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 enable serine C-palmitoyltransferase activity. Involved in response to immobilization stress. Predicted to be located in endoplasmic reticulum membrane. Predicted to be part of serine 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; 3-chloropropane-1,2-diol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously 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 Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr86112,679,623 - 112,762,470 (-)NCBIGRCr8
mRatBN7.26106,948,682 - 107,031,532 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl6106,950,949 - 107,031,542 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx6107,116,961 - 107,199,840 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.06107,415,779 - 107,498,659 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.06106,785,468 - 106,868,346 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.06111,334,408 - 111,417,960 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6111,339,136 - 111,417,954 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06120,616,251 - 120,699,243 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46111,546,037 - 111,622,959 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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



  
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Original Reference(s)
Sptlc2RatCOVID-19  ISOSPTLC2 (Homo sapiens)9068941mRNA:increased expression:peripheral blood mononuclear cell (human)RGDPMID:32228226 and REF_RGD_ID:28912744
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Original Reference(s)
Sptlc2RatCharcot-Marie-Tooth disease  ISOSPTLC2 (Homo sapiens)8554872ClinVar Annotator: match by term: Charcot-Marie-Tooth diseaseClinVarPMID:17081983 more ...
Sptlc2Ratgenetic disease  ISOSPTLC2 (Homo sapiens)8554872ClinVar Annotator: match by term: Inborn genetic diseasesClinVarPMID:17576681 more ...
Sptlc2Rathereditary sensory and autonomic neuropathy type 1C  ISOSPTLC2 (Homo sapiens)8554872ClinVar more ...ClinVarPMID:16199547 more ...
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Original Reference(s)
Sptlc2Ratpsoriasis  ISSSptlc2 (Mus musculus)13592920OMIM:177900 more ...MouseDO 
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Original Reference(s)
Sptlc2Rathereditary sensory and autonomic neuropathy type 1C  ISOSPTLC2 (Homo sapiens)7240710 OMIM 

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Original Reference(s)
Sptlc2Rat(+)-schisandrin B multiple interactionsEXP 6480464schizandrin B inhibits the reaction [Carbon Tetrachloride results in increased expression of SPTLC2 mRNA]CTDPMID:31150632
Sptlc2Rat(-)-epigallocatechin 3-gallate multiple interactionsISOSPTLC2 (Homo sapiens)6480464[potassium chromate(VI) co-treated with epigallocatechin gallate] results in decreased expression of SPTLC2 mRNACTDPMID:22079256
Sptlc2Rat(1->4)-beta-D-glucan multiple interactionsISOSptlc2 (Mus musculus)6480464[perfluorooctane sulfonic acid co-treated with Cellulose] results in increased expression of SPTLC2 mRNACTDPMID:36331819
Sptlc2Rat1,2-dimethylhydrazine decreases expressionISOSptlc2 (Mus musculus)64804641 and 2-Dimethylhydrazine results in decreased expression of SPTLC2 mRNACTDPMID:22206623
Sptlc2Rat1-benzylpiperazine increases expressionEXP 6480464N-benzylpiperazine results in increased expression of SPTLC2 mRNACTDPMID:26821219
Sptlc2Rat17beta-estradiol increases expressionISOSptlc2 (Mus musculus)6480464Estradiol results in increased expression of SPTLC2 mRNACTDPMID:15289156
Sptlc2Rat2,2',4,4',5,5'-hexachlorobiphenyl increases expressionISOSPTLC2 (Homo sapiens)64804642 more ...CTDPMID:34627992
Sptlc2Rat2,3,7,8-tetrachlorodibenzodioxine affects expressionISOSptlc2 (Mus musculus)6480464Tetrachlorodibenzodioxin affects the expression of SPTLC2 mRNACTDPMID:21570461
Sptlc2Rat2,3,7,8-tetrachlorodibenzodioxine multiple interactionsISOSPTLC2 (Homo sapiens)6480464Tetrachlorodibenzodioxin promotes the reaction [[AHR protein binds to ARNT protein] which binds to SPTLC2 promoter]CTDPMID:34097992
Sptlc2Rat2,3,7,8-tetrachlorodibenzodioxine increases expressionISOSptlc2 (Mus musculus)6480464Tetrachlorodibenzodioxin results in increased expression of SPTLC2 mRNACTDPMID:28238261
Sptlc2Rat2,3,7,8-tetrachlorodibenzodioxine increases expressionISOSPTLC2 (Homo sapiens)6480464Tetrachlorodibenzodioxin results in increased expression of SPTLC2 mRNACTDPMID:23152189
Sptlc2Rat2,3,7,8-Tetrachlorodibenzofuran multiple interactionsISOSptlc2 (Mus musculus)64804642 more ...CTDPMID:34097992
Sptlc2Rat2,3,7,8-Tetrachlorodibenzofuran increases expressionISOSptlc2 (Mus musculus)64804642 more ...CTDPMID:34097992
Sptlc2Rat2-acetamidofluorene increases expressionISOSptlc2 (Mus musculus)64804642-Acetylaminofluorene results in increased expression of SPTLC2 mRNACTDPMID:17317680
Sptlc2Rat2-hydroxypropanoic acid decreases expressionISOSPTLC2 (Homo sapiens)6480464Lactic Acid results in decreased expression of SPTLC2 mRNACTDPMID:30851411
Sptlc2Rat2-palmitoylglycerol increases expressionISOSPTLC2 (Homo sapiens)64804642-palmitoylglycerol results in increased expression of SPTLC2 mRNACTDPMID:37199045
Sptlc2Rat3,3',5-triiodo-L-thyronine increases expressionISOSPTLC2 (Homo sapiens)6480464Triiodothyronine results in increased expression of SPTLC2 mRNACTDPMID:23397585
Sptlc2Rat3,4-methylenedioxymethamphetamine decreases expressionISOSptlc2 (Mus musculus)6480464N-Methyl-3 and 4-methylenedioxyamphetamine results in decreased expression of SPTLC2 mRNACTDPMID:26251327
Sptlc2Rat3-chloropropane-1,2-diol increases expressionEXP 6480464alpha-Chlorohydrin results in increased expression of SPTLC2 proteinCTDPMID:34915118
Sptlc2Rat3-methylcholanthrene multiple interactionsISOSPTLC2 (Homo sapiens)6480464Methylcholanthrene promotes the reaction [AHR protein binds to SPTLC2 promoter]CTDPMID:20348232

