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

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Gene: Sptssa (serine palmitoyltransferase, small subunit A) Rattus norvegicus
Analyze
Symbol: Sptssa
Name: serine palmitoyltransferase, small subunit A
RGD ID: 1565821
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 be located in endoplasmic reticulum. Predicted to be part of serine C-palmitoyltransferase complex. 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); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC500651; MGC112883; serine palmitoyltransferase small subunit A; small subunit of serine palmitoyltransferase A; Ssspta
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
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
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. 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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:19416851   PMID:23510452   PMID:25691431  


Genomics

Comparative Map Data
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
(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
(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
(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
102 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:87
Count of miRNA genes:78
Interacting mature miRNAs:81
Transcripts:ENSRNOT00000005825
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6172227641Rat
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
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)61173566972593685Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)61173566972593685Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)615107216107351382Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat
1331779Rf38Renal function QTL 382.876kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)63207442872227641Rat
6893340Cm77Cardiac mass QTL 770.260.57heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)63330954981132889Rat
1300143Rf14Renal function QTL 142.92renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)63443413777102317Rat
634307Bp141Blood pressure QTL 1414arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)63523041780230417Rat
9590290Uminl2Urine mineral level QTL 23.960.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)63878398983783989Rat
9590306Scort18Serum corticosterone level QTL 182.880.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)63878398983783989Rat
9590140Scort4Serum corticosterone level QTL 414.490.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)63878398983783989Rat
634330Pia16Pristane induced arthritis QTL 163.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)645790088104200226Rat
4889848Pur25Proteinuria QTL 25140.003urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)65672856290198260Rat
6893332Cm74Cardiac mass QTL 740.40.64heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)657730540104085867Rat
1558641Cm47Cardiac mass QTL 472.90.001heart mass (VT:0007028)heart wet weight (CMO:0000069)657730540104085867Rat
70176Mcsm1Mammary carcinoma susceptibility modifier QTL 1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)658632962103632962Rat
12801471Schws9Schwannoma susceptibility QTL 9nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)661747639106747639Rat
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
1641904Alcrsp4Alcohol response QTL 4response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)667262953112262953Rat
1300075Glom7Glomerulus QTL 75.60.0000002kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)671201409116201409Rat


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 43 57 41 19 41 8 10 74 35 38 11 8
Low 1 3
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000005825   ⟹   ENSRNOP00000005825
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl672,144,714 - 72,156,214 (-)Ensembl
Rnor_6.0 Ensembl675,540,174 - 75,551,625 (-)Ensembl
RefSeq Acc Id: NM_001047743   ⟹   NP_001041208
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8677,879,931 - 77,891,344 (-)NCBI
mRatBN7.2672,144,714 - 72,156,130 (-)NCBI
Rnor_6.0675,540,132 - 75,551,545 (-)NCBI
Rnor_5.0685,080,132 - 85,091,844 (-)NCBI
RGSC_v3.4674,962,387 - 74,973,800 (-)RGD
Celera670,991,533 - 71,002,947 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001041208 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH98829 (Get FASTA)   NCBI Sequence Viewer  
  EDM03407 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000005825
  ENSRNOP00000005825.3
  ENSRNOP00055018790
  ENSRNOP00060030592
  ENSRNOP00065005122
GenBank Protein Q4G019 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_001041208   ⟸   NM_001047743
- UniProtKB: Q4G019 (UniProtKB/Swiss-Prot),   A6HBK2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000005825   ⟸   ENSRNOT00000005825

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q4G019-F1-model_v2 AlphaFold Q4G019 1-71 view protein structure

Transcriptome

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

Promoters
RGD ID:13694597
Promoter ID:EPDNEW_R5121
Type:initiation region
Name:Sptssa_1
Description:serine palmitoyltransferase, small subunit A
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_6.0675,551,560 - 75,551,620EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565821 AgrOrtholog
BioCyc Gene G2FUF-37538 BioCyc
Ensembl Genes ENSRNOG00000004292 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00055013504 UniProtKB/Swiss-Prot
  ENSRNOG00060021422 UniProtKB/Swiss-Prot
  ENSRNOG00065005034 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000005825 ENTREZGENE
  ENSRNOT00000005825.7 UniProtKB/Swiss-Prot
  ENSRNOT00055023151 UniProtKB/Swiss-Prot
  ENSRNOT00060037086 UniProtKB/Swiss-Prot
  ENSRNOT00065007371 UniProtKB/Swiss-Prot
InterPro Ser_palmitoyltrfase_ssu-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:500651 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 500651 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
RatGTEx ENSRNOG00000004292 RatGTEx
  ENSRNOG00055013504 RatGTEx
  ENSRNOG00060021422 RatGTEx
  ENSRNOG00065005034 RatGTEx
UniProt A6HBK2 ENTREZGENE, UniProtKB/TrEMBL
  Q4G019 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-08-16 Sptssa  serine palmitoyltransferase, small subunit A  MGC112883  LOC500651  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-02-09 MGC112883  LOC500651      Symbol and Name status set to provisional 70820 PROVISIONAL