Sptlc2 (serine palmitoyltransferase, long chain base subunit 2) - Rat Genome Database

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Gene: Sptlc2 (serine palmitoyltransferase, long chain base subunit 2) Rattus norvegicus
Analyze
Symbol: Sptlc2
Name: serine palmitoyltransferase, long chain base subunit 2
RGD ID: 1305447
Description: Predicted to have serine C-palmitoyltransferase activity. Predicted to be involved in adipose tissue development; positive regulation of lipophagy; and sphingolipid biosynthetic process. Predicted to localize to serine C-palmitoyltransferase complex. Human ortholog(s) of this gene implicated in hereditary sensory and autonomic neuropathy type 1C. Orthologous to human SPTLC2 (serine palmitoyltransferase long chain base subunit 2); PARTICIPATES IN Fabry disease pathway; Gaucher's disease pathway; Krabbe disease pathway; INTERACTS WITH (+)-schisandrin B; 1-benzylpiperazine; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LCB 2; LOC366697; long chain base biosynthesis protein 2; MGC124851; Pomt2; protein-O-mannosyltransferase 2; serine palmitoyltransferase 2; serine-palmitoyl-CoA transferase 2; SPT 2
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
mRatBN7.26106,948,681 - 107,031,584 (-)NCBI
Rnor_6.0 Ensembl6111,339,136 - 111,417,954 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.06111,334,408 - 111,417,960 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.06120,616,251 - 120,699,243 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46111,546,037 - 111,622,959 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.16111,245,978 - 111,626,585 (-)NCBI
Celera6104,771,427 - 104,849,755 (-)NCBICelera
Cytogenetic Map6q31NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(-)-epigallocatechin 3-gallate  (ISO)
1,2-dimethylhydrazine  (ISO)
1-benzylpiperazine  (EXP)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-acetamidofluorene  (ISO)
2-hydroxypropanoic acid  (ISO)
3,3',5-triiodo-L-thyronine  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-methylcholanthrene  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
8'-apo-beta,psi-caroten-8'-al  (ISO)
acetamide  (EXP)
aflatoxin B1  (ISO)
amphetamine  (EXP)
Aroclor 1254  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[e]pyrene  (ISO)
beta-carotene  (ISO)
butanal  (ISO)
calcitriol  (ISO)
choline  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
cyclosporin A  (ISO)
deoxynivalenol  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP)
diethylstilbestrol  (ISO)
divanadium pentaoxide  (ISO)
dorsomorphin  (ISO)
entinostat  (ISO)
ethanol  (ISO)
flutamide  (EXP)
folic acid  (ISO)
genistein  (ISO)
gentamycin  (EXP)
GW 4064  (ISO)
isoprenaline  (ISO)
L-methionine  (ISO)
lithocholic acid  (ISO)
methapyrilene  (ISO)
methotrexate  (ISO)
nickel atom  (ISO)
paracetamol  (ISO)
pentachlorophenol  (ISO)
pentanal  (ISO)
perfluorooctanoic acid  (ISO)
phenethyl caffeate  (ISO)
phenobarbital  (ISO)
pirinixic acid  (ISO)
piroxicam  (ISO)
potassium chromate  (ISO)
rac-lactic acid  (ISO)
SB 431542  (ISO)
sodium fluoride  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP)
triclocarban  (EXP)
urethane  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:9363775   PMID:11816724   PMID:12477932   PMID:16216550   PMID:18614015   PMID:19416851   PMID:20920666   PMID:25332431   PMID:25691431   PMID:25771159   PMID:26573920   PMID:27818258  
PMID:28698261  


