Snx3 (sorting nexin 3) - Rat Genome Database

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Pathways
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Gene: Snx3 (sorting nexin 3) Rattus norvegicus
Analyze
Symbol: Snx3
Name: sorting nexin 3
RGD ID: 1595151
Description: Predicted to enable phosphatidylinositol phosphate binding activity; protein phosphatase binding activity; and retromer complex binding activity. Predicted to be involved in several processes, including endosomal transport; intralumenal vesicle formation; and negative regulation of transport. Predicted to act upstream of or within several processes, including hemoglobin biosynthetic process; regulation of intracellular protein transport; and transferrin transport. Predicted to be located in cytoplasmic vesicle and cytosol. Predicted to be part of retromer complex. Predicted to be active in early endosome membrane. Orthologous to human SNX3 (sorting nexin 3); PARTICIPATES IN retromer-mediated pathway; INTERACTS WITH 6-propyl-2-thiouracil; amitrole; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC684097; similar to sorting nexin 3; sorting nexin-3
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82047,574,051 - 47,607,577 (+)NCBIGRCr8
mRatBN7.22045,992,446 - 46,025,361 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2045,992,720 - 46,025,379 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2047,710,148 - 47,742,787 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02047,360,312 - 47,392,951 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02048,053,233 - 48,086,017 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02047,225,382 - 47,263,390 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2047,225,619 - 47,263,390 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02048,923,090 - 48,932,814 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera2053,947,195 - 53,979,808 (-)NCBICelera
Cytogenetic Map20q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
clathrin-coated vesicle  (ISO,ISS)
cytoplasm  (ISO)
cytosol  (ISO)
early endosome  (ISO,ISS)
early endosome membrane  (IBA,IEA,ISO)
early phagosome  (ISO,ISS)
endosome membrane  (ISO,ISS)
retromer complex  (IBA,IEA,ISO)

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. 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.
3. GOA pipeline RGD automated data pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Comprehensive gene review and curation 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 AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82047,574,051 - 47,607,577 (+)NCBIGRCr8
mRatBN7.22045,992,446 - 46,025,361 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2045,992,720 - 46,025,379 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2047,710,148 - 47,742,787 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02047,360,312 - 47,392,951 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02048,053,233 - 48,086,017 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02047,225,382 - 47,263,390 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2047,225,619 - 47,263,390 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02048,923,090 - 48,932,814 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera2053,947,195 - 53,979,808 (-)NCBICelera
Cytogenetic Map20q13NCBI
SNX3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386108,211,222 - 108,261,040 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6108,211,222 - 108,261,246 (-)EnsemblGRCh38hg38GRCh38
GRCh376108,532,426 - 108,582,244 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 366108,639,410 - 108,689,156 (-)NCBINCBI36Build 36hg18NCBI36
Build 346108,639,410 - 108,689,156NCBI
Celera6109,279,209 - 109,328,955 (-)NCBICelera
Cytogenetic Map6q21NCBI
HuRef6106,100,989 - 106,150,564 (-)NCBIHuRef
CHM1_16108,795,674 - 108,845,435 (-)NCBICHM1_1
T2T-CHM13v2.06109,388,338 - 109,438,159 (-)NCBIT2T-CHM13v2.0
Snx3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391042,378,050 - 42,411,365 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1042,378,026 - 42,411,377 (+)EnsemblGRCm39 Ensembl
GRCm381042,502,054 - 42,535,369 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1042,502,030 - 42,535,381 (+)EnsemblGRCm38mm10GRCm38
MGSCv371042,221,860 - 42,255,175 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361042,190,444 - 42,223,782 (+)NCBIMGSCv36mm8
Celera1043,369,479 - 43,403,088 (+)NCBICelera
Cytogenetic Map10B2NCBI
cM Map1022.89NCBI
Snx3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541133,340,274 - 33,345,500 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541133,339,974 - 33,344,563 (-)NCBIChiLan1.0ChiLan1.0
SNX3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v25128,216,245 - 128,269,590 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan16126,106,433 - 126,156,957 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v06106,010,633 - 106,063,331 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.16109,874,095 - 109,924,185 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6109,874,105 - 109,924,185 (-)Ensemblpanpan1.1panPan2
SNX3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11265,252,175 - 65,294,620 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1265,252,175 - 65,294,611 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1265,067,774 - 65,110,209 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01266,127,936 - 66,170,477 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1266,127,942 - 66,170,467 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11265,483,130 - 65,525,574 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01265,329,591 - 65,371,812 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01265,602,544 - 65,644,998 (-)NCBIUU_Cfam_GSD_1.0
Snx3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946100,197,614 - 100,245,855 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365644,471,652 - 4,520,785 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365644,472,171 - 4,520,732 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SNX3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl174,306,455 - 74,349,335 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1174,306,450 - 74,349,735 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2183,576,787 - 83,585,208 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SNX3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11365,590,413 - 65,640,368 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1365,589,801 - 65,640,876 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604037,916,042 - 37,966,796 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Snx3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462478014,043,003 - 14,080,380 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462478014,043,002 - 14,080,380 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Snx3
203 total Variants
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201175751554435887Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201175751554435887Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)201761783247606836Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201769755054435887Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)201919072154435887Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202510672254435887Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202510672254435887Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202510672254435887Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202520973454435887Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)202924438854435887Rat