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Biological Process
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Original Reference(s)
Sptlc2Ratadipose tissue development involved_inISSUniProtKB:P973631600115GO_REF:0000024UniProtGO_REF:0000024
Sptlc2Ratadipose tissue development involved_inISOSptlc2 (Mus musculus)1624291 PMID:27818258 and PMID:28698261RGDPMID:27818258 and PMID:28698261
Sptlc2Ratadipose tissue development involved_inIEAUniProtKB:P97363 and ensembl:ENSMUSP000000214241600115GO_REF:0000107EnsemblGO_REF:0000107
Sptlc2Ratbiosynthetic process involved_inIEAInterPro:IPR0048391600115GO_REF:0000002InterProGO_REF:0000002
Sptlc2Ratceramide biosynthetic process acts_upstream_of_or_withinISOSPTLC2 (Homo sapiens)1624291 PMID:25691431RGDPMID:25691431
Sptlc2Ratceramide biosynthetic process acts_upstream_of_or_withinIEAUniProtKB:O15270 and ensembl:ENSP000002164841600115GO_REF:0000107EnsemblGO_REF:0000107
Sptlc2Ratceramide biosynthetic process acts_upstream_of_or_withinISOSptlc2 (Mus musculus)1624291MGI:3815117 PMID:16216550RGDPMID:16216550
Sptlc2Ratceramide biosynthetic process involved_inIBAMGI:108074 more ...1600115GO_REF:0000033GO_CentralGO_REF:0000033
Sptlc2Ratceramide biosynthetic process acts_upstream_of_or_withinIEAUniProtKB:P97363 and ensembl:ENSMUSP000000214241600115GO_REF:0000107EnsemblGO_REF:0000107
Sptlc2Ratlipid metabolic process involved_inIEAUniProtKB-KW:KW-04431600115GO_REF:0000043UniProtGO_REF:0000043
Sptlc2Ratpositive regulation of lipophagy acts_upstream_of_or_withinISOSPTLC2 (Homo sapiens)1624291 PMID:25332431RGDPMID:25332431
Sptlc2Ratpositive regulation of lipophagy acts_upstream_of_or_withinIEAUniProtKB:O15270 and ensembl:ENSP000002164841600115GO_REF:0000107EnsemblGO_REF:0000107
Sptlc2Ratresponse to immobilization stress  IEP 213230152 RGD 
Sptlc2Ratsphinganine biosynthetic process acts_upstream_of_or_withinISOSptlc2 (Mus musculus)1624291 PMID:9363775RGDPMID:9363775
Sptlc2Ratsphinganine biosynthetic process acts_upstream_of_or_withinIEAUniProtKB:P97363 and ensembl:ENSMUSP000000214241600115GO_REF:0000107EnsemblGO_REF:0000107
Sptlc2Ratsphingolipid biosynthetic process involved_inISOSPTLC2 (Homo sapiens)1624291 PMID:26573920RGDPMID:26573920
Sptlc2Ratsphingolipid biosynthetic process involved_inIEAUniProtKB:P97363 and ensembl:ENSMUSP000000214241600115GO_REF:0000107EnsemblGO_REF:0000107
Sptlc2Ratsphingolipid biosynthetic process acts_upstream_of_or_withinIEAUniProtKB:O15270 and ensembl:ENSP000002164841600115GO_REF:0000107EnsemblGO_REF:0000107
Sptlc2Ratsphingolipid biosynthetic process involved_inISOSptlc2 (Mus musculus)1624291 PMID:28698261RGDPMID:28698261
Sptlc2Ratsphingolipid biosynthetic process involved_inISSUniProtKB:P973631600115GO_REF:0000024UniProtGO_REF:0000024
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Cellular Component
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Original Reference(s)
Sptlc2Ratendoplasmic reticulum located_inIEAUniProtKB-KW:KW-02561600115GO_REF:0000043UniProtGO_REF:0000043
Sptlc2Ratendoplasmic reticulum membrane located_inIEAUniProtKB-SubCell:SL-00971600115GO_REF:0000044UniProtGO_REF:0000044
Sptlc2Ratmembrane located_inIEAGO:00301481600115GO_REF:0000108GOCGO_REF:0000108
Sptlc2Ratmembrane located_inIEAGO:00465121600115GO_REF:0000108GOCGO_REF:0000108
Sptlc2Ratmembrane located_inIEAGO:00465131600115GO_REF:0000108GOCGO_REF:0000108
Sptlc2Ratmembrane located_inIEAUniProtKB-KW:KW-04721600115GO_REF:0000043UniProtGO_REF:0000043
Sptlc2Ratserine palmitoyltransferase complex part_ofISOSPTLC2 (Homo sapiens)1624291 PMID:19416851 and PMID:33558761RGDPMID:19416851 and PMID:33558761
Sptlc2Ratserine palmitoyltransferase complex part_ofIBAPANTHER:PTN000343811 more ...1600115GO_REF:0000033GO_CentralGO_REF:0000033
Sptlc2Ratserine palmitoyltransferase complex part_ofIEAUniProtKB:O15270 and ensembl:ENSP000002164841600115GO_REF:0000107EnsemblGO_REF:0000107
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Molecular Function
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Original Reference(s)
Sptlc2Ratacyltransferase activity enablesIEAUniProtKB-KW:KW-00121600115GO_REF:0000043UniProtGO_REF:0000043
Sptlc2Ratprotein binding enablesISOSPTLC2 (Homo sapiens)1624291UniProtKB:O15269 more ...RGDPMID:19416851 and PMID:35271311
Sptlc2Ratpyridoxal phosphate binding enablesIEAInterPro:IPR0048391600115GO_REF:0000002InterProGO_REF:0000002
Sptlc2Ratserine C-palmitoyltransferase activity contributes_toISOSPTLC2 (Homo sapiens)1624291 PMID:25332431 and PMID:25691431RGDPMID:25332431 and PMID:25691431
Sptlc2Ratserine C-palmitoyltransferase activity enablesIEAEC:2.3.1.501600115GO_REF:0000003UniProtGO_REF:0000003
Sptlc2Ratserine C-palmitoyltransferase activity enablesIEARHEA:147611600115GO_REF:0000116RHEAGO_REF:0000116
Sptlc2Ratserine C-palmitoyltransferase activity contributes_toISOSptlc2 (Mus musculus)1624291 PMID:9363775RGDPMID:9363775
Sptlc2Ratserine C-palmitoyltransferase activity enablesIBAFB:FBgn0002524 more ...1600115GO_REF:0000033GO_CentralGO_REF:0000033
Sptlc2Ratserine C-palmitoyltransferase activity contributes_toIEAUniProtKB:P97363 and ensembl:ENSMUSP000000214241600115GO_REF:0000107EnsemblGO_REF:0000107
Sptlc2Ratserine C-palmitoyltransferase activity enablesISOSPTLC2 (Homo sapiens)1624291 PMID:19416851 more ...RGDPMID:19416851 more ...
Sptlc2Ratserine C-palmitoyltransferase activity enablesIEAUniProtKB:O15270 and ensembl:ENSP000002164841600115GO_REF:0000107EnsemblGO_REF:0000107
Sptlc2Ratserine C-palmitoyltransferase activity enablesISSUniProtKB:O152701600115GO_REF:0000024UniProtGO_REF:0000024
Sptlc2Rattransferase activity enablesIEAUniProtKB-KW:KW-08081600115GO_REF:0000043UniProtGO_REF:0000043
Sptlc2Rattransferase activity enablesIEAInterPro:IPR0019171600115GO_REF:0000002InterProGO_REF:0000002
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Imported Annotations - SMPDB