Genomics

Comparative Map Data
Sptlc2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.26106,948,681 - 107,031,584 (-)NCBI
Rnor_6.0 Ensembl6111,339,136 - 111,417,954 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.06111,334,408 - 111,417,960 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.06120,616,251 - 120,699,243 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46111,546,037 - 111,622,959 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.16111,245,978 - 111,626,585 (-)NCBI
Celera6104,771,427 - 104,849,755 (-)NCBICelera
Cytogenetic Map6q31NCBI
SPTLC2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1477,505,997 - 77,616,773 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl1477,505,997 - 77,616,637 (-)EnsemblGRCh38hg38GRCh38
GRCh381477,505,997 - 77,616,663 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371477,972,340 - 78,082,980 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361477,043,023 - 77,152,863 (-)NCBINCBI36hg18NCBI36
Build 341477,043,024 - 77,152,863NCBI
Celera1458,011,851 - 58,121,636 (-)NCBI
Cytogenetic Map14q24.3NCBI
HuRef1458,138,337 - 58,249,054 (-)NCBIHuRef
CHM1_11477,911,814 - 78,022,586 (-)NCBICHM1_1
Sptlc2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391287,351,832 - 87,435,129 (-)NCBIGRCm39mm39
GRCm39 Ensembl1287,351,832 - 87,435,129 (-)Ensembl
GRCm381287,305,058 - 87,388,355 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1287,305,058 - 87,388,355 (-)EnsemblGRCm38mm10GRCm38
MGSCv371288,648,839 - 88,729,180 (-)NCBIGRCm37mm9NCBIm37
MGSCv361288,196,992 - 88,277,333 (-)NCBImm8
Celera1288,772,417 - 88,852,773 (-)NCBICelera
Cytogenetic Map12D2NCBI
Sptlc2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554381,385,431 - 1,491,578 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554381,385,431 - 1,491,534 (-)NCBIChiLan1.0ChiLan1.0
SPTLC2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11477,266,545 - 77,370,663 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1477,266,545 - 77,370,663 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01458,066,123 - 58,170,472 (-)NCBIMhudiblu_PPA_v0panPan3
SPTLC2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1850,291,797 - 50,401,202 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl850,271,010 - 50,401,313 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha849,979,477 - 50,088,850 (-)NCBI
ROS_Cfam_1.0850,525,698 - 50,635,391 (-)NCBI
UMICH_Zoey_3.1850,188,135 - 50,297,514 (-)NCBI
UNSW_CanFamBas_1.0850,211,301 - 50,320,641 (-)NCBI
UU_Cfam_GSD_1.0850,609,185 - 50,719,362 (-)NCBI
LOC101967158
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864025,664,744 - 25,778,794 (+)NCBI
SpeTri2.0NW_0049364886,313,189 - 6,404,425 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SPTLC2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl7100,544,478 - 100,638,907 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.17100,545,360 - 100,638,973 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.27106,672,604 - 106,730,716 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SPTLC2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12454,769,072 - 54,876,963 (-)NCBI
Sptlc2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473424,281,482 - 24,400,870 (+)NCBI

Position Markers
D19271  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26106,953,252 - 106,953,411 (+)MAPPER
Rnor_6.06111,338,980 - 111,339,138NCBIRnor6.0
Rnor_5.06120,620,823 - 120,620,981UniSTSRnor5.0
Celera6104,773,271 - 104,773,429UniSTS
Cytogenetic Map6q31UniSTS
RH138750  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26107,008,557 - 107,008,777 (+)MAPPER
Rnor_6.06111,394,494 - 111,394,713NCBIRnor6.0
Rnor_5.06120,675,810 - 120,676,029UniSTSRnor5.0
RGSC_v3.46111,599,983 - 111,600,202UniSTSRGSC3.4
Celera6104,827,505 - 104,827,724UniSTS
RH 3.4 Map6748.9UniSTS
Cytogenetic Map6q31UniSTS
RH131889  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26106,952,847 - 106,953,045 (+)MAPPER
Rnor_6.06111,338,575 - 111,338,772NCBIRnor6.0
Rnor_5.06120,620,418 - 120,620,615UniSTSRnor5.0
Celera6104,772,866 - 104,773,063UniSTS
RH 3.4 Map6748.9UniSTS
Cytogenetic Map6q31UniSTS
RH134867  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26106,951,098 - 106,951,279 (+)MAPPER
Rnor_6.06111,336,826 - 111,337,006NCBIRnor6.0
Rnor_5.06120,618,669 - 120,618,849UniSTSRnor5.0
Celera6104,771,117 - 104,771,297UniSTS
RH 3.4 Map6744.1UniSTS
Cytogenetic Map6q31UniSTS
BE115266  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26106,957,199 - 106,957,394 (+)MAPPER
Rnor_6.06111,342,663 - 111,342,857NCBIRnor6.0
Rnor_5.06120,624,089 - 120,624,283UniSTSRnor5.0
RGSC_v3.46111,546,617 - 111,546,811UniSTSRGSC3.4
Celera6104,776,449 - 104,776,643UniSTS
RH 3.4 Map6743.6UniSTS
Cytogenetic Map6q31UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70196BpQTLcluster7Blood pressure QTL cluster 76.82arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)675623277120623277Rat
724513Uae14Urinary albumin excretion QTL 146.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)688996335139410483Rat
724524Uae2Urinary albumin excretion QTL 22.70.0005urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)676902247114203334Rat
724536Uae7Urinary albumin excretion QTL 73.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)675623277136143011Rat
1331725Bp212Blood pressure QTL 2123.52475arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)697949772133849286Rat
737827Hcar11Hepatocarcinoma resistance QTL 114.4liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)686422697115379601Rat
1331789Rf37Renal function QTL 373.224kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)675623277120276465Rat
1331797Bp213Blood pressure QTL 2133.291arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)6108154445133849286Rat
1331799Bp211Blood pressure QTL 2113.66407arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)675623277136426962Rat
1581550Pur8Proteinuria QTL 8total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)675623393136142742Rat
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
738034Anxrr5Anxiety related response QTL 55.9exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)688507712133507712Rat
1641904Alcrsp4Alcohol response QTL 4response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)671206251116206251Rat
1581563Uae33Urinary albumin excretion QTL 33urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)675623393136142742Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)62537030111715717Rat
2313399Anxrr28Anxiety related response QTL 28aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)6104381930138066274Rat
1358355Srcrt4Stress Responsive Cort QTL 46.39blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)6104363890147991367Rat
1300075Glom7Glomerulus QTL 75.60.0000002kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)675449871120449871Rat
1300076Glom8Glomerulus QTL 870.000000009kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)691703409136703409Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
2303624Vencon5Ventilatory control QTL 54.45respiration trait (VT:0001943)minute ventilation (VE) (CMO:0000132)692879510137879510Rat
61414Pia3Pristane induced arthritis QTL 34.5joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)699273921144792678Rat
8552796Vie3Viral induced encephalitis QTL 32.6brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)6101207574147991367Rat
10054138Gmadr3Adrenal mass QTL 33.680.00045adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)689631358134631358Rat
10054123Srcrt6Stress Responsive Cort QTL 62.50.0043blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)689631358134631358Rat
4145118Mcs26Mammary carcinoma susceptibility QTL 260.0001mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)6111134524138065254Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)67009971115379601Rat
12801411Schws8Schwannoma susceptibility QTL 8nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)699273921144273921Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:126
Count of miRNA genes:106
Interacting mature miRNAs:113
Transcripts:ENSRNOT00000016324
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.


