Snx6 (sorting nexin 6) - Rat Genome Database

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Gene: Snx6 (sorting nexin 6) Mus musculus
Analyze
Symbol: Snx6
Name: sorting nexin 6
RGD ID: 1312209
MGI Page MGI
Description: Enables type I transforming growth factor beta receptor binding activity. Involved in regulation of postsynaptic membrane neurotransmitter receptor levels. Is active in glutamatergic synapse. Is expressed in brain; cerebral cortex ventricular layer; and cortical plate. Orthologous to human SNX6 (sorting nexin 6).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 2010006G21Rik; 2610032J07Rik; 2810425K19Rik; AU018928; C85963; sorting nexin-6
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391254,793,124 - 54,842,464 (-)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
cM Map1223.46NCBI
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. 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.
2. Functional annotation of a full-length mouse cDNA collection. Kawai J, etal., Nature. 2001 Feb 8;409(6821):685-90.
3. Large-scale cDNA analysis reveals phased gene expression patterns during preimplantation mouse development. Ko MS, etal., Development 2000 Apr;127(8):1737-49.
4. MGDs mouse GO annotations MGD data from the GO Consortium
5. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8889548   PMID:10349636   PMID:10922068   PMID:11042159   PMID:11076861   PMID:12477932   PMID:12520002   PMID:14610273   PMID:15489334   PMID:15782199   PMID:16141072   PMID:16141073  
PMID:17967808   PMID:18523162   PMID:18655203   PMID:18799693   PMID:21266196   PMID:21267068   PMID:21873635   PMID:24457600   PMID:25535984   PMID:27103069   PMID:28134614   PMID:29666193  
PMID:32325033   PMID:32554809   PMID:34321999  


Genomics

Comparative Map Data
Snx6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391254,793,124 - 54,842,464 (-)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
cM Map1223.46NCBI
SNX6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381434,561,093 - 34,630,148 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 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
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8677,966,141 - 78,009,343 (-)NCBIGRCr8
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_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0672,960,493 - 73,003,614 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0672,390,562 - 72,433,730 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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
(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
NHGRI_mPanPan1-v21535,879,343 - 35,948,427 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11435,096,838 - 35,164,633 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01415,319,526 - 15,388,326 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11433,511,019 - 33,576,699 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1433,511,019 - 33,576,705 (-)Ensemblpanpan1.1panPan2
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 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
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
1880 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:230
Count of miRNA genes:170
Interacting mature miRNAs:197
Transcripts:ENSMUST00000005798
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4142234Tmc1m3_mTmc1 modifier 3 (mouse)Not determined12541844077031203Mouse
27226753Femd7_mfemur midshaft diameter 7, 10 week (mouse)12955000084146774Mouse
13207568Tcq14_mtotal cholesterol QTL 14 (mouse)121166000197176774Mouse
13524839Ppiq10_mprepulse inhibition QTL 10 (mouse)121304319554945798Mouse
1558978Cplaq10_mcircadian period of locomotor activity 10 (mouse)Not determined121534102679040364Mouse
1301574Lmblgq5_mlimb length QTL 5 (mouse)Not determined121759644780956883Mouse
1302172Skts5_mskin tumor susceptibility 5 (mouse)Not determined122214886656149016Mouse
1301989Hdlq18_mHDL QTL 18 (mouse)Not determined122916068563160884Mouse
1300636Gct2_mgranulosa cell tumorigenesis 2 (mouse)Not determined122916068563160884Mouse
4141843Moen3_mmodifier of engrailed QTL 3 (mouse)Not determined122980158463801733Mouse
14747008Mancz10_mmandible centroid size 10 (mouse)122986352263863522Mouse
10402492Dipa8_mdrug induced psychomotor activation 8 (mouse)Not determined123493387268934019Mouse
1300818Bbaa10_mB.burgdorferi-associated arthritis 10 (mouse)Not determined123509100465511019Mouse
4142002Tbqt3_mtibia bone quality traits 3 (mouse)Not determined1235285496109936243Mouse
1357479Splwt1_mspleen weight 1 (mouse)Not determined124169317590887526Mouse
1357757Lnopy2_mlens opacity 2 (mouse)Not determined125284662686846796Mouse
1357749Vtbt13_mvertebral trabecular bone trait 13 (mouse)Not determined125313200287132145Mouse
12904004Opfaq11_mopen field activity QTL 11 (mouse)125315562457276756Mouse
12832727Ahrq1_mairway hyperresponsiveness QTL 1 (mouse)125469591082665939Mouse

Markers in Region
RH127247  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381254,746,362 - 54,746,583UniSTSGRCm38
MGSCv371255,847,349 - 55,847,570UniSTSGRCm37
Cytogenetic Map12C1UniSTS
Whitehead/MRC_RH12524.24UniSTS
RH136517  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381254,746,381 - 54,746,556UniSTSGRCm38
MGSCv371255,847,368 - 55,847,543UniSTSGRCm37
Cytogenetic Map12C1UniSTS


Expression


Sequence


RefSeq Acc Id: ENSMUST00000005798   ⟹   ENSMUSP00000005798
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1254,793,134 - 54,842,488 (-)Ensembl
GRCm38.p6 Ensembl1254,746,349 - 54,795,703 (-)Ensembl
RefSeq Acc Id: ENSMUST00000218066
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1254,814,836 - 54,842,269 (-)Ensembl
GRCm38.p6 Ensembl1254,768,051 - 54,795,484 (-)Ensembl
RefSeq Acc Id: ENSMUST00000218337
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1254,814,788 - 54,817,767 (-)Ensembl
GRCm38.p6 Ensembl1254,768,003 - 54,770,982 (-)Ensembl
RefSeq Acc Id: ENSMUST00000218934   ⟹   ENSMUSP00000151488
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1254,793,435 - 54,842,267 (-)Ensembl
GRCm38.p6 Ensembl1254,746,650 - 54,795,482 (-)Ensembl
RefSeq Acc Id: ENSMUST00000219302
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1254,829,871 - 54,842,437 (-)Ensembl
GRCm38.p6 Ensembl1254,783,086 - 54,795,652 (-)Ensembl
RefSeq Acc Id: ENSMUST00000219722
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1254,803,660 - 54,807,268 (-)Ensembl
GRCm38.p6 Ensembl1254,756,875 - 54,760,483 (-)Ensembl
RefSeq Acc Id: ENSMUST00000219781   ⟹   ENSMUSP00000151460
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1254,812,434 - 54,842,449 (-)Ensembl
GRCm38.p6 Ensembl1254,765,649 - 54,795,664 (-)Ensembl
RefSeq Acc Id: ENSMUST00000219865
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1254,841,960 - 54,842,472 (-)Ensembl
GRCm38.p6 Ensembl1254,795,175 - 54,795,687 (-)Ensembl
RefSeq Acc Id: NM_001416020   ⟹   NP_001402949
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391254,793,124 - 54,842,464 (-)NCBI
RefSeq Acc Id: NM_026998   ⟹   NP_081274
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391254,793,124 - 54,842,464 (-)NCBI
GRCm381254,746,357 - 54,795,662 (-)NCBI
MGSCv371255,847,344 - 55,896,649 (-)RGD
Celera1256,055,971 - 56,093,720 (-)RGD
cM Map12 ENTREZGENE
Sequence:
RefSeq Acc Id: NP_081274   ⟸   NM_026998
- Peptide Label: isoform 1
- UniProtKB: Q9CZ03 (UniProtKB/Swiss-Prot),   Q6P8X1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSMUSP00000151488   ⟸   ENSMUST00000218934
RefSeq Acc Id: ENSMUSP00000151460   ⟸   ENSMUST00000219781
RefSeq Acc Id: ENSMUSP00000005798   ⟸   ENSMUST00000005798
RefSeq Acc Id: NP_001402949   ⟸   NM_001416020
- Peptide Label: isoform 2
Protein Domains
BAR   PX   Sorting nexin/Vps5-like C-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6P8X1-F1-model_v2 AlphaFold Q6P8X1 1-406 view protein structure

Promoters
RGD ID:8678276
Promoter ID:EPDNEW_M17169
Type:initiation region
Name:Snx6_1
Description:Mus musculus sorting nexin 6 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381254,795,679 - 54,795,739EPDNEW
RGD ID:6823435
Promoter ID:MM_KWN:11657
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day4,   3T3L1_Day6,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Liver,   Lung,   MEF_B4,   MEF_B6,   Spleen
Transcripts:NM_026998,   UC007NNW.1
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361255,896,419 - 55,896,919 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1919433 AgrOrtholog
Ensembl Genes ENSMUSG00000005656 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000005798 ENTREZGENE
  ENSMUST00000005798.9 UniProtKB/Swiss-Prot
  ENSMUST00000218934.2 UniProtKB/TrEMBL
  ENSMUST00000219781.2 UniProtKB/TrEMBL
Gene3D-CATH 1.20.1270.60 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.1520.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro AH/BAR_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Phox UniProtKB/Swiss-Prot
  PX_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PX_SNX6 UniProtKB/Swiss-Prot
  SNX5/SNX6/SNX32 UniProtKB/Swiss-Prot
  SNX6 UniProtKB/Swiss-Prot
  Vps5_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:72183 UniProtKB/Swiss-Prot
MGD MGI:1919433 ENTREZGENE
NCBI Gene 72183 ENTREZGENE
PANTHER PTHR45850:SF4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SORTING NEXIN FAMILY MEMBER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam PF00787 UniProtKB/Swiss-Prot
  Vps5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Snx6 PhenoGen
PIRSF Snx5_Snx6 UniProtKB/Swiss-Prot
PROSITE PS50195 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF103657 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF64268 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A1W2P6Y0_MOUSE UniProtKB/TrEMBL
  A0A1W2P701_MOUSE UniProtKB/TrEMBL
  Q6P8X1 ENTREZGENE
  Q8R0Z4_MOUSE UniProtKB/TrEMBL
  Q9CZ03 ENTREZGENE
  SNX6_MOUSE UniProtKB/Swiss-Prot
UniProt Secondary Q9CZ03 UniProtKB/Swiss-Prot