Snx6 (sorting nexin 6) - Rat Genome Database

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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
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2672,230,950 - 72,274,157 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl672,229,870 - 72,315,911 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx672,653,827 - 72,696,948 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0672,960,493 - 73,003,614 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0672,390,562 - 72,433,730 (-)NCBIRnor_WKY
Rnor_6.0675,626,927 - 75,670,172 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl675,626,927 - 75,670,135 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0685,165,508 - 85,210,033 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4675,052,945 - 75,096,566 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1675,056,107 - 75,099,694 (-)NCBI
Celera671,076,843 - 71,119,862 (-)NCBICelera
Cytogenetic Map6q23NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Molecular Pathway Annotations     Click to see Annotation Detail View
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 AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2672,230,950 - 72,274,157 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl672,229,870 - 72,315,911 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx672,653,827 - 72,696,948 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0672,960,493 - 73,003,614 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0672,390,562 - 72,433,730 (-)NCBIRnor_WKY
Rnor_6.0675,626,927 - 75,670,172 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl675,626,927 - 75,670,135 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0685,165,508 - 85,210,033 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4675,052,945 - 75,096,566 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1675,056,107 - 75,099,694 (-)NCBI
Celera671,076,843 - 71,119,862 (-)NCBICelera
Cytogenetic Map6q23NCBI
SNX6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381434,561,093 - 34,630,148 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1434,561,093 - 34,630,160 (-)EnsemblGRCh38hg38GRCh38
GRCh371435,030,299 - 35,099,354 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361434,100,369 - 34,169,117 (-)NCBINCBI36Build 36hg18NCBI36
Build 341434,100,366 - 34,169,088NCBI
Celera1414,894,794 - 14,963,537 (-)NCBICelera
Cytogenetic Map14q13.1NCBI
HuRef1415,145,531 - 15,213,532 (-)NCBIHuRef
CHM1_11435,029,388 - 35,098,166 (-)NCBICHM1_1
T2T-CHM13v2.01428,757,116 - 28,826,173 (-)NCBIT2T-CHM13v2.0
Snx6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391254,793,124 - 54,842,663 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1254,793,134 - 54,842,488 (-)EnsemblGRCm39 Ensembl
GRCm381254,746,339 - 54,795,749 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1254,746,349 - 54,795,703 (-)EnsemblGRCm38mm10GRCm38
MGSCv371255,847,344 - 55,896,649 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361255,667,983 - 55,713,796 (-)NCBIMGSCv36mm8
Celera1256,055,971 - 56,093,720 (-)NCBICelera
Cytogenetic Map12C1NCBI
Snx6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540926,319,951 - 26,352,994 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540926,323,940 - 26,353,675 (+)NCBIChiLan1.0ChiLan1.0
SNX6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11433,511,019 - 33,576,699 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1433,511,019 - 33,576,705 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01415,319,526 - 15,388,326 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
SNX6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1813,460,676 - 13,520,282 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl813,460,947 - 13,520,423 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha813,269,463 - 13,318,180 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0813,570,000 - 13,629,505 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl813,568,968 - 13,629,568 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1813,279,627 - 13,328,216 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0813,331,900 - 13,392,335 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0813,621,984 - 13,681,194 (-)NCBIUU_Cfam_GSD_1.0
Snx6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864045,314,543 - 45,374,404 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364948,821,147 - 8,879,446 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049364948,819,695 - 8,880,298 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SNX6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl765,156,478 - 65,205,239 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1765,156,476 - 65,205,249 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2769,988,387 - 69,995,163 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SNX6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12411,389,436 - 11,433,126 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2411,388,329 - 11,433,545 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666053339,232 - 407,901 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Snx6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248382,105,619 - 2,145,268 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248382,105,558 - 2,146,064 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Snx6
100 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.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)610894415110548006Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)61173566972593685Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)61173566972593685Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)615107216107351382Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat
6893340Cm77Cardiac mass QTL 770.260.57heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)63330954981132889Rat
1300143Rf14Renal function QTL 142.92renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)63443413777102317Rat
634307Bp141Blood pressure QTL 1414arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)63523041780230417Rat
9590290Uminl2Urine mineral level QTL 23.960.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)63878398983783989Rat
9590306Scort18Serum corticosterone level QTL 182.880.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)63878398983783989Rat
9590140Scort4Serum corticosterone level QTL 414.490.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)63878398983783989Rat
634330Pia16Pristane induced arthritis QTL 163.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)645790088104200226Rat
4889848Pur25Proteinuria QTL 25140.003urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)65672856290198260Rat
6893332Cm74Cardiac mass QTL 740.40.64heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)657730540104085867Rat
1558641Cm47Cardiac mass QTL 472.90.001heart mass (VT:0007028)heart wet weight (CMO:0000069)657730540104085867Rat
70176Mcsm1Mammary carcinoma susceptibility modifier QTL 1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)658632962103632962Rat
12801471Schws9Schwannoma susceptibility QTL 9nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)661747639106747639Rat
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
1641904Alcrsp4Alcohol response QTL 4response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)667262953112262953Rat
1300075Glom7Glomerulus QTL 75.60.0000002kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)671201409116201409Rat
1331789Rf37Renal function QTL 373.224kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)672202632115200186Rat
70196BpQTLcluster7Blood pressure QTL cluster 76.82arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)672202632117202632Rat
724536Uae7Urinary albumin excretion QTL 73.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)672202632130729475Rat
1331799Bp211Blood pressure QTL 2113.66407arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)672202632130919985Rat
2301964Bp323Blood pressure QTL 3234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)67222764181132889Rat
1581550Pur8Proteinuria QTL 8urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)672227641130729205Rat
1581563Uae33Urinary albumin excretion QTL 33urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)672227641130729205Rat