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 42 39 23 19 23 1 1 74 35 38 11 1
Low 1 18 18 18 7 10 3 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000016324   ⟹   ENSRNOP00000016324
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl6111,339,136 - 111,417,813 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000085458   ⟹   ENSRNOP00000071651
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl6111,342,024 - 111,417,954 (-)Ensembl
RefSeq Acc Id: NM_001037097   ⟹   NP_001032174
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26106,951,409 - 107,031,532 (-)NCBI
Rnor_6.06111,337,136 - 111,417,913 (-)NCBI
Rnor_5.06120,616,251 - 120,699,243 (-)NCBI
RGSC_v3.46111,546,037 - 111,622,959 (-)RGD
Celera6104,771,427 - 104,849,755 (-)RGD
Sequence:
RefSeq Acc Id: XM_008764823   ⟹   XP_008763045
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.06111,334,408 - 111,417,960 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039112649   ⟹   XP_038968577
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26106,948,681 - 107,031,584 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001032174 (Get FASTA)   NCBI Sequence Viewer  
  XP_038968577 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI07663 (Get FASTA)   NCBI Sequence Viewer  
  EDL81646 (Get FASTA)   NCBI Sequence Viewer  
  EDL81647 (Get FASTA)   NCBI Sequence Viewer  
  Q3B7D2 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001032174   ⟸   NM_001037097
- UniProtKB: Q3B7D2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008763045   ⟸   XM_008764823
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000071651   ⟸   ENSRNOT00000085458
RefSeq Acc Id: ENSRNOP00000016324   ⟸   ENSRNOT00000016324
RefSeq Acc Id: XP_038968577   ⟸   XM_039112649
- Peptide Label: isoform X1
Protein Domains
Aminotran_1_2

Transcriptome

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

Promoters
RGD ID:13694758
Promoter ID:EPDNEW_R5283
Type:initiation region
Name:Sptlc2_1
Description:serine palmitoyltransferase, long chain base subunit 2
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_6.06111,417,840 - 111,417,900EPDNEW

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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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:1305447 AgrOrtholog
Ensembl Genes ENSRNOG00000012210 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000016324 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000071651 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000016324 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000085458 UniProtKB/TrEMBL
Gene3D-CATH 3.40.640.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.90.1150.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7936642 IMAGE-MGC_LOAD
InterPro Aminotrans_II_pyridoxalP_BS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Aminotransferase_I/II UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PyrdxlP-dep_Trfase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PyrdxlP-dep_Trfase_dom1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PyrdxlP-dep_Trfase_major UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:366697 UniProtKB/Swiss-Prot
MGC_CLONE MGC:124851 IMAGE-MGC_LOAD
NCBI Gene 366697 ENTREZGENE
Pfam Aminotran_1_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Sptlc2 PhenoGen
PROSITE AA_TRANSFER_CLASS_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF53383 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K103_RAT UniProtKB/TrEMBL
  A0A5H1ZRU9_RAT UniProtKB/TrEMBL
  Q3B7D2 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary F1LSV4 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-06 Sptlc2  serine palmitoyltransferase, long chain base subunit 2  Pomt2  protein-O-mannosyltransferase 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Pomt2  protein-O-mannosyltransferase 2  Pomt2_predicted  protein-O-mannosyltransferase 2 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Pomt2_predicted  protein-O-mannosyltransferase 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED