Snx12 (sorting nexin 12) - Rat Genome Database

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Gene: Snx12 (sorting nexin 12) Rattus norvegicus
Analyze
Symbol: Snx12
Name: sorting nexin 12
RGD ID: 1565585
Description: Predicted to enable enzyme binding activity and phosphatidylinositol-3-phosphate binding activity. Predicted to be involved in several processes, including endosomal transport; negative regulation of protein metabolic process; and regulation of vesicle-mediated transport. Predicted to be located in early endosome. Predicted to be part of retromer complex. Predicted to be active in early endosome membrane. Orthologous to human SNX12 (sorting nexin 12); INTERACTS WITH acetamide; cadmium dichloride; flutamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC363478; RGD1565585; similar to sorting nexin 12; sorting nexin-12
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X70,267,013 - 70,396,948 (-)NCBIGRCr8
mRatBN7.2X66,226,995 - 66,356,945 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX66,227,053 - 66,356,950 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX67,714,611 - 67,840,239 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X71,215,008 - 71,340,627 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X68,775,912 - 68,901,534 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X70,989,822 - 71,127,330 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX70,989,822 - 71,127,278 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X71,841,036 - 71,979,425 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X89,180,623 - 89,302,886 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX66,587,920 - 66,712,807 (-)NCBICelera
Cytogenetic MapXq22NCBI
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

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:22709416   PMID:22719997   PMID:23376485  


Genomics

Comparative Map Data
Snx12
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X70,267,013 - 70,396,948 (-)NCBIGRCr8
mRatBN7.2X66,226,995 - 66,356,945 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX66,227,053 - 66,356,950 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX67,714,611 - 67,840,239 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X71,215,008 - 71,340,627 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X68,775,912 - 68,901,534 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X70,989,822 - 71,127,330 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX70,989,822 - 71,127,278 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X71,841,036 - 71,979,425 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X89,180,623 - 89,302,886 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX66,587,920 - 66,712,807 (-)NCBICelera
Cytogenetic MapXq22NCBI
SNX12
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X71,059,247 - 71,073,426 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX71,056,332 - 71,073,426 (-)EnsemblGRCh38hg38GRCh38
GRCh37X70,279,097 - 70,293,276 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X70,197,513 - 70,204,956 (-)NCBINCBI36Build 36hg18NCBI36
Build 34X70,063,808 - 70,071,252NCBI
CeleraX70,634,675 - 70,642,112 (-)NCBICelera
Cytogenetic MapXq13.1NCBI
HuRefX64,098,078 - 64,112,533 (-)NCBIHuRef
CHM1_1X70,171,505 - 70,185,641 (-)NCBICHM1_1
T2T-CHM13v2.0X69,493,335 - 69,507,559 (-)NCBIT2T-CHM13v2.0
Snx12
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X100,132,973 - 100,266,185 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX100,141,392 - 100,266,169 (-)EnsemblGRCm39 Ensembl
GRCm38X101,089,367 - 101,222,583 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX101,097,786 - 101,222,563 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X98,293,125 - 98,417,902 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X97,414,987 - 97,425,209 (-)NCBIMGSCv36mm8
CeleraX88,016,094 - 88,138,712 (-)NCBICelera
Cytogenetic MapXDNCBI
cM MapX43.72NCBI
Snx12
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495547510,474,697 - 10,641,723 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495547510,632,938 - 10,641,452 (-)NCBIChiLan1.0ChiLan1.0
SNX12
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X70,735,214 - 70,745,919 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X70,735,563 - 70,749,428 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X60,327,484 - 60,336,682 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X70,382,421 - 70,395,737 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX70,384,164 - 70,395,737 (-)Ensemblpanpan1.1panPan2
SNX12
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X55,441,271 - 55,450,767 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX46,268,481 - 46,277,836 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X56,410,302 - 56,419,651 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX56,236,112 - 56,420,547 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X54,378,561 - 54,387,910 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X55,709,985 - 55,719,334 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X55,637,110 - 55,646,459 (-)NCBIUU_Cfam_GSD_1.0
Snx12
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X46,761,429 - 46,772,472 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936762523,564 - 542,757 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936762523,641 - 534,646 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SNX12
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX57,089,136 - 57,108,750 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X57,099,521 - 57,108,636 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X64,630,295 - 64,639,393 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SNX12
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X60,849,241 - 60,866,846 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660652,715,531 - 2,725,717 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Snx12
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249031,118,965 - 1,367,179 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046249031,357,298 - 1,366,849 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Snx12
105 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:28
Count of miRNA genes:22
Interacting mature miRNAs:26
Transcripts:ENSRNOT00000068098
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
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X65612192120568734Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat

