Sptssa (serine palmitoyltransferase, small subunit A) - Rat Genome Database

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Gene: Sptssa (serine palmitoyltransferase, small subunit A) Mus musculus
Analyze
Symbol: Sptssa
Name: serine palmitoyltransferase, small subunit A
RGD ID: 1618252
MGI Page MGI
Description: Predicted to contribute to serine C-palmitoyltransferase activity. Predicted to be involved in ceramide biosynthetic process; protein localization; and sphingosine biosynthetic process. Predicted to act upstream of or within sphingolipid metabolic process. Predicted to be located in endoplasmic reticulum. Predicted to be part of serine C-palmitoyltransferase complex. Is expressed in several structures, including aorta; brain; retina; spleen; and submandibular gland. Human ortholog(s) of this gene implicated in hereditary spastic paraplegia 90A and hereditary spastic paraplegia 90B. Orthologous to human SPTSSA (serine palmitoyltransferase small subunit A).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 1110002B05Rik; AA407909; AA409588; AU041967; serine palmitoyltransferase small subunit A; small subunit of serine palmitoyltransferase A; Ssspta
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: Gm19847  
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391254,692,159 - 54,703,357 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1254,692,177 - 54,703,358 (-)EnsemblGRCm39 Ensembl
GRCm381254,645,374 - 54,656,572 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1254,645,392 - 54,656,573 (-)EnsemblGRCm38mm10GRCm38
MGSCv371255,746,361 - 55,757,559 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361255,567,018 - 55,578,124 (-)NCBIMGSCv36mm8
Celera1255,961,951 - 55,973,156 (-)NCBICelera
Cytogenetic Map12C1NCBI
cM Map1223.46NCBI
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

References - curated
# Reference Title Reference Citation
1. Mouse MP Annotation Import Pipeline RGD automated import pipeline
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10349636   PMID:10725249   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12477932   PMID:15163632   PMID:15489334   PMID:15782199   PMID:16110338   PMID:16141072  
PMID:16141073   PMID:21267068   PMID:21677750   PMID:21873635   PMID:24194600   PMID:25269881   PMID:25691431   PMID:26272612   PMID:27626380   PMID:28700664   PMID:33662400   PMID:34321999  


