Snx6 (sorting nexin 6) - Rat Genome Database

Name: Snx6
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: Snx6 (sorting nexin 6) Rattus norvegicus

Analyze

Symbol:

Snx6

Name:

sorting nexin 6

RGD ID:

1304647

Description:

Predicted to enable dynactin binding activity; protein homodimerization activity; and type I transforming growth factor beta receptor binding activity. Involved in cellular response to epidermal growth factor stimulus. Located in endosome. Orthologous to human SNX6 (sorting nexin 6); PARTICIPATES IN retromer-mediated pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; gentamycin.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

LOC362738; sorting nexin-6

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):	SNX6 (sorting nexin 6)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Snx6 (sorting nexin 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Snx6 (sorting nexin 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	SNX6 (sorting nexin 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	SNX6 (sorting nexin 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Snx6 (sorting nexin 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	SNX6 (sorting nexin 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	SNX6 (sorting nexin 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Snx6 (sorting nexin 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	SNX6 (sorting nexin 6)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Snx6 (sorting nexin 6)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	snx6 (sorting nexin 6)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	Snx6	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	snx-6	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	snx6	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	6	77,966,141 - 78,009,343 (-)	NCBI		GRCr8
mRatBN7.2	6	72,230,950 - 72,274,157 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	6	72,229,870 - 72,315,911 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	6	72,653,827 - 72,696,948 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	6	72,960,493 - 73,003,614 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	6	72,390,562 - 72,433,730 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	6	75,626,927 - 75,670,172 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	6	75,626,927 - 75,670,135 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	6	85,165,508 - 85,210,033 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	6	75,052,945 - 75,096,566 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	6	75,056,107 - 75,099,694 (-)	NCBI
Celera	6	71,076,843 - 71,119,862 (-)	NCBI		Celera
Cytogenetic Map	6	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

Brain-Lung-Thyroid Syndrome (ISO)

genetic disease (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(1->4)-beta-D-glucan (ISO)

1,2-dichloroethane (ISO)

1,2-dimethylhydrazine (ISO)

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

2,4-dinitrotoluene (EXP)

4,4'-diaminodiphenylmethane (ISO)

4,4'-sulfonyldiphenol (ISO)

4-hydroxyphenyl retinamide (ISO)

5-fluorouracil (ISO)

antirheumatic drug (ISO)

aristolochic acid A (ISO)

Aroclor 1254 (ISO)

atrazine (ISO)

benzo[a]pyrene (ISO)

bisphenol A (ISO)

clozapine (ISO)

copper(II) sulfate (ISO)

coumestrol (ISO)

cyclosporin A (ISO)

dibutyl phthalate (ISO)

dicrotophos (ISO)

Enterolactone (ISO)

enzyme inhibitor (ISO)

folic acid (ISO)

gentamycin (EXP)

gold atom (ISO)

gold(0) (ISO)

hypochlorous acid (ISO)

ivermectin (ISO)

lead diacetate (EXP)

lead(0) (EXP)

methidathion (ISO)

ozone (ISO)

paracetamol (ISO)

pentachlorophenol (ISO)

perfluorohexanesulfonic acid (ISO)

perfluorooctane-1-sulfonic acid (ISO)

Salinomycin (ISO)

sodium arsenite (EXP)

sunitinib (ISO)

tetrachloromethane (ISO)

thioacetamide (EXP)

titanium dioxide (ISO)

uranium atom (ISO)

valproic acid (ISO)

vitamin E (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

cellular response to amyloid-beta (ISO)

cellular response to epidermal growth factor stimulus (IDA)

intracellular protein transport (ISO)

negative regulation of DNA-templated transcription (ISO)

negative regulation of neuron apoptotic process (ISO)

negative regulation of transforming growth factor beta receptor signaling pathway (ISO)

regulation of histamine secretion by mast cell (ISO)

regulation of postsynaptic membrane neurotransmitter receptor levels (ISO)

retrograde transport, endosome to Golgi (IBA,ISO)

Cellular Component

cytoplasm (ISO)

cytosol (IEA)

early endosome membrane (ISO)

endosome (IBA,IDA,ISO)

glutamatergic synapse (ISO)

lysosome (IEA,ISO)

postsynaptic early endosome (ISO)

retromer complex (ISO)

tubular endosome (ISO)