Markers in Region
RH129490  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X66,340,031 - 66,340,245 (+)MAPPERmRatBN7.2
Rnor_6.0X71,110,424 - 71,110,637NCBIRnor6.0
Rnor_5.0X71,962,502 - 71,962,715UniSTSRnor5.0
RGSC_v3.4X89,286,032 - 89,286,245UniSTSRGSC3.4
CeleraX66,695,953 - 66,696,166UniSTS
Cytogenetic MapXq31UniSTS
RH142505  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X66,351,680 - 66,351,802 (+)MAPPERmRatBN7.2
Rnor_6.0X71,122,072 - 71,122,193NCBIRnor6.0
Rnor_5.0X71,974,150 - 71,974,271UniSTSRnor5.0
RGSC_v3.4X89,297,680 - 89,297,801UniSTSRGSC3.4
CeleraX66,707,601 - 66,707,722UniSTS
Cytogenetic MapXq31UniSTS
BF395935  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X66,321,922 - 66,322,047 (+)MAPPERmRatBN7.2
Rnor_6.0X71,092,525 - 71,092,649NCBIRnor6.0
Rnor_5.0X71,944,603 - 71,944,727UniSTSRnor5.0
RGSC_v3.4X89,267,572 - 89,267,696UniSTSRGSC3.4
CeleraX66,677,712 - 66,677,836UniSTS
Cytogenetic MapXq31UniSTS
BI293668  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X66,348,824 - 66,348,961 (+)MAPPERmRatBN7.2
Rnor_6.0X71,119,216 - 71,119,352NCBIRnor6.0
Rnor_5.0X71,971,294 - 71,971,430UniSTSRnor5.0
RGSC_v3.4X89,294,824 - 89,294,960UniSTSRGSC3.4
CeleraX66,704,745 - 66,704,881UniSTS
Cytogenetic MapXq31UniSTS
RH137926  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X66,334,902 - 66,335,074 (+)MAPPERmRatBN7.2
Rnor_6.0X71,105,300 - 71,105,471NCBIRnor6.0
Rnor_5.0X71,957,378 - 71,957,549UniSTSRnor5.0
RGSC_v3.4X89,280,907 - 89,281,078UniSTSRGSC3.4
CeleraX66,690,831 - 66,691,002UniSTS
Cytogenetic MapXq31UniSTS


