOAD
	MGC:187477	IMAGE-MGC_LOAD
NCBI Gene	684097	ENTREZGENE
Pfam	PF00787	UniProtKB/Swiss-Prot
PhenoGen	Snx3	PhenoGen
PROSITE	PS50195	UniProtKB/Swiss-Prot
SMART	SM00312	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF64268	UniProtKB/Swiss-Prot
UniProt	Q5U211	ENTREZGENE, UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2010-12-08	Snx3	sorting nexin 3	LOC684097	similar to sorting nexin 3	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-11-20	LOC684097	similar to sorting nexin 3			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 Disease Annotations - OMIM

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