Genomics

Comparative Map Data
Sptssa
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391254,692,159 - 54,703,357 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1254,692,177 - 54,703,358 (-)EnsemblGRCm39 Ensembl
GRCm381254,645,374 - 54,656,572 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1254,645,392 - 54,656,573 (-)EnsemblGRCm38mm10GRCm38
MGSCv371255,746,361 - 55,757,559 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361255,567,018 - 55,578,124 (-)NCBIMGSCv36mm8
Celera1255,961,951 - 55,973,156 (-)NCBICelera
Cytogenetic Map12C1NCBI
cM Map1223.46NCBI
SPTSSA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381434,432,788 - 34,462,240 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1434,432,788 - 34,462,240 (-)EnsemblGRCh38hg38GRCh38
GRCh371434,901,994 - 34,931,446 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361433,971,895 - 34,001,219 (-)NCBINCBI36Build 36hg18NCBI36
Build 341433,971,904 - 34,001,313NCBI
Celera1414,767,183 - 14,796,506 (-)NCBICelera
Cytogenetic Map14q13.1NCBI
HuRef1415,020,179 - 15,049,457 (-)NCBIHuRef
CHM1_11434,900,608 - 34,930,130 (-)NCBICHM1_1
T2T-CHM13v2.01428,631,319 - 28,661,012 (-)NCBIT2T-CHM13v2.0
Sptssa
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8677,879,931 - 77,891,344 (-)NCBIGRCr8
mRatBN7.2672,144,714 - 72,156,130 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl672,144,714 - 72,156,214 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx672,565,588 - 72,577,037 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0672,872,259 - 72,883,710 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0672,302,687 - 72,314,091 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0675,540,132 - 75,551,545 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl675,540,174 - 75,551,625 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0685,080,132 - 85,091,844 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4674,962,387 - 74,973,800 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera670,991,533 - 71,002,947 (-)NCBICelera
Cytogenetic Map6q23NCBI
Sptssa
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495540926,460,208 - 26,460,854 (+)NCBIChiLan1.0ChiLan1.0
SPTSSA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21535,751,896 - 35,779,566 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11434,968,397 - 34,996,068 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01415,190,833 - 15,219,882 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
LOC102151865
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1813,265,424 - 13,339,212 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha813,077,984 - 13,151,811 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0813,284,591 - 13,447,278 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1812,965,994 - 13,127,949 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0813,049,110 - 13,211,027 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0813,427,103 - 13,501,270 (-)NCBIUU_Cfam_GSD_1.0
Sptssa
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864045,211,157 - 45,233,059 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364948,716,829 - 8,739,066 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364948,717,821 - 8,738,923 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SPTSSA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl765,302,858 - 65,326,728 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1765,302,887 - 65,325,877 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2770,090,613 - 70,113,604 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SPTSSA
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12411,264,578 - 11,298,816 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2411,266,343 - 11,298,668 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666053201,739 - 236,078 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sptssa
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248382,206,917 - 2,231,518 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248382,207,003 - 2,231,838 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Sptssa
395 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:202
Count of miRNA genes:168
Interacting mature miRNAs:175
Transcripts:ENSMUST00000056228
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4142234Tmc1m3_mTmc1 modifier 3 (mouse)Not determined12541844077031203Mouse
27226753Femd7_mfemur midshaft diameter 7, 10 week (mouse)12955000084146774Mouse
13207568Tcq14_mtotal cholesterol QTL 14 (mouse)121166000197176774Mouse
13524839Ppiq10_mprepulse inhibition QTL 10 (mouse)121304319554945798Mouse
1558978Cplaq10_mcircadian period of locomotor activity 10 (mouse)Not determined121534102679040364Mouse
1301574Lmblgq5_mlimb length QTL 5 (mouse)Not determined121759644780956883Mouse
1302172Skts5_mskin tumor susceptibility 5 (mouse)Not determined122214886656149016Mouse
1301989Hdlq18_mHDL QTL 18 (mouse)Not determined122916068563160884Mouse
1300636Gct2_mgranulosa cell tumorigenesis 2 (mouse)Not determined122916068563160884Mouse
4141843Moen3_mmodifier of engrailed QTL 3 (mouse)Not determined122980158463801733Mouse
14747008Mancz10_mmandible centroid size 10 (mouse)122986352263863522Mouse
10402492Dipa8_mdrug induced psychomotor activation 8 (mouse)Not determined123493387268934019Mouse
1300818Bbaa10_mB.burgdorferi-associated arthritis 10 (mouse)Not determined123509100465511019Mouse
4142002Tbqt3_mtibia bone quality traits 3 (mouse)Not determined1235285496109936243Mouse
1357479Splwt1_mspleen weight 1 (mouse)Not determined124169317590887526Mouse
1357757Lnopy2_mlens opacity 2 (mouse)Not determined125284662686846796Mouse
1357749Vtbt13_mvertebral trabecular bone trait 13 (mouse)Not determined125313200287132145Mouse
12904004Opfaq11_mopen field activity QTL 11 (mouse)125315562457276756Mouse
12832727Ahrq1_mairway hyperresponsiveness QTL 1 (mouse)125469591082665939Mouse

Markers in Region
D17995  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381254,645,481 - 54,645,594UniSTSGRCm38
MGSCv371255,746,468 - 55,746,581UniSTSGRCm37
Celera1255,962,058 - 55,962,171UniSTS
Cytogenetic Map12C1UniSTS
Whitehead_YAC12 UniSTS
D12Mit285  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381254,649,125 - 54,649,249UniSTSGRCm38
MGSCv371255,750,112 - 55,750,236UniSTSGRCm37
Celera1255,965,702 - 55,965,826UniSTS
Cytogenetic Map12C1UniSTS
cM Map1225.0UniSTS
Whitehead Genetic1219.7UniSTS
Whitehead/MRC_RH12552.72UniSTS
Whitehead_YAC12 UniSTS
RH124648  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381254,645,526 - 54,645,643UniSTSGRCm38
MGSCv371255,746,513 - 55,746,630UniSTSGRCm37
Celera1255,962,103 - 55,962,220UniSTS
Cytogenetic Map12C1UniSTS
RH125747  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381254,645,452 - 54,645,701UniSTSGRCm38
MGSCv371255,746,439 - 55,746,688UniSTSGRCm37
Celera1255,962,029 - 55,962,278UniSTS
Cytogenetic Map12C1UniSTS
Whitehead/MRC_RH12554.13UniSTS
RH125858  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381254,645,423 - 54,645,607UniSTSGRCm38
MGSCv371255,746,410 - 55,746,594UniSTSGRCm37
Celera1255,962,000 - 55,962,184UniSTS
Cytogenetic Map12C1UniSTS
Whitehead/MRC_RH12552.72UniSTS


Expression


Sequence


RefSeq Acc Id: ENSMUST00000056228   ⟹   ENSMUSP00000053671
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1254,692,177 - 54,703,358 (-)Ensembl
GRCm38.p6 Ensembl1254,645,392 - 54,656,573 (-)Ensembl
RefSeq Acc Id: ENSMUST00000218147   ⟹   ENSMUSP00000151214
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1254,692,186 - 54,703,281 (-)Ensembl
GRCm38.p6 Ensembl1254,645,401 - 54,656,496 (-)Ensembl
RefSeq Acc Id: ENSMUST00000220090
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1254,692,749 - 54,702,983 (-)Ensembl
GRCm38.p6 Ensembl1254,645,964 - 54,656,198 (-)Ensembl
RefSeq Acc Id: NM_134054   ⟹   NP_598815
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391254,692,159 - 54,703,357 (-)NCBI
GRCm381254,645,374 - 54,656,572 (-)ENTREZGENE
MGSCv371255,746,361 - 55,757,559 (-)RGD
Celera1255,961,951 - 55,973,156 (-)RGD
cM Map12 ENTREZGENE
Sequence:
RefSeq Acc Id: NP_598815   ⟸   NM_134054
- UniProtKB: Q8BHT2 (UniProtKB/Swiss-Prot),   Q8R207 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSMUSP00000151214   ⟸   ENSMUST00000218147
RefSeq Acc Id: ENSMUSP00000053671   ⟸   ENSMUST00000056228

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8R207-F1-model_v2 AlphaFold Q8R207 1-71 view protein structure

Promoters
RGD ID:8678290
Promoter ID:EPDNEW_M17167
Type:initiation region
Name:Sptssa_1
Description:Mus musculus serine palmitoyltransferase, small subunit A , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381254,656,508 - 54,656,568EPDNEW
RGD ID:6822525
Promoter ID:MM_KWN:11647
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day4,   3T3L1_Day6,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Liver,   Lung,   MEF_B4,   MEF_B6,   Spleen
Transcripts:NM_134054
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361255,757,341 - 55,757,841 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1913399 AgrOrtholog
Ensembl Genes ENSMUSG00000044408 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000056228 ENTREZGENE
  ENSMUST00000056228.8 UniProtKB/Swiss-Prot
  ENSMUST00000218147.2 UniProtKB/TrEMBL
InterPro Ser_palmitoyltrfase_ssu-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:104725 UniProtKB/Swiss-Prot
MGD MGI:1913399 ENTREZGENE
NCBI Gene 104725 ENTREZGENE
PANTHER SERINE PALMITOYLTRANSFERASE SMALL SUBUNIT A UniProtKB/Swiss-Prot
  SERINE PALMITOYLTRANSFERASE SMALL SUBUNIT A UniProtKB/Swiss-Prot
  SERINE PALMITOYLTRANSFERASE SMALL SUBUNIT A UniProtKB/TrEMBL
  SERINE PALMITOYLTRANSFERASE SMALL SUBUNIT A UniProtKB/TrEMBL
Pfam SPT_ssu-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Sptssa PhenoGen
UniProt A0A1W2P6D8_MOUSE UniProtKB/TrEMBL
  Q8BHT2 ENTREZGENE
  Q8R207 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q8BHT2 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-09-25 Sptssa  serine palmitoyltransferase, small subunit A  1110002B05Rik  RIKEN cDNA 1110002B05 gene  Symbol and/or name change 5135510 APPROVED