Snx12 (sorting nexin 12) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Snx12 (sorting nexin 12) Rattus norvegicus
Analyze
Symbol: Snx12
Name: sorting nexin 12
RGD ID: 1565585
Description: Predicted to have 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 localize to early endosome membrane and retromer complex. Orthologous to human SNX12 (sorting nexin 12); INTERACTS WITH acetamide; cadmium dichloride; flutamide.
Type: protein-coding
RefSeq Status: VALIDATED
Also 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 Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X66,226,995 - 66,356,945 (-)NCBI
Rnor_6.0 EnsemblX70,989,822 - 71,127,278 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X70,989,822 - 71,127,330 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X71,841,036 - 71,979,425 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X89,180,623 - 89,302,886 (-)NCBIRGSC3.4rn4RGSC3.4
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

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
mRatBN7.2X66,226,995 - 66,356,945 (-)NCBI
Rnor_6.0 EnsemblX70,989,822 - 71,127,278 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X70,989,822 - 71,127,330 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X71,841,036 - 71,979,425 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X89,180,623 - 89,302,886 (-)NCBIRGSC3.4rn4RGSC3.4
CeleraX66,587,920 - 66,712,807 (-)NCBICelera
Cytogenetic MapXq22NCBI
SNX12
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX71,056,332 - 71,073,426 (-)EnsemblGRCh38hg38GRCh38
GRCh38X71,059,247 - 71,073,426 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X70,279,097 - 70,293,276 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X70,197,513 - 70,204,956 (-)NCBINCBI36hg18NCBI36
Build 34X70,063,808 - 70,071,252NCBI
CeleraX70,634,675 - 70,642,112 (-)NCBI
Cytogenetic MapXq13.1NCBI
HuRefX64,098,078 - 64,112,533 (-)NCBIHuRef
CHM1_1X70,171,505 - 70,185,641 (-)NCBICHM1_1
Snx12
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X100,132,973 - 100,266,185 (-)NCBIGRCm39mm39
GRCm39 EnsemblX100,141,392 - 100,266,169 (-)Ensembl
GRCm38X101,089,367 - 101,222,583 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX101,097,786 - 101,222,563 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X98,293,125 - 98,417,902 (-)NCBIGRCm37mm9NCBIm37
MGSCv36X97,414,987 - 97,425,209 (-)NCBImm8
CeleraX88,016,094 - 88,138,712 (-)NCBICelera
Cytogenetic MapXDNCBI
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
PanPan1.1X70,382,421 - 70,395,737 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX70,384,164 - 70,395,737 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X60,327,484 - 60,336,682 (-)NCBIMhudiblu_PPA_v0panPan3
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 (-)NCBI
ROS_Cfam_1.0X56,410,302 - 56,419,651 (-)NCBI
UMICH_Zoey_3.1X54,378,561 - 54,387,910 (-)NCBI
UNSW_CanFamBas_1.0X55,709,985 - 55,719,334 (-)NCBI
UU_Cfam_GSD_1.0X55,637,110 - 55,646,459 (-)NCBI
Snx12
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X46,761,429 - 46,772,472 (+)NCBI
SpeTri2.0NW_004936762523,641 - 534,646 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SNX12
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX57,085,544 - 57,108,533 (-)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 - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X60,849,241 - 60,866,846 (-)NCBI
Snx12
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046249031,357,298 - 1,366,849 (-)NCBI

Position Markers
RH129490  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X66,340,031 - 66,340,245 (+)MAPPER
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 (+)MAPPER
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 (+)MAPPER
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 (+)MAPPER
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 (+)MAPPER
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


QTLs in Region (Rnor_6.0)
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)X15688119127888215Rat
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)X44320616158345622Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX44557974120045269Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X70352120127888215Rat

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.


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 38 30 14 19 14 8 11 74 35 34 11 8
Low 5 27 27 27 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000068098   ⟹   ENSRNOP00000061412
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX70,994,077 - 71,127,278 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076403   ⟹   ENSRNOP00000068481
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX71,117,528 - 71,127,237 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076590   ⟹   ENSRNOP00000068508
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX71,117,528 - 71,121,034 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076635   ⟹   ENSRNOP00000068200
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
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_006257078   ⟹   XP_006257140
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X66,226,995 - 66,356,945 (-)NCBI
Rnor_6.0X70,989,822 - 71,127,330 (-)NCBI
Rnor_5.0X71,841,036 - 71,979,425 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006257079   ⟹   XP_006257141
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X66,226,995 - 66,356,945 (-)NCBI
RefSeq Acc Id: XM_039099899   ⟹   XP_038955827
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X66,278,766 - 66,356,945 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001102287   ⟸   NM_001108817
- UniProtKB: D4A719 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006257140   ⟸   XM_006257078
- Peptide Label: isoform X2
- UniProtKB: D4A719 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006257141   ⟸   XM_006257079
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017457597   ⟸   XM_017602108
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000061412   ⟸   ENSRNOT00000068098
RefSeq Acc Id: ENSRNOP00000068200   ⟸   ENSRNOT00000076635
RefSeq Acc Id: ENSRNOP00000068481   ⟸   ENSRNOT00000076403
RefSeq Acc Id: ENSRNOP00000068508   ⟸   ENSRNOT00000076590
RefSeq Acc Id: XP_038955826   ⟸   XM_039099898
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038955827   ⟸   XM_039099899
- Peptide Label: isoform X5
Protein Domains
PX

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

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565585 AgrOrtholog
Ensembl Genes ENSRNOG00000004036 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000061412 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000068200 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000068481 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000068508 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000068098 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000076403 UniProtKB/TrEMBL
  ENSRNOT00000076590 UniProtKB/TrEMBL
  ENSRNOT00000076635 UniProtKB/TrEMBL
Gene3D-CATH 3.30.1520.10 UniProtKB/TrEMBL
InterPro IPR001683 UniProtKB/TrEMBL
  PX_dom_sf UniProtKB/TrEMBL
KEGG Report rno:363478 UniProtKB/TrEMBL
NCBI Gene 363478 ENTREZGENE
Pfam PF00787 UniProtKB/TrEMBL
PhenoGen Snx12 PhenoGen
PROSITE PS50195 UniProtKB/TrEMBL
SMART SM00312 UniProtKB/TrEMBL
Superfamily-SCOP 64268 UniProtKB/TrEMBL
UniProt A0A096MKE2_RAT UniProtKB/TrEMBL
  A0A096MKG7_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