Molecular Function

dynactin binding (IBA,ISO)

phosphatidylinositol binding (IEA)

protein binding (ISO)

protein homodimerization activity (ISO)

type I transforming growth factor beta receptor binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

retromer-mediated pathway (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	An epidermal growth factor (EGF) -dependent interaction between GIT1 and sorting nexin 6 promotes degradation of the EGF receptor.	Cavet ME, etal., FASEB J. 2008 Oct;22(10):3607-16. doi: 10.1096/fj.07-094086. Epub 2008 Jun 3.
2.	Retromer and sorting nexins in endosomal sorting.	Gallon M and Cullen PJ, Biochem Soc Trans. 2015 Feb;43(1):33-47. doi: 10.1042/BST20140290.
3.	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.
4.	Rat ISS GO annotations from GOA human gene data--August 2006	GOA data from the GO Consortium
5.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
6.	GOA pipeline	RGD automated data pipeline
7.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
9.	Comprehensive gene review and curation	RGD comprehensive gene curation

Additional References at PubMed

PMID:11279102	PMID:12477932	PMID:18253931	PMID:19619496	PMID:19935774	PMID:20830743	PMID:21266196	PMID:27541017

Genomics

Comparative Map Data

Snx6
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	6	77,966,141 - 78,009,343 (-)	NCBI		GRCr8
mRatBN7.2	6	72,230,950 - 72,274,157 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	6	72,229,870 - 72,315,911 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	6	72,653,827 - 72,696,948 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	6	72,960,493 - 73,003,614 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	6	72,390,562 - 72,433,730 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	6	75,626,927 - 75,670,172 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	6	75,626,927 - 75,670,135 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	6	85,165,508 - 85,210,033 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	6	75,052,945 - 75,096,566 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	6	75,056,107 - 75,099,694 (-)	NCBI
Celera	6	71,076,843 - 71,119,862 (-)	NCBI		Celera
Cytogenetic Map	6	q23	NCBI

SNX6
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	14	34,561,093 - 34,630,148 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	14	34,561,093 - 34,630,160 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	14	35,030,299 - 35,099,354 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	14	34,100,369 - 34,169,117 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	14	34,100,366 - 34,169,088	NCBI
Celera	14	14,894,794 - 14,963,537 (-)	NCBI		Celera
Cytogenetic Map	14	q13.1	NCBI
HuRef	14	15,145,531 - 15,213,532 (-)	NCBI		HuRef
CHM1_1	14	35,029,388 - 35,098,166 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	14	28,757,116 - 28,826,173 (-)	NCBI		T2T-CHM13v2.0

Snx6
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	12	54,793,124 - 54,842,464 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	12	54,793,134 - 54,842,488 (-)	Ensembl		GRCm39 Ensembl
GRCm38	12	54,746,339 - 54,795,749 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	12	54,746,349 - 54,795,703 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	12	55,847,344 - 55,896,649 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	12	55,667,983 - 55,713,796 (-)	NCBI		MGSCv36	mm8
Celera	12	56,055,971 - 56,093,720 (-)	NCBI		Celera
Cytogenetic Map	12	C1	NCBI
cM Map	12	23.46	NCBI

Snx6
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955409	26,319,951 - 26,352,994 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955409	26,323,940 - 26,353,675 (+)	NCBI	ChiLan1.0	ChiLan1.0

SNX6
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	15	35,879,343 - 35,948,427 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	14	35,096,838 - 35,164,633 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	14	15,319,526 - 15,388,326 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	14	33,511,019 - 33,576,699 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	14	33,511,019 - 33,576,705 (-)	Ensembl	panpan1.1		panPan2

SNX6
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	8	13,460,676 - 13,520,282 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	8	13,460,947 - 13,520,423 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	8	13,269,463 - 13,318,180 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	8	13,570,000 - 13,629,505 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	8	13,568,968 - 13,629,568 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	8	13,279,627 - 13,328,216 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	8	13,331,900 - 13,392,335 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	8	13,621,984 - 13,681,194 (-)	NCBI		UU_Cfam_GSD_1.0

Snx6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024408640	45,314,543 - 45,374,404 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936494	8,821,147 - 8,879,446 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936494	8,819,695 - 8,880,298 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SNX6
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	7	65,156,478 - 65,205,239 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	7	65,156,476 - 65,205,249 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	7	69,988,387 - 69,995,163 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

SNX6
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	24	11,389,436 - 11,433,126 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	24	11,388,329 - 11,433,545 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666053	339,232 - 407,901 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Snx6
(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_004624838	2,105,619 - 2,145,268 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624838	2,105,558 - 2,146,064 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Snx6
129 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	120
Count of miRNA genes:	82
Interacting mature miRNAs:	105
Transcripts:	ENSRNOT00000007300
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
4145119	Mcs25	Mammary carcinoma susceptibility QTL 25		0.0001	mammary gland integrity trait (VT:0010552)	ratio of deaths to total study population during a period of time (CMO:0001023)	6	10894415	110548006	Rat
1578665	Bss16	Bone structure and strength QTL 16	4.4		femur morphology trait (VT:0000559)	bone trabecular cross-sectional area (CMO:0002311)	6	11735669	72593685	Rat
1578668	Bmd14	Bone mineral density QTL 14	3.8		femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	6	11735669	72593685	Rat
1576309	Emca7	Estrogen-induced mammary cancer QTL 7	4		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	6	15107216	107351382	Rat
2293839	Kiddil2	Kidney dilation QTL 2	4.8		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	6	20866422	81133036	Rat
2293841	Kiddil4	Kidney dilation QTL 4	4.4		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	6	20866422	81133036	Rat
6893340	Cm77	Cardiac mass QTL 77	0.26	0.57	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	6	33309549	81132889	Rat
1300143	Rf14	Renal function QTL 14	2.92		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	6	34434137	77102317	Rat
634307	Bp141	Blood pressure QTL 141	4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	6	35230417	80230417	Rat
9590290	Uminl2	Urine mineral level QTL 2	3.96	0.001	urine mineral amount (VT:0015086)	urine electrolyte level (CMO:0000593)	6	38783989	83783989	Rat
9590306	Scort18	Serum corticosterone level QTL 18	2.88	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	6	38783989	83783989	Rat
9590140	Scort4	Serum corticosterone level QTL 4	14.49	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	6	38783989	83783989	Rat
634330	Pia16	Pristane induced arthritis QTL 16	3.9		joint integrity trait (VT:0010548)	arthritic paw count (CMO:0001460)	6	45790088	104200226	Rat
4889848	Pur25	Proteinuria QTL 25	14	0.003	urine total protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	6	56728562	90198260	Rat
6893332	Cm74	Cardiac mass QTL 74	0.4	0.64	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	6	57730540	104085867	Rat
1558641	Cm47	Cardiac mass QTL 47	2.9	0.001	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	6	57730540	104085867	Rat
70176	Mcsm1	Mammary carcinoma susceptibility modifier QTL 1			mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	6	58632962	103632962	Rat
12801471	Schws9	Schwannoma susceptibility QTL 9			nervous system integrity trait (VT:0010566)	percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)	6	61747639	106747639	Rat
731173	Uae22	Urinary albumin excretion QTL 22	10.1		urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	6	65531555	140994061	Rat
2290393	Uae37	Urinary albumin excretion QTL 37		0.0001	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	6	65531555	140994061	Rat
1641904	Alcrsp4	Alcohol response QTL 4			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	6	67262953	112262953	Rat
1300075	Glom7	Glomerulus QTL 7	5.6	0.0000002	kidney glomerulus morphology trait (VT:0005325)	count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)	6	71201409	116201409	Rat
1331789	Rf37	Renal function QTL 37	3.224		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal vascular resistance (CMO:0001900)	6	72202632	115200186	Rat
70196	BpQTLcluster7	Blood pressure QTL cluster 7	6.82		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	6	72202632	117202632	Rat
724536	Uae7	Urinary albumin excretion QTL 7	3.5		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	6	72202632	130729475	Rat
1331799	Bp211	Blood pressure QTL 211	3.66407		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	6	72202632	130919985	Rat
2301964	Bp323	Blood pressure QTL 323	4.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	6	72227641	81132889	Rat
1581550	Pur8	Proteinuria QTL 8			urine total protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	6	72227641	130729205	Rat
1581563	Uae33	Urinary albumin excretion QTL 33			urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	6	72227641	130729205	Rat

Markers in Region

RH129893

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	6	72,231,123 - 72,231,315 (+)	MAPPER	mRatBN7.2
Rnor_6.0	6	75,627,101 - 75,627,292	NCBI	Rnor6.0
Rnor_5.0	6	85,166,999 - 85,167,190	UniSTS	Rnor5.0
RGSC_v3.4	6	75,053,119 - 75,053,310	UniSTS	RGSC3.4
Celera	6	71,077,017 - 71,077,208	UniSTS
Cytogenetic Map	6	q23	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	41	56	40	19	40	6	6	74	35	40	11	6
Low		2	1	1		1	2	5			1		2
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001108711	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017594224	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC168856	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473947	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ218076	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000006	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSRNOT00000007300 ⟹ ENSRNOP00000007300

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	6	72,231,007 - 72,315,911 (-)	Ensembl
Rnor_6.0 Ensembl	6	75,626,927 - 75,670,135 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000117817 ⟹ ENSRNOP00000081270

