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 have phosphatidylinositol phosphate binding activity and protein phosphatase binding activity. Predicted to be involved in several processes, including endosomal transport; negative regulation of transport; and regulation of protein metabolic process. Predicted to localize to cytoplasmic vesicle; cytosol; and retromer complex. 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

Also 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 (African 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:

Rnor_6.0 - RGSC Genome Assembly v6.0

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
Rnor_6.0 Ensembl	20	47,225,619 - 47,263,390 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	20	47,225,382 - 47,263,390 (+)	NCBI	Rnor6.0	Rnor_6.0	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)

benzo[a]pyrene (ISO)

bisphenol A (EXP)

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)

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
Rnor_6.0 Ensembl	20	47,225,619 - 47,263,390 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	20	47,225,382 - 47,263,390 (+)	NCBI	Rnor6.0	Rnor_6.0	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.p13 Ensembl	6	108,211,222 - 108,261,246 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	6	108,211,222 - 108,261,040 (-)	NCBI	GRCh38	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	108,795,378 - 108,845,435 (-)	NCBI		CHM1_1

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
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 - African green monkey)

Vervet Assembly	Chr	Position (strand)	Source	Genome Browsers
Vervet Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	13	65,590,413 - 65,640,368 (+)	NCBI
ChlSab1.1 Ensembl	13	65,589,801 - 65,640,876 (+)	Ensembl

Snx3
(Heterocephalus glaber - naked mole-rat)

Molerat Assembly	Chr	Position (strand)	Source	Genome Browsers
Molerat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624780	14,043,002 - 14,080,380 (+)	NCBI

Position Markers

REN49968

Rat Assembly	Chr	Position (strand)	Source	JBrowse
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 (Rnor_6.0)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1641915	Colcr9	Colorectal carcinoma resistance QTL 9	2.97	0.0024	intestine integrity trait (VT:0010554)	benign colorectal tumor number (CMO:0001795)	20	2999707	47999707	Rat
1598816	Memor12	Memory QTL 12	2.4		exploratory behavior trait (VT:0010471)	average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)	20	4108956	49108956	Rat
9590092	Insglur9	Insulin/glucose ratio QTL 9	18.38	0.001	blood insulin amount (VT:0001560)	calculated plasma insulin level (CMO:0002170)	20	13834309	56205956	Rat
7411652	Foco24	Food consumption QTL 24		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	20	13834309	56205956	Rat
2317880	Alcrsp25	Alcohol response QTL 25	2.3		response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	20	17827096	56205956	Rat
4889610	Pancm3	Pancreatic morphology QTL 3	3.75	0.001	pancreas mass (VT:0010144)	pancreas wet weight (CMO:0000626)	20	18872150	49108956	Rat
2303626	Vencon10	Ventilatory control QTL 10		0.001	respiration trait (VT:0001943)	respiration rate (CMO:0000289)	20	20858470	56205956	Rat
2303578	Gluco50	Glucose level QTL 50	2		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	20	26608843	56205956	Rat
2303587	Bw93	Body weight QTL 93	13		body mass (VT:0001259)	body weight (CMO:0000012)	20	26608843	56205956	Rat
2300188	Bmd68	Bone mineral density QTL 68	6.4	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	20	26608843	56205956	Rat
1331747	Hrtrt16	Heart rate QTL 16	3.163		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	20	26712323	56205956	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	30913481	56205956	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
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
Rnor_6.0 Ensembl	20	47,253,664 - 47,263,390 (+)	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

Protein Domains

Transcriptome

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

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

ACI/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

ACI/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

BBDP/Wor (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

BN/SsN (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Buf/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

COP/CrCrl (MCW & UW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob) University of Wisconsin (Dr. James Shull)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Charles River Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)

F344/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

F344/NRrrc (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

FHH/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHH/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

FHL/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHL/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

GH/OmrMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

GK/Ox (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LE/Stm (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/Crl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/NCrlBR (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LH/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LL/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LN/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

M520/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

MHS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MNS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MR/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

SBH/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBH/Ygl sequenced by MCW

SBH/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SBN/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBN/Ygl sequenced by MCW

SBN/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHR/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHRSP/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SR/JrHsd (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Harlan Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SR/JrHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/Jr (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/JrHsdMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SS/JrHsdMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WAG/Rij (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

WKY/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WN/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1595151	AgrOrtholog
Ensembl Genes	ENSRNOG00000046705	Ensembl, ENTREZGENE
Ensembl Transcript	ENSRNOT00000074532	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)

Imported Disease Annotations - OMIM

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Imported Disease Annotations - OMIM

RGD Manual Annotations