Markers in Region
RH129893  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2672,231,123 - 72,231,315 (+)MAPPERmRatBN7.2
Rnor_6.0675,627,101 - 75,627,292NCBIRnor6.0
Rnor_5.0685,166,999 - 85,167,190UniSTSRnor5.0
RGSC_v3.4675,053,119 - 75,053,310UniSTSRGSC3.4
Celera671,077,017 - 71,077,208UniSTS
Cytogenetic Map6q23UniSTS


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

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000007300   ⟹   ENSRNOP00000007300
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl672,231,007 - 72,315,911 (-)Ensembl
Rnor_6.0 Ensembl675,626,927 - 75,670,135 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000117817   ⟹   ENSRNOP00000081270
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl672,229,870 - 72,274,131 (-)Ensembl
RefSeq Acc Id: NM_001108711   ⟹   NP_001102181
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2672,230,950 - 72,274,157 (-)NCBI
Rnor_6.0675,626,927 - 75,670,135 (-)NCBI
Rnor_5.0685,165,508 - 85,210,033 (-)NCBI
RGSC_v3.4675,052,945 - 75,096,566 (-)RGD
Celera671,076,843 - 71,119,862 (-)RGD
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  
Reference Sequences
RefSeq Acc Id: NP_001102181   ⟸   NM_001108711
- UniProtKB: B5DEY8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000007300   ⟸   ENSRNOT00000007300
RefSeq Acc Id: ENSRNOP00000081270   ⟸   ENSRNOT00000117817
Protein Domains
PX

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 AssemblyChrPosition (strand)Source
Rnor_6.0675,670,111 - 75,670,171EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1304647 AgrOrtholog
BioCyc Gene G2FUF-37506 BioCyc
Ensembl Genes ENSRNOG00000005249 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000007300.6 UniProtKB/TrEMBL
  ENSRNOP00000081270 ENTREZGENE
  ENSRNOP00000081270.1 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
Pfam PF00787 UniProtKB/TrEMBL
  Vps5 UniProtKB/TrEMBL
PhenoGen Snx6 PhenoGen
PIRSF Snx5_Snx6 UniProtKB/TrEMBL
PROSITE PS50195 UniProtKB/TrEMBL
Superfamily-SCOP 64268 UniProtKB/TrEMBL
  SSF103657 UniProtKB/TrEMBL
UniProt A0A8I5ZS69_RAT 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