Snx20 (sorting nexin 20) - Rat Genome Database

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Gene: Snx20 (sorting nexin 20) Rattus norvegicus
Analyze
Symbol: Snx20
Name: sorting nexin 20
RGD ID: 1307787
Description: Predicted to enable phosphatidylinositol-3-phosphate binding activity and phosphatidylinositol-4,5-bisphosphate binding activity. Predicted to be involved in protein transport. Predicted to be located in endosome; nucleoplasm; and plasma membrane. Predicted to be active in early endosome membrane. Orthologous to human SNX20 (sorting nexin 20); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acetamide; aflatoxin B1.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC307742; MGC108869; RGD1307787; selectin ligand interactor cytoplasmic-1; similar to RIKEN cDNA 9130017C17 gene; Slic1; sorting nexin-20
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81934,609,397 - 34,618,569 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1934,609,412 - 34,618,567 (+)EnsemblGRCr8
mRatBN7.21918,435,935 - 18,445,108 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1918,435,935 - 18,445,107 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1920,115,486 - 20,124,660 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01925,310,096 - 25,319,280 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01928,267,854 - 28,277,004 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01919,395,655 - 19,404,846 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1919,395,655 - 19,404,835 (+)Ensemblrn6Rnor6.0
Rnor_5.01930,428,393 - 30,436,777 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41919,715,997 - 19,726,145 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1918,322,643 - 18,331,589 (+)NCBICelera
RGSC_v3.11919,720,822 - 19,730,970 (+)NCBI
Cytogenetic Map19p11NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (IEA)
early endosome membrane  (IBA,IEA,ISO,ISS)
nucleus  (IEA)
plasma membrane  (IEA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. 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.
2. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:25882846  


Genomics

Comparative Map Data
Snx20
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81934,609,397 - 34,618,569 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1934,609,412 - 34,618,567 (+)EnsemblGRCr8
mRatBN7.21918,435,935 - 18,445,108 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1918,435,935 - 18,445,107 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1920,115,486 - 20,124,660 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01925,310,096 - 25,319,280 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01928,267,854 - 28,277,004 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01919,395,655 - 19,404,846 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1919,395,655 - 19,404,835 (+)Ensemblrn6Rnor6.0
Rnor_5.01930,428,393 - 30,436,777 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41919,715,997 - 19,726,145 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1918,322,643 - 18,331,589 (+)NCBICelera
RGSC_v3.11919,720,822 - 19,730,970 (+)NCBI
Cytogenetic Map19p11NCBI
SNX20
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381650,666,300 - 50,681,312 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1650,666,300 - 50,681,743 (-)Ensemblhg38GRCh38
GRCh371650,700,211 - 50,715,223 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361649,264,387 - 49,272,667 (-)NCBIBuild 36Build 36hg18NCBI36
Celera1635,215,527 - 35,230,577 (-)NCBICelera
Cytogenetic Map16q12.1NCBI
HuRef1636,588,004 - 36,603,054 (-)NCBIHuRef
CHM1_11652,107,729 - 52,122,779 (-)NCBICHM1_1
T2T-CHM13v2.01656,463,916 - 56,478,923 (-)NCBIT2T-CHM13v2.0
Snx20
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39889,353,189 - 89,362,769 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl889,353,191 - 89,362,756 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38888,626,561 - 88,636,133 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl888,626,563 - 88,636,128 (-)Ensemblmm10GRCm38
MGSCv37891,150,727 - 91,160,027 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36891,516,933 - 91,526,233 (-)NCBIMGSCv36mm8
Celera892,907,268 - 92,916,455 (-)NCBICelera
Cytogenetic Map8C3NCBI
cM Map843.51NCBI
Snx20
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554338,727,493 - 8,731,398 (-)Ensembl
ChiLan1.0NW_0049554338,725,950 - 8,734,699 (-)NCBIChiLan1.0ChiLan1.0
SNX20
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21860,124,381 - 60,138,701 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11666,030,121 - 66,044,337 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01630,928,545 - 30,944,509 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11649,814,315 - 49,822,209 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1649,809,077 - 49,818,459 (-)EnsemblpanPan2panpan1.1
SNX20
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1264,681,329 - 64,689,825 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl264,681,303 - 64,692,486 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha261,254,013 - 61,262,796 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0265,226,579 - 65,235,362 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl265,226,554 - 65,237,740 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1262,050,248 - 62,059,016 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0263,070,208 - 63,078,984 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0263,957,752 - 63,966,522 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
SNX20
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl634,176,748 - 34,191,570 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1634,176,753 - 34,188,233 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
SNX20
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1536,467,839 - 36,481,083 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl536,469,366 - 36,480,514 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604740,021,561 - 40,031,658 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Snx20
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247576,014,238 - 6,019,378 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247576,011,750 - 6,019,378 (+)NCBIHetGla 1.0HetGla 1.0hetGla2