Imported Annotations - KEGG (archival)

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Original Reference(s)
Sptlc2Ratsphingolipid metabolic pathway  IEA 6907045 KEGGrno:00600

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#
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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
5. SMPDB Annotation Import Pipeline Pipeline to import SMPDB annotations from SMPDB into RGD
6. GOA pipeline RGD automated data pipeline
7. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
9. Enriched Environment Enhances the Myelin Regulatory Factor by mTOR Signaling and Protects the Myelin Membrane Against Oxidative Damage in Rats Exposed to Chronic Immobilization Stress. Thamizhoviya G and Vanisree AJ, Neurochem Res. 2021 Dec;46(12):3314-3324. doi: 10.1007/s11064-021-03433-8. Epub 2021 Aug 27.
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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   PMID:36828166  



Sptlc2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr86112,679,623 - 112,762,470 (-)NCBIGRCr8
mRatBN7.26106,948,682 - 107,031,532 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl6106,950,949 - 107,031,542 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx6107,116,961 - 107,199,840 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.06107,415,779 - 107,498,659 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.06106,785,468 - 106,868,346 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.06111,334,408 - 111,417,960 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6111,339,136 - 111,417,954 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06120,616,251 - 120,699,243 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46111,546,037 - 111,622,959 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
GRCh381477,505,997 - 77,616,637 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1477,505,997 - 77,616,637 (-)EnsemblGRCh38hg38GRCh38
GRCh371477,972,340 - 78,082,980 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361477,043,023 - 77,152,863 (-)NCBINCBI36Build 36hg18NCBI36
Build 341477,043,024 - 77,152,863NCBI
Celera1458,011,851 - 58,121,636 (-)NCBICelera
Cytogenetic Map14q24.3NCBI
HuRef1458,138,337 - 58,249,054 (-)NCBIHuRef
CHM1_11477,911,814 - 78,022,586 (-)NCBICHM1_1
T2T-CHM13v2.01471,715,382 - 71,825,999 (-)NCBIT2T-CHM13v2.0
Sptlc2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391287,351,832 - 87,435,129 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1287,351,832 - 87,435,129 (-)EnsemblGRCm39 Ensembl
GRCm381287,305,058 - 87,388,355 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1287,305,058 - 87,388,355 (-)EnsemblGRCm38mm10GRCm38
MGSCv371288,648,839 - 88,729,180 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361288,196,992 - 88,277,333 (-)NCBIMGSCv36mm8
Celera1288,772,417 - 88,852,773 (-)NCBICelera
Cytogenetic Map12D2NCBI
cM Map1241.52NCBI
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
NHGRI_mPanPan1-v21578,591,247 - 78,702,589 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11477,807,751 - 77,918,929 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01458,066,123 - 58,170,472 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11477,266,545 - 77,370,663 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1477,266,545 - 77,370,663 (-)Ensemblpanpan1.1panPan2
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 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0850,525,698 - 50,635,391 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl850,530,838 - 50,635,427 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1850,188,135 - 50,297,514 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0850,211,301 - 50,320,641 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0850,609,185 - 50,719,362 (-)NCBIUU_Cfam_GSD_1.0
LOC101967158
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864025,664,744 - 25,778,794 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364886,315,715 - 6,419,882 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0 EnsemblNW_0049364886,289,833 - 6,296,849 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
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 - 100,638,905 (-)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 - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12454,769,072 - 54,876,963 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605342,955,305 - 43,064,586 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sptlc2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473424,281,482 - 24,400,870 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

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Variants in Sptlc2
362 total Variants

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.


1 to 10 of 29 rows
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD ID
Symbol
Name
LOD
P Value
Trait
Sub Trait
Chr
Start
Stop
Species
12801411Schws8Schwannoma susceptibility QTL 8nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)694968928139968928Rat
1331797Bp213Blood pressure QTL 2133.291arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)6104085867128713626Rat
1331799Bp211Blood pressure QTL 2113.66407arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)672202632130919985Rat
71111Iddm8Insulin dependent diabetes mellitus QTL 81.90.002blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)6105156861140994061Rat
1358355Srcrt4Stress Responsive Cort QTL 46.39blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)6100364669140994061Rat
2313399Anxrr28Anxiety related response QTL 28aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)6100671796132340886Rat
1331789Rf37Renal function QTL 373.224kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)672202632115200186Rat
1331725Bp212Blood pressure QTL 2123.52475arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)693701310128713626Rat
8552796Vie3Viral induced encephalitis QTL 32.6brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)696833997140994061Rat
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)610894415110548006Rat

1 to 10 of 29 rows
D19271  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26106,953,252 - 106,953,411 (+)MAPPERmRatBN7.2
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 (+)MAPPERmRatBN7.2
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 (+)MAPPERmRatBN7.2
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 (+)MAPPERmRatBN7.2
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 (+)MAPPERmRatBN7.2
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




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



Ensembl Acc Id: ENSRNOT00000016324   ⟹   ENSRNOP00000016324
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl6111,339,136 - 111,417,813 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000085458   ⟹   ENSRNOP00000071651
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl6106,950,949 - 107,031,542 (-)Ensembl
Rnor_6.0 Ensembl6111,342,024 - 111,417,954 (-)Ensembl
RefSeq Acc Id: NM_001037097   ⟹   NP_001032174
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr86112,679,623 - 112,762,470 (-)NCBI
mRatBN7.26106,948,682 - 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:
Protein RefSeqs NP_001032174 (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  
Ensembl Protein ENSRNOP00000071651
GenBank Protein Q3B7D2 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001032174   ⟸   NM_001037097
- UniProtKB: F1LSV4 (UniProtKB/Swiss-Prot),   Q3B7D2 (UniProtKB/TrEMBL),   A6JEA2 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000071651   ⟸   ENSRNOT00000085458
Ensembl Acc Id: ENSRNOP00000016324   ⟸   ENSRNOT00000016324
Aminotransferase class I/classII large

Name Modeler Protein Id AA Range Protein Structure
AF-Q3B7D2-F1-model_v2 AlphaFold Q3B7D2 1-560 view protein structure


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

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


1 to 27 of 27 rows
Database
Acc Id
Source(s)
BioCyc Gene G2FUF-36719 BioCyc
Ensembl Genes ENSRNOG00000012210 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000085458 ENTREZGENE
Gene3D-CATH 3.40.640.10 UniProtKB/Swiss-Prot
  3.90.1150.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7936642 IMAGE-MGC_LOAD
InterPro Aminotrans_II_pyridoxalP_BS UniProtKB/Swiss-Prot
  Aminotransferase_I/II UniProtKB/Swiss-Prot
  AON_synthase_class-II UniProtKB/Swiss-Prot
  PyrdxlP-dep_Trfase UniProtKB/Swiss-Prot
  PyrdxlP-dep_Trfase_dom1 UniProtKB/Swiss-Prot
  PyrdxlP-dep_Trfase_major UniProtKB/Swiss-Prot
KEGG Report rno:366697 UniProtKB/Swiss-Prot
MGC_CLONE MGC:124851 IMAGE-MGC_LOAD
NCBI Gene 366697 ENTREZGENE
PANTHER CLASS II AMINOTRANSFERASE/8-AMINO-7-OXONONANOATE SYNTHASE UniProtKB/Swiss-Prot
  SERINE PALMITOYLTRANSFERASE 2 UniProtKB/Swiss-Prot
Pfam Aminotran_1_2 UniProtKB/Swiss-Prot
PhenoGen Sptlc2 PhenoGen
PROSITE AA_TRANSFER_CLASS_2 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000012210 RatGTEx
Superfamily-SCOP SSF53383 UniProtKB/Swiss-Prot
UniProt A0A0G2K103_RAT UniProtKB/TrEMBL
  A6JEA2 ENTREZGENE, UniProtKB/TrEMBL
  F1LSV4 ENTREZGENE
  Q3B7D2 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary F1LSV4 UniProtKB/Swiss-Prot
1 to 27 of 27 rows


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