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
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000068098   ⟹   ENSRNOP00000061412
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX66,341,396 - 66,356,950 (-)Ensembl
Rnor_6.0 EnsemblX70,994,077 - 71,127,278 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000076403   ⟹   ENSRNOP00000068481
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX66,347,138 - 66,356,936 (-)Ensembl
Rnor_6.0 EnsemblX71,117,528 - 71,127,237 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000076590   ⟹   ENSRNOP00000068508
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX71,117,528 - 71,121,034 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000076635   ⟹   ENSRNOP00000068200
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX66,227,053 - 66,356,889 (-)Ensembl
Rnor_6.0 EnsemblX70,989,822 - 71,127,272 (-)Ensembl
RefSeq Acc Id: NM_001108817   ⟹   NP_001102287
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X70,271,268 - 70,396,896 (-)NCBI
mRatBN7.2X66,231,250 - 66,356,887 (-)NCBI
Rnor_6.0X70,994,077 - 71,127,278 (-)NCBI
Rnor_5.0X71,841,036 - 71,979,425 (-)NCBI
RGSC_v3.4X89,180,623 - 89,302,886 (-)RGD
CeleraX66,587,920 - 66,712,807 (-)RGD
Sequence:
RefSeq Acc Id: XM_006257079   ⟹   XP_006257141
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X70,387,146 - 70,396,948 (-)NCBI
mRatBN7.2X66,347,135 - 66,356,945 (-)NCBI
Rnor_6.0X71,117,528 - 71,127,329 (-)NCBI
Rnor_5.0X71,841,036 - 71,979,425 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017602108   ⟹   XP_017457597
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X70,333,737 - 70,396,948 (-)NCBI
mRatBN7.2X66,302,267 - 66,356,945 (-)NCBI
Rnor_6.0X71,073,367 - 71,127,330 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039099898   ⟹   XP_038955826
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X70,267,013 - 70,396,948 (-)NCBI
mRatBN7.2X66,226,995 - 66,356,945 (-)NCBI
RefSeq Acc Id: XM_039099899   ⟹   XP_038955827
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X70,318,502 - 70,396,948 (-)NCBI
mRatBN7.2X66,278,766 - 66,356,945 (-)NCBI
RefSeq Acc Id: XM_063280144   ⟹   XP_063136214
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X70,374,766 - 70,396,948 (-)NCBI
RefSeq Acc Id: XM_063280145   ⟹   XP_063136215
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X70,346,588 - 70,396,948 (-)NCBI
RefSeq Acc Id: NP_001102287   ⟸   NM_001108817
- UniProtKB: A0A096MJN6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006257141   ⟸   XM_006257079
- Peptide Label: isoform X5
- UniProtKB: A0A096MJN6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017457597   ⟸   XM_017602108
- Peptide Label: isoform X2
- UniProtKB: A0A096MJN6 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000061412   ⟸   ENSRNOT00000068098
Ensembl Acc Id: ENSRNOP00000068200   ⟸   ENSRNOT00000076635
Ensembl Acc Id: ENSRNOP00000068481   ⟸   ENSRNOT00000076403
Ensembl Acc Id: ENSRNOP00000068508   ⟸   ENSRNOT00000076590
RefSeq Acc Id: XP_038955826   ⟸   XM_039099898
- Peptide Label: isoform X1
- UniProtKB: A0A096MJN6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038955827   ⟸   XM_039099899
- Peptide Label: isoform X6
- UniProtKB: A0A096MJN6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063136215   ⟸   XM_063280145
- Peptide Label: isoform X4
RefSeq Acc Id: XP_063136214   ⟸   XM_063280144
- Peptide Label: isoform X3
- UniProtKB: D4A719 (UniProtKB/TrEMBL)
Protein Domains
PX

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A719-F1-model_v2 AlphaFold D4A719 1-170 view protein structure

Transcriptome

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

Promoters
RGD ID:13701873
Promoter ID:EPDNEW_R12394
Type:initiation region
Name:Snx12_1
Description:sorting nexin 12
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_6.0X71,127,239 - 71,127,299EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565585 AgrOrtholog
BioCyc Gene G2FUF-2112 BioCyc
Ensembl Genes ENSRNOG00000004036 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000068098.4 UniProtKB/TrEMBL
  ENSRNOT00000076403.2 UniProtKB/TrEMBL
  ENSRNOT00000076635.3 UniProtKB/TrEMBL
Gene3D-CATH 3.30.1520.10 UniProtKB/TrEMBL
InterPro IPR001683 UniProtKB/TrEMBL
  PX_dom_sf UniProtKB/TrEMBL
  Sorting_Nexin UniProtKB/TrEMBL
NCBI Gene 363478 ENTREZGENE
PANTHER RE52028P UniProtKB/TrEMBL
  SORTING NEXIN-12 UniProtKB/TrEMBL
Pfam PF00787 UniProtKB/TrEMBL
PhenoGen Snx12 PhenoGen
PROSITE PS50195 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000004036 RatGTEx
SMART SM00312 UniProtKB/TrEMBL
Superfamily-SCOP 64268 UniProtKB/TrEMBL
UniProt A0A096MJN6 ENTREZGENE, UniProtKB/TrEMBL
  A0A096MKE2_RAT UniProtKB/TrEMBL
  D4A719 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Snx12  sorting nexin 12   Snx12_predicted  sorting nexin 12 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Snx12_predicted  sorting nexin 12 (predicted)  RGD1565585_predicted  similar to sorting nexin 12 (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-07 RGD1565585_predicted  similar to sorting nexin 12 (predicted)  LOC363478  similar to sorting nexin 12  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC363478  similar to sorting nexin 12      Symbol and Name status set to provisional 70820 PROVISIONAL