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	6	72,229,870 - 72,274,131 (-)	Ensembl

RefSeq Acc Id:

NM_001108711 ⟹ NP_001102181

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	6	77,966,141 - 78,009,343 (-)	NCBI
mRatBN7.2	6	72,230,950 - 72,274,157 (-)	NCBI
Rnor_6.0	6	75,626,927 - 75,670,135 (-)	NCBI
Rnor_5.0	6	85,165,508 - 85,210,033 (-)	NCBI
RGSC_v3.4	6	75,052,945 - 75,096,566 (-)	RGD
Celera	6	71,076,843 - 71,119,862 (-)	RGD

Sequence:

show sequence

TCGTGGCCTTGCTTGTGAGTCTGCGCGAGACCTGGACTCGAAGCAGCCATGATGGAAGGCCTGG
ATGACGGCCCCGACTTCCTCTCGGAGGAAGACCGCGGACTTAAATCAATAAATGTAGATCTCCA
AAGTGATGCTGCTCTACAAGTGGACATTTCGGACGCTCTTAGTGAAAGGGATAAAGTCAAATTC
ACTGTTCACACAAAGAGTTCATTGCCAAATTTTAAGCAAAATGAGTTTTCAGTCGTTCGACAAC
ATGAGGAATTTATCTGGCTTCATGATTCCTTTGTTGAAAATGAAGACTATGCAGGTTACATTAT
CCCACCAGCACCACCAAGACCCGACTTTGATGCTTCACGGGAAAAACTGCAGAAGCTTGGAGAA
GGGGAAGGGTCAATGACAAAGGAAGAATTCACGAAGATGAAACAGGAGCTGGAAGCTGAGTATC
TGGCAATCTTCAAGAAGACAGTTGCGATGCATGAGGTGTTCCTGTGTCGTGTTGCCGCGCATCC
CATTTTGAGAAAAGATTTAAATTTCCACGTCTTCTTGGAATATAATCAAGATTTGAGTGTTCGA
GGAAAAAACAAAAAAGAAAAACTCGAGGATTTCTTTAAAAACATGGTTAAGTCAGCGGATGGAG
TAATTGTTTCAGGAGTAAAGGATGTAGATGACTTCTTTGAACATGAACGAACATTCCTTCTAGA
ATATCACAACCGAGTTAAGGATGCATCTGCTAAGTCTGACAGAATGACAAGATCTCACAAAAGT
GCTGCTGATGATTACAATAGAATTGGGTCTTCACTATATGCTTTAGGAACTCAGGACTCCACAG
ATATATGCAAGTTTTTCCTCAAAGTTTCAGAACTGTTTGATAAAACAAGAAAAATAGAAGCTCG
GGTGTCTGCTGATGAGGACCTCAAGCTTTCTGACCTACTAAAGTACTACTTGCGGGAGTCTCAA
GCAGCTAAGGACCTTCTCTATCGAAGGTCTAGGTCGCTGGTGGACTATGAAAATGCCAATAAAG
CACTGGACAAAGCAAGAGCAAAAAACAAAGATGTACTGCAGGCTGAGACCTCCCAACAGCTGTG
CTGTCAGAAGTTTGAAAAGATATCCGAATCTGCAAAACAAGAACTGATAGATTTTAAGACAAGA
AGAGTTGCTGCATTCAGAAAAAATTTAGTGGAACTTGCAGAACTAGAACTGAAGCATGCAAAGG
GTAACCTCCAGCTACTGCAGAACTGCCTTGCGGTTTTAAATGGAGACACATAGGCTTCACTCCA
CCTTCTGTTGAAAAGGGCTGCCTTCAGATCTGGTTTGTTTTCCTGAGGACCTCCGGCATCTAAG
CTCACTGGGAACAAAAGAAACAGCGGGCACAGTGCATCGGCTCTTCTGAGAGACCGTGGAGCAG
CAGGGCTCACCCTGCCACCTCGCACTCCACCTTCCAAGAAGCCCAAAGTTGAACCCTCTCTTTC
TTTAAGTAGCCTGTCTCAACTGTGTTTATCTCGTATGTGGCGATTCTGTGCCTGCAGGCCTTAT
TACCTAGGAATCGCTCGTCCAGTTTTAACATTCTCAGTACATTGTTCACGCAATTTAAAGGTTG
CCTTTCTGATTTTTTTTAAGCATCCTGTTCCTTAGTTCTTTCATGTATTCGTGTAAAGCATCTT
AATGAGACTTACTTTGAATTAATGAACGTAGAAGTTATGGGTCAGACTTTATGTAAGCTTTATA
CGTATGATCTCTGAAGAGAAGCAGATGCATTAGTATGTTTGCCTTAAACTCGTGGACTAAACCA
ATATTGTAAACCGCCGAGACACCAGCGGCATTTTTACTCCGTGCTCCTTGTATCGCTCTGGAAT
TCGGGGTAGCCATAATAAACCTACTCCGCTAGTATGCTTTACAGTGCAGGTCTTTTTTCTTCCC
CTCCTACCTTTCTT