Variants

.
Variants in Snx20
38 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:41
Count of miRNA genes:39
Interacting mature miRNAs:41
Transcripts:ENSRNOT00000019130
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
8552935Pigfal10Plasma insulin-like growth factor 1 level QTL 105.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)19799775052997750Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)191922068964220689Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19799775052997750Rat
631840Niddm38Non-insulin dependent diabetes mellitus QTL 383.86blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)191032907674246245Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)19574806450748064Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)193236531174246245Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)193628974246245Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)192409397369093973Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191083361874246245Rat
2303628Vencon9Ventilatory control QTL 90.005respiration trait (VT:0001943)minute ventilation (CMO:0000132)192318858668188586Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)193253961574246245Rat
1558656Prcs1Prostate cancer susceptibility QTL 15prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)193128753251431640Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19799775052997750Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19799775052997750Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)193177788874246245Rat
1554318Bmd5Bone mineral density QTL 512.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)192318858668188586Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)192010930665109306Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19219431774246245Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19219431774246245Rat
61407Scl12Serum cholesterol level QTL 120.001blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)193009938347207961Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 163 91 90 59 92 59 6 356 192 11 136 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000019130   ⟹   ENSRNOP00000019130
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1934,609,412 - 34,618,567 (+)Ensembl
mRatBN7.2 Ensembl1918,435,935 - 18,445,107 (+)Ensembl
Rnor_6.0 Ensembl1919,395,655 - 19,404,835 (+)Ensembl
RefSeq Acc Id: NM_001024999   ⟹   NP_001020170
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81934,609,397 - 34,618,569 (+)NCBI
mRatBN7.21918,435,935 - 18,445,108 (+)NCBI
Rnor_6.01919,395,655 - 19,404,836 (+)NCBI
Rnor_5.01930,428,393 - 30,436,777 (+)NCBI
RGSC_v3.41919,715,997 - 19,726,145 (+)RGD
Celera1918,322,643 - 18,331,589 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001020170 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH91194 (Get FASTA)   NCBI Sequence Viewer  
  EDL87528 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000019130
  ENSRNOP00000019130.4
GenBank Protein Q5BK61 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001020170   ⟸   NM_001024999
- UniProtKB: Q5BK61 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSRNOP00000019130   ⟸   ENSRNOT00000019130
Protein Domains
PX

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5BK61-F1-model_v2 AlphaFold Q5BK61 1-313 view protein structure

Transcriptome

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

Promoters
RGD ID:13700975
Promoter ID:EPDNEW_R11499
Type:multiple initiation site
Name:Snx20_1
Description:sorting nexin 20
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_6.01919,395,643 - 19,395,703EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307787 AgrOrtholog
BioCyc Gene G2FUF-6279 BioCyc
Ensembl Genes ENSRNOG00000014202 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000019130 ENTREZGENE
  ENSRNOT00000019130.6 UniProtKB/Swiss-Prot
Gene3D-CATH 3.30.1520.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7373920 IMAGE-MGC_LOAD
InterPro Phox UniProtKB/Swiss-Prot
  PX_dom_sf UniProtKB/Swiss-Prot
  SNX20/SNX21 UniProtKB/Swiss-Prot
KEGG Report rno:307742 UniProtKB/Swiss-Prot
MGC_CLONE MGC:108869 IMAGE-MGC_LOAD
NCBI Gene 307742 ENTREZGENE
PANTHER PTHR20939 UniProtKB/Swiss-Prot
  SORTING NEXIN-20 UniProtKB/Swiss-Prot
Pfam PF00787 UniProtKB/Swiss-Prot
PhenoGen Snx20 PhenoGen
PROSITE PS50195 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000014202 RatGTEx
SMART SM00312 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF64268 UniProtKB/Swiss-Prot
UniProt Q5BK61 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-24 Snx20  sorting nexin 20  Slic1  selectin ligand interactor cytoplasmic-1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Slic1  selectin ligand interactor cytoplasmic-1  RGD1307787  similar to RIKEN cDNA 9130017C17 gene  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 RGD1307787  similar to RIKEN cDNA 9130017C17 gene  RGD1307787_predicted  similar to RIKEN cDNA 9130017C17 gene (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1307787_predicted  similar to RIKEN cDNA 9130017C17 gene (predicted)  LOC307742_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC307742_predicted  similar to RIKEN cDNA 9130017C17 gene (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL