SPTLC3 (serine palmitoyltransferase long chain base subunit 3) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: SPTLC3 (serine palmitoyltransferase long chain base subunit 3) Canis lupus familiaris
Analyze
Symbol: SPTLC3
Name: serine palmitoyltransferase long chain base subunit 3
RGD ID: 12140909
Description: ENCODES a protein that exhibits acyltransferase activity (inferred); pyridoxal phosphate binding (inferred); serine C-palmitoyltransferase activity (inferred); INVOLVED IN sphingoid biosynthetic process (ortholog); ASSOCIATED WITH genetic disease (ortholog); sensory peripheral neuropathy (ortholog); FOUND IN serine C-palmitoyltransferase complex (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: serine palmitoyltransferase 3
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1249,447,575 - 9,597,544 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl249,447,859 - 9,595,975 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha249,258,320 - 9,409,355 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0249,860,196 - 10,010,807 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl249,861,421 - 10,011,073 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1249,471,327 - 9,619,877 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0249,555,159 - 9,706,174 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0249,904,468 - 10,055,517 (-)NCBIUU_Cfam_GSD_1.0
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

Biological Process

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
SPTLC3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1249,447,575 - 9,597,544 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl249,447,859 - 9,595,975 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha249,258,320 - 9,409,355 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0249,860,196 - 10,010,807 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl249,861,421 - 10,011,073 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1249,471,327 - 9,619,877 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0249,555,159 - 9,706,174 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0249,904,468 - 10,055,517 (-)NCBIUU_Cfam_GSD_1.0
SPTLC3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382013,008,972 - 13,169,103 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2013,008,972 - 13,169,103 (+)EnsemblGRCh38hg38GRCh38
GRCh372012,989,620 - 13,149,750 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362012,937,627 - 13,095,411 (+)NCBINCBI36Build 36hg18NCBI36
Celera2013,059,733 - 13,217,481 (+)NCBICelera
Cytogenetic Map20p12.1NCBI
HuRef2012,941,029 - 13,101,523 (+)NCBIHuRef
CHM1_12012,989,665 - 13,147,485 (+)NCBICHM1_1
T2T-CHM13v2.02013,048,743 - 13,212,449 (+)NCBIT2T-CHM13v2.0
Sptlc3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392139,335,833 - 139,478,981 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2139,335,833 - 139,479,594 (+)EnsemblGRCm39 Ensembl
GRCm382139,493,913 - 139,637,061 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2139,493,913 - 139,637,674 (+)EnsemblGRCm38mm10GRCm38
MGSCv372139,319,656 - 139,463,410 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362139,185,361 - 139,329,115 (+)NCBIMGSCv36mm8
Celera2140,671,316 - 140,814,560 (+)NCBICelera
Cytogenetic Map2F3NCBI
cM Map268.52NCBI
Sptlc3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83147,301,570 - 147,431,696 (+)NCBIGRCr8
mRatBN7.23126,847,878 - 126,978,010 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3126,847,878 - 126,978,010 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3130,707,371 - 130,835,985 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03139,291,458 - 139,420,089 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03136,994,594 - 137,123,206 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03132,560,437 - 132,689,313 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3132,560,506 - 132,692,737 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03139,023,075 - 139,151,792 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43127,691,668 - 127,825,206 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13127,597,526 - 127,729,920 (+)NCBI
Celera3125,501,233 - 125,630,510 (+)NCBICelera
Cytogenetic Map3q36NCBI
Sptlc3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541522,531,626 - 22,682,564 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541522,532,193 - 22,686,071 (+)NCBIChiLan1.0ChiLan1.0
SPTLC3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22113,894,378 - 14,053,615 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12013,891,210 - 14,052,725 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02012,966,584 - 13,125,802 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12012,952,501 - 13,111,347 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2012,952,524 - 13,111,347 (+)Ensemblpanpan1.1panPan2
Sptlc3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640158,213,063 - 158,353,439 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364856,644,188 - 6,784,828 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364856,647,930 - 6,784,792 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SPTLC3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1721,769,484 - 21,903,264 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11721,769,388 - 21,903,269 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21724,339,933 - 24,473,785 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SPTLC3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1241,900,389 - 42,067,842 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl241,900,447 - 42,070,112 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660542,190,751 - 2,332,203 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sptlc3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474113,956,570 - 14,152,600 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474113,956,688 - 14,152,127 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in SPTLC3
1937 total Variants

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 reproductive system respiratory system adipose tissue
High
Medium 6
Low 4 14 6 12 9 1
Below cutoff 1 5 8 6 6 6 8 1 5

Sequence


RefSeq Acc Id: ENSCAFT00000009031   ⟹   ENSCAFP00000008376
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl249,447,859 - 9,595,975 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000084594   ⟹   ENSCAFP00000057797
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl249,447,859 - 9,556,181 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845041452   ⟹   ENSCAFP00845032503
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl249,861,421 - 10,011,073 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845041567   ⟹   ENSCAFP00845032590
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl249,861,421 - 10,010,780 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845041646   ⟹   ENSCAFP00845032660
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl249,861,421 - 9,987,445 (-)Ensembl
RefSeq Acc Id: XM_022408974   ⟹   XP_022264682
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1249,447,575 - 9,597,214 (-)NCBI
Dog10K_Boxer_Tasha249,258,320 - 9,409,355 (-)NCBI
Sequence:
RefSeq Acc Id: XM_038433124   ⟹   XP_038289052
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0249,860,196 - 10,010,807 (-)NCBI
RefSeq Acc Id: XM_038433125   ⟹   XP_038289053
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0249,860,196 - 10,010,807 (-)NCBI
RefSeq Acc Id: XM_038508321   ⟹   XP_038364249
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1249,471,327 - 9,619,877 (-)NCBI
RefSeq Acc Id: XM_038508322   ⟹   XP_038364250
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1249,471,327 - 9,619,877 (-)NCBI
RefSeq Acc Id: XM_038571598   ⟹   XP_038427526
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0249,904,468 - 10,055,517 (-)NCBI
RefSeq Acc Id: XM_038571599   ⟹   XP_038427527
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0249,904,468 - 10,055,517 (-)NCBI
RefSeq Acc Id: XM_038635847   ⟹   XP_038491775
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0249,555,159 - 9,706,174 (-)NCBI
RefSeq Acc Id: XM_038635848   ⟹   XP_038491776
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0249,555,159 - 9,706,174 (-)NCBI
RefSeq Acc Id: XM_542889   ⟹   XP_542889
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1249,447,575 - 9,597,544 (-)NCBI
Dog10K_Boxer_Tasha249,258,320 - 9,409,355 (-)NCBI
Sequence:
RefSeq Acc Id: XP_542889   ⟸   XM_542889
- Peptide Label: isoform X1
- UniProtKB: A0A8C0LPW1 (UniProtKB/TrEMBL),   A0A8I3PMG7 (UniProtKB/TrEMBL),   A0A8P0PNN3 (UniProtKB/TrEMBL),   A0A8I3PIX5 (UniProtKB/TrEMBL),   A0A8P0T9T4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_022264682   ⟸   XM_022408974
- Peptide Label: isoform X2
- UniProtKB: A0A8C0Q8N0 (UniProtKB/TrEMBL),   A0A8C0LTM3 (UniProtKB/TrEMBL),   A0A8I3PNE9 (UniProtKB/TrEMBL),   A0A8I3PIX5 (UniProtKB/TrEMBL),   A0A8P0T9T4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCAFP00000057797   ⟸   ENSCAFT00000084594
RefSeq Acc Id: ENSCAFP00000008376   ⟸   ENSCAFT00000009031
RefSeq Acc Id: XP_038364249   ⟸   XM_038508321
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038364250   ⟸   XM_038508322
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038491775   ⟸   XM_038635847
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038491776   ⟸   XM_038635848
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038289052   ⟸   XM_038433124
- Peptide Label: isoform X1
- UniProtKB: A0A8C0LPW1 (UniProtKB/TrEMBL),   A0A8I3PMG7 (UniProtKB/TrEMBL),   A0A8P0PNN3 (UniProtKB/TrEMBL),   A0A8I3PIX5 (UniProtKB/TrEMBL),   A0A8P0T9T4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038289053   ⟸   XM_038433125
- Peptide Label: isoform X2
- UniProtKB: A0A8C0Q8N0 (UniProtKB/TrEMBL),   A0A8C0LTM3 (UniProtKB/TrEMBL),   A0A8I3PNE9 (UniProtKB/TrEMBL),   A0A8I3PIX5 (UniProtKB/TrEMBL),   A0A8P0T9T4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038427526   ⟸   XM_038571598
- Peptide Label: isoform X1
- UniProtKB: A0A8C0LPW1 (UniProtKB/TrEMBL),   A0A8I3PIX5 (UniProtKB/TrEMBL),   A0A8I3PMG7 (UniProtKB/TrEMBL),   A0A8P0PNN3 (UniProtKB/TrEMBL),   A0A8P0T9T4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038427527   ⟸   XM_038571599
- Peptide Label: isoform X2
- UniProtKB: A0A8C0LTM3 (UniProtKB/TrEMBL),   A0A8C0Q8N0 (UniProtKB/TrEMBL),   A0A8I3PIX5 (UniProtKB/TrEMBL),   A0A8I3PNE9 (UniProtKB/TrEMBL),   A0A8P0T9T4 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCAFP00845032590   ⟸   ENSCAFT00845041567
RefSeq Acc Id: ENSCAFP00845032503   ⟸   ENSCAFT00845041452
RefSeq Acc Id: ENSCAFP00845032660   ⟸   ENSCAFT00845041646

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000005607 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030017569 UniProtKB/TrEMBL
  ENSCAFG00040006060 UniProtKB/TrEMBL
  ENSCAFG00845023443 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000009031.5 UniProtKB/TrEMBL
  ENSCAFT00000084594.2 UniProtKB/TrEMBL
  ENSCAFT00000109552.1 UniProtKB/TrEMBL
  ENSCAFT00030032464.1 UniProtKB/TrEMBL
  ENSCAFT00030032543.1 UniProtKB/TrEMBL
  ENSCAFT00040011331.1 UniProtKB/TrEMBL
  ENSCAFT00040011359.1 UniProtKB/TrEMBL
  ENSCAFT00845041452 ENTREZGENE
  ENSCAFT00845041452.1 UniProtKB/TrEMBL
  ENSCAFT00845041567 ENTREZGENE
  ENSCAFT00845041567.1 UniProtKB/TrEMBL
  ENSCAFT00845041646.1 UniProtKB/TrEMBL
Gene3D-CATH 3.40.640.10 UniProtKB/TrEMBL
  3.90.1150.10 UniProtKB/TrEMBL
InterPro Aminotrans_II_pyridoxalP_BS UniProtKB/TrEMBL
  Aminotransferase_I/II UniProtKB/TrEMBL
  PyrdxlP-dep_Trfase UniProtKB/TrEMBL
  PyrdxlP-dep_Trfase_major UniProtKB/TrEMBL
  PyrdxlP-dep_Trfase_small UniProtKB/TrEMBL
NCBI Gene SPTLC3 ENTREZGENE
PANTHER CLASS II AMINOTRANSFERASE/8-AMINO-7-OXONONANOATE SYNTHASE UniProtKB/TrEMBL
  SERINE PALMITOYLTRANSFERASE 3 UniProtKB/TrEMBL
Pfam Aminotran_1_2 UniProtKB/TrEMBL
PROSITE AA_TRANSFER_CLASS_2 UniProtKB/TrEMBL
Superfamily-SCOP SSF53383 UniProtKB/TrEMBL
UniProt A0A8C0LPW1 ENTREZGENE
  A0A8C0LTM3 ENTREZGENE
  A0A8C0P1K5_CANLF UniProtKB/TrEMBL
  A0A8C0Q8N0 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3PIX5 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3PMG7 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3PNE9 ENTREZGENE, UniProtKB/TrEMBL
  A0A8P0PNN3 ENTREZGENE, UniProtKB/TrEMBL
  A0A8P0T9T4 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:46781 ENTREZGENE