hide sequence

Protein Sequences


Protein RefSeqs	NP_001102181	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAI68856	(Get FASTA)	NCBI Sequence Viewer
	EDM03414	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000007300.6
	ENSRNOP00000081270
	ENSRNOP00000081270.1

RefSeq Acc Id:

NP_001102181 ⟸ NM_001108711

- UniProtKB:

B5DEY8 (UniProtKB/TrEMBL), A0A8I5ZS69 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MMEGLDDGPDFLSEEDRGLKSINVDLQSDAALQVDISDALSERDKVKFTVHTKSSLPNFKQNEF
SVVRQHEEFIWLHDSFVENEDYAGYIIPPAPPRPDFDASREKLQKLGEGEGSMTKEEFTKMKQE
LEAEYLAIFKKTVAMHEVFLCRVAAHPILRKDLNFHVFLEYNQDLSVRGKNKKEKLEDFFKNMV
KSADGVIVSGVKDVDDFFEHERTFLLEYHNRVKDASAKSDRMTRSHKSAADDYNRIGSSLYALG
TQDSTDICKFFLKVSELFDKTRKIEARVSADEDLKLSDLLKYYLRESQAAKDLLYRRSRSLVDY
ENANKALDKARAKNKDVLQAETSQQLCCQKFEKISESAKQELIDFKTRRVAAFRKNLVELAELE
LKHAKGNLQLLQNCLAVLNGDT

hide sequence

RefSeq Acc Id:

ENSRNOP00000007300 ⟸ ENSRNOT00000007300

RefSeq Acc Id:

ENSRNOP00000081270 ⟸ ENSRNOT00000117817

Protein Domains

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-B5DEY8-F1-model_v2	AlphaFold	B5DEY8	1-406	view protein structure

Transcriptome

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

Promoters

RGD ID:

13694599

Promoter ID:

EPDNEW_R5123

Type:

multiple initiation site

Name:

Snx6_1

Description:

sorting nexin 6

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	6	75,670,111 - 75,670,171	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1304647	AgrOrtholog
BioCyc Gene	G2FUF-37506	BioCyc
Ensembl Genes	ENSRNOG00000005249	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000007300.6	UniProtKB/TrEMBL
	ENSRNOT00000117817	ENTREZGENE
	ENSRNOT00000117817.1	UniProtKB/TrEMBL
Gene3D-CATH	1.20.1270.60	UniProtKB/TrEMBL
	3.30.1520.10	UniProtKB/TrEMBL
InterPro	AH/BAR-dom	UniProtKB/TrEMBL
	IPR001683	UniProtKB/TrEMBL
	PX_dom_sf	UniProtKB/TrEMBL
	PX_SNX6	UniProtKB/TrEMBL
	Snx5_Snx6	UniProtKB/TrEMBL
	SNX6	UniProtKB/TrEMBL
	Vps5_C	UniProtKB/TrEMBL
KEGG Report	rno:362738	UniProtKB/TrEMBL
NCBI Gene	362738	ENTREZGENE
PANTHER	PTHR45850:SF4	UniProtKB/TrEMBL
	SORTING NEXIN FAMILY MEMBER	UniProtKB/TrEMBL
Pfam	PF00787	UniProtKB/TrEMBL
	Vps5	UniProtKB/TrEMBL
PhenoGen	Snx6	PhenoGen
PIRSF	Snx5_Snx6	UniProtKB/TrEMBL
PROSITE	PS50195	UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000005249	RatGTEx
Superfamily-SCOP	64268	UniProtKB/TrEMBL
	SSF103657	UniProtKB/TrEMBL
UniProt	A0A8I5ZS69	ENTREZGENE, UniProtKB/TrEMBL
	B5DEY8	ENTREZGENE, UniProtKB/TrEMBL
	F7FPM8_RAT	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-04-30	Snx6	sorting nexin 6	Snx6_predicted	sorting nexin 6 (predicted)	'predicted' is removed	2292626	APPROVED
2005-01-12	Snx6_predicted	sorting nexin 6 (predicted)			Symbol and Name status set to approved	70820	APPROVED

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

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Imported Disease Annotations - ClinVar

RGD Manual Annotations