Markers in Region
REN49968  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22046,013,127 - 46,013,385 (+)MAPPERmRatBN7.2
Rnor_6.02047,251,161 - 47,251,418NCBIRnor6.0
Rnor_5.02048,920,585 - 48,920,842UniSTSRnor5.0
Celera2053,959,169 - 53,959,426UniSTS


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

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000074532
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2045,992,965 - 46,025,361 (+)Ensembl
Rnor_6.0 Ensembl2047,225,619 - 47,263,389 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000075924
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2045,992,720 - 46,025,379 (+)Ensembl
Rnor_6.0 Ensembl2047,253,664 - 47,263,390 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000103931   ⟹   ENSRNOP00000082616
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2045,993,047 - 46,025,361 (+)Ensembl
RefSeq Acc Id: NM_001044283   ⟹   NP_001037748
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82047,574,940 - 47,607,577 (+)NCBI
mRatBN7.22045,992,721 - 46,025,361 (+)NCBI
Rnor_6.02047,225,382 - 47,263,390 (+)NCBI
Rnor_5.02048,923,090 - 48,932,814 (+)NCBI
Celera2053,947,195 - 53,979,808 (-)RGD
Sequence:
RefSeq Acc Id: XM_039099063   ⟹   XP_038954991
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82047,574,051 - 47,607,577 (+)NCBI
mRatBN7.22045,992,446 - 46,025,361 (+)NCBI
RefSeq Acc Id: XM_039099064   ⟹   XP_038954992
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82047,574,051 - 47,607,577 (+)NCBI
mRatBN7.22045,992,446 - 46,025,361 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001037748   ⟸   NM_001044283
- UniProtKB: Q5U211 (UniProtKB/Swiss-Prot),   A6K6Y8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_038954991   ⟸   XM_039099063
- Peptide Label: isoform X1
- UniProtKB: B0BMY2 (UniProtKB/TrEMBL),   A0A8I6A603 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038954992   ⟸   XM_039099064
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000082616   ⟸   ENSRNOT00000103931
Protein Domains
PX

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

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1595151 AgrOrtholog
BioCyc Gene G2FUF-3359 BioCyc
Ensembl Genes ENSRNOG00000046705 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSRNOG00055000791 UniProtKB/Swiss-Prot
  ENSRNOG00060006605 UniProtKB/Swiss-Prot
  ENSRNOG00065008686 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000074532 ENTREZGENE
  ENSRNOT00000074532.4 UniProtKB/Swiss-Prot
  ENSRNOT00000075924.2 UniProtKB/TrEMBL
  ENSRNOT00000103931.1 UniProtKB/TrEMBL
  ENSRNOT00055001369 UniProtKB/Swiss-Prot
  ENSRNOT00060010863 UniProtKB/Swiss-Prot
  ENSRNOT00065013811 UniProtKB/Swiss-Prot
Gene3D-CATH 3.30.1520.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7301775 IMAGE-MGC_LOAD
  IMAGE:7301779 IMAGE-MGC_LOAD
  IMAGE:7458016 IMAGE-MGC_LOAD
InterPro Phox UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PX_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PX_SNX3_Vert UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:684097 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:105945 IMAGE-MGC_LOAD
  MGC:125029 IMAGE-MGC_LOAD
  MGC:187477 IMAGE-MGC_LOAD
NCBI Gene 684097 ENTREZGENE
PANTHER RE52028P UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SORTING NEXIN-3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam PF00787 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Snx3 PhenoGen
PROSITE PS50195 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000046705 RatGTEx
  ENSRNOG00055000791 RatGTEx
  ENSRNOG00060006605 RatGTEx
  ENSRNOG00065008686 RatGTEx
SMART SM00312 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF64268 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I5ZVK8_RAT UniProtKB/TrEMBL
  A0A8I6A603 ENTREZGENE, UniProtKB/TrEMBL
  A6K6Y8 ENTREZGENE, UniProtKB/TrEMBL
  B0BMY2 ENTREZGENE, UniProtKB/TrEMBL
  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