Snx20 (sorting nexin 20) - Rat Genome Database

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Gene: Snx20 (sorting nexin 20) Mus musculus
Analyze
Symbol: Snx20
Name: sorting nexin 20
RGD ID: 1317182
MGI Page MGI
Description: Enables phosphatidylinositol-3-phosphate binding activity and phosphatidylinositol-4,5-bisphosphate binding activity. Predicted to act upstream of or within protein transport. Located in early endosome membrane. Orthologous to human SNX20 (sorting nexin 20); INTERACTS WITH 1,2-dimethylhydrazine; 4-hydroxyphenyl retinamide; 7,12-dimethyltetraphene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: 9130017C17Rik; sorting nexin-20
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39889,353,189 - 89,362,769 (-)NCBIGRCm39mm39
GRCm39 Ensembl889,353,191 - 89,362,756 (-)Ensembl
GRCm38888,626,561 - 88,636,133 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl888,626,563 - 88,636,128 (-)EnsemblGRCm38mm10GRCm38
MGSCv37891,150,727 - 91,160,027 (-)NCBIGRCm37mm9NCBIm37
MGSCv36891,516,933 - 91,526,233 (-)NCBImm8
Celera892,907,268 - 92,916,455 (-)NCBICelera
Cytogenetic Map8C3NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

Additional References at PubMed
PMID:10349636   PMID:11042159   PMID:11076861   PMID:12477932   PMID:16141072   PMID:16141073   PMID:18196517   PMID:21873635   PMID:25882846  


Genomics

Comparative Map Data
Snx20
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39889,353,189 - 89,362,769 (-)NCBIGRCm39mm39
GRCm39 Ensembl889,353,191 - 89,362,756 (-)Ensembl
GRCm38888,626,561 - 88,636,133 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl888,626,563 - 88,636,128 (-)EnsemblGRCm38mm10GRCm38
MGSCv37891,150,727 - 91,160,027 (-)NCBIGRCm37mm9NCBIm37
MGSCv36891,516,933 - 91,526,233 (-)NCBImm8
Celera892,907,268 - 92,916,455 (-)NCBICelera
Cytogenetic Map8C3NCBI
SNX20
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1650,666,300 - 50,681,353 (-)EnsemblGRCh38hg38GRCh38
GRCh381650,666,300 - 50,681,312 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371650,700,211 - 50,715,223 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361649,264,387 - 49,272,667 (-)NCBINCBI36hg18NCBI36
Celera1635,215,527 - 35,230,577 (-)NCBI
Cytogenetic Map16q12.1NCBI
HuRef1636,588,004 - 36,603,054 (-)NCBIHuRef
CHM1_11652,107,729 - 52,122,779 (-)NCBICHM1_1
Snx20
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21918,435,935 - 18,445,108 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1918,435,935 - 18,445,107 (+)Ensembl
Rnor_6.01919,395,655 - 19,404,846 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1919,395,655 - 19,404,835 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01930,428,393 - 30,436,777 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41919,715,997 - 19,726,145 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11919,720,822 - 19,730,970 (+)NCBI
Celera1918,322,643 - 18,331,589 (+)NCBICelera
Cytogenetic Map19p11NCBI
Snx20
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554338,727,493 - 8,731,398 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554338,725,950 - 8,734,699 (-)NCBIChiLan1.0ChiLan1.0
SNX20
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11649,814,315 - 49,822,209 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1649,809,077 - 49,818,459 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01630,928,545 - 30,944,509 (-)NCBIMhudiblu_PPA_v0panPan3
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 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha261,254,013 - 61,262,796 (+)NCBI
ROS_Cfam_1.0265,226,579 - 65,235,362 (+)NCBI
UMICH_Zoey_3.1262,050,248 - 62,059,016 (+)NCBI
UNSW_CanFamBas_1.0263,070,208 - 63,078,984 (+)NCBI
UU_Cfam_GSD_1.0263,957,752 - 63,966,522 (+)NCBI
SNX20
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl634,176,748 - 34,191,570 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl536,469,366 - 36,480,514 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604740,021,561 - 40,031,658 (+)NCBIVero_WHO_p1.0
Snx20
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247576,011,750 - 6,019,378 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
BE199892  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38888,626,895 - 88,627,041UniSTSGRCm38
MGSCv37891,150,794 - 91,150,940UniSTSGRCm37
Celera892,907,335 - 92,907,481UniSTS
Cytogenetic Map8C4UniSTS
Whitehead/MRC_RH81046.25UniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4140967Bmd39_mbone mineral density 39 (mouse)Not determined832016544117238700Mouse
1558875Eae31_mexperimental allergic encephalomyelitis susceptibility 31 (mouse)Not determined834642776114837007Mouse
1301013Capsq4_mcapsaicin sensitivity related QTL 4 (mouse)Not determined83616300092728652Mouse
27226754Femd6_mfemur midshaft diameter 6, 10 week (mouse)837400000109600000Mouse
12904744Carcdq1_mcardiac collagen deposition QTL 1 (mouse)83970925694689598Mouse
1301952Im3_mimmunoregulatory 3 (mouse)Not determined85470661488706763Mouse
10412287Carg3_mCandida albicans resistance gene 3 (mouse)Not determined85554502889545028Mouse
11353828Gf7_mgonadal fat pad weight 7 (mouse)85820147992201479Mouse
10043975Obq31_mobesity QTL 31 (mouse)Not determined85840977692409776Mouse
1301688Orch6_mautoimmune orchitis resistance 6 (mouse)Not determined86078685094786976Mouse
4141285Tgq18_mtriglyceride QTL 18 (mouse)Not determined6346010797460107Mouse
4141797Skmw16_mskeletal muscle weight 16 (mouse)Not determined86393954797939696Mouse
1357787Vtbt5_mvertebral trabecular bone trait 5 (mouse)Not determined86535776899357920Mouse
10043992Hbnr11_mHeligmosomoides bakeri nematode resistance 11 (mouse)Not determined86560020799600347Mouse
1301767Fcsa2_mfemoral cross-sectional area 2 (mouse)Not determined870305375104305495Mouse
4142283Imraq2_mimmune response to AAV2 QTL 2 (mouse)Not determined870305375104305495Mouse
1558780Idd22_minsulin dependent diabetes susceptibility 22 (mouse)Not determined871102903105103009Mouse
4141395Char2a_mP. chabaudi malaria resistance QTL 2a (mouse)Not determined7113678390202598Mouse
4142023W3q5_mweight 3 weeks QTL 5 (mouse)Not determined71287817123895615Mouse
1357708Orq1_movulation rate QTL 1 (mouse)Not determined871287817123895615Mouse
1301872Cd4ts3_mCD4 T cell subset 3 (mouse)Not determined871396181105396393Mouse
1300920Pitm3_mprion incubation time 3 (mouse)Not determined873202495107202598Mouse
27095912Pglq14_mpelvic girdle length QTL 14, 16 week (mouse)873400000126100000Mouse
1558890Lith18_mlithogenic gene 18 (mouse)Not determined875675517109675623Mouse
1357470Obq16_mobesity QTL 16 (mouse)Not determined875685348109685497Mouse
1301808Nhdlq1_mnon-HDL QTL 1 (mouse)Not determined875685348109685497Mouse
1301874Hdlq16_mHDL QTL 16 (mouse)Not determined875685348109685497Mouse
10412234Nhdlq14_mnon-HDL QTL 14 (mouse)Not determined875685348109685497Mouse
1301099Cbm2_mcerebellum weight 2 (mouse)Not determined878518613112518703Mouse
1301581Char2_mP. chabaudi malaria resistance QTL 2 (mouse)Not determined879082178113082403Mouse
12904012Cfq10_mconditioned fear QTL 10 (mouse)88006677589014359Mouse
10755530Wbc2_mwhite blood cell count 2 (mouse)881092664115092664Mouse
10755519Wbc1_mwhite blood cell count 1 (mouse)881619151115619151Mouse
1301766Desp1_mdespair 1 (mouse)Not determined884759576118759741Mouse
1302049Heal1_mwound healing/regeneration 1 (mouse)Not determined885716921119717069Mouse
1301253Skmw2_mskeletal muscle weight 2 (mouse)Not determined885716921119717069Mouse
10045619Heal14_mwound healing/regeneration 14 (mouse)Not determined885716921119717069Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:157
Count of miRNA genes:132
Interacting mature miRNAs:147
Transcripts:ENSMUST00000034087
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.


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000034087   ⟹   ENSMUSP00000034087
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl889,353,191 - 89,362,756 (-)Ensembl
GRCm38.p6 Ensembl888,626,563 - 88,636,128 (-)Ensembl
RefSeq Acc Id: ENSMUST00000209806
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl889,357,735 - 89,362,729 (-)Ensembl
GRCm38.p6 Ensembl888,631,107 - 88,636,101 (-)Ensembl
RefSeq Acc Id: NM_027840   ⟹   NP_082116
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39889,353,456 - 89,362,756 (-)NCBI
GRCm38888,626,828 - 88,636,128 (-)NCBI
MGSCv37891,150,727 - 91,160,027 (-)RGD
Celera892,907,268 - 92,916,455 (-)RGD
cM Map8 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_006531371   ⟹   XP_006531434
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39889,353,189 - 89,362,769 (-)NCBI
GRCm38888,626,561 - 88,636,131 (-)NCBI
Sequence:
RefSeq Acc Id: XM_011248503   ⟹   XP_011246805
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39889,353,189 - 89,362,769 (-)NCBI
GRCm38888,626,561 - 88,636,133 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_082116   ⟸   NM_027840
- UniProtKB: Q9D2Y5 (UniProtKB/Swiss-Prot),   A0A0R4J0D0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006531434   ⟸   XM_006531371
- Peptide Label: isoform X1
- UniProtKB: Q9D2Y5 (UniProtKB/Swiss-Prot),   A0A0R4J0D0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_011246805   ⟸   XM_011248503
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSMUSP00000034087   ⟸   ENSMUST00000034087
Protein Domains
PX

Promoters
RGD ID:8667825
Promoter ID:EPDNEW_M11944
Type:initiation region
Name:Snx20_1
Description:Mus musculus sorting nexin 20 , 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
GRCm38888,636,067 - 88,636,127EPDNEW
RGD ID:6843754
Promoter ID:MM_KWN:55215
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Lung,   Spleen
Transcripts:ENSMUST00000034087
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36891,159,634 - 91,160,134 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1918857 AgrOrtholog
Ensembl Genes ENSMUSG00000031662 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSMUSP00000034087 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000034087 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 3.30.1520.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Phox UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PX_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SNX20/SNX21 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TPR-like_helical_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:71607 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGD MGI:1918857 ENTREZGENE
NCBI Gene 71607 ENTREZGENE
PANTHER PTHR20939 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam PF00787 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Snx20 PhenoGen
PROSITE PS50195 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SM00312 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48452 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF64268 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0R4J0D0 ENTREZGENE, UniProtKB/TrEMBL
  Q9D2Y5 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q3U0B6 UniProtKB/Swiss-Prot
  Q544B6 UniProtKB/Swiss-Prot
  Q8CHQ3 UniProtKB/Swiss-Prot