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Gene: Sptlc3 (serine palmitoyltransferase, long chain base subunit 3) Rattus norvegicus

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Symbol:

Sptlc3

Name:

serine palmitoyltransferase, long chain base subunit 3

RGD ID:

1310030

Description:

Predicted to enable serine C-palmitoyltransferase activity. Predicted to be involved in ceramide biosynthetic process and sphingosine biosynthetic process. Predicted to act upstream of or within sphingoid biosynthetic process. Predicted to be located in endoplasmic reticulum and membrane. Predicted to be part of serine palmitoyltransferase complex. Orthologous to human SPTLC3 (serine palmitoyltransferase long chain base subunit 3); PARTICIPATES IN sphingolipid metabolic pathway; INTERACTS WITH 17beta-estradiol 3-benzoate; acrylamide; bisphenol A.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

LOC296188; RGD1310030; serine palmitoyltransferase 3; similar to dJ718P11.1.1 (novel class II aminotransferase similar to serine palmotyltransferase (isoform 1)); similar to RIKEN cDNA C130053K05 gene

RGD Orthologs

Alliance Orthologs

More Info

more info ...

Allele / Splice:

Sptlc3^{Tn(sb-T2/Bart3)2.147Mcwi}

Genetic Models:

F344-Sptlc3^{Tn(sb-T2/Bart3)2.147Mcwi}

Latest Assembly:

GRCr8 - GRCr8 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	3	147,301,570 - 147,431,696 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	3	147,301,801 - 147,434,044 (+)	Ensembl				GRCr8
mRatBN7.2	3	126,847,878 - 126,978,010 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	126,847,878 - 126,978,010 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	3	130,707,371 - 130,835,985 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	3	139,291,458 - 139,420,089 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	3	136,994,594 - 137,123,206 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	3	132,560,437 - 132,689,313 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	132,560,506 - 132,692,737 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	3	139,023,075 - 139,151,792 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	3	127,691,668 - 127,825,206 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	3	125,501,233 - 125,630,510 (+)	NCBI		Celera
RGSC_v3.1	3	127,597,526 - 127,729,920 (+)	NCBI
Cytogenetic Map	3	q36	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

sensory peripheral neuropathy (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(1->4)-beta-D-glucan (ISO)

(S)-nicotine (ISO)

1,2,4-trichloro-5-(2,5-dichlorophenyl)benzene (ISO)

17beta-estradiol 3-benzoate (EXP)

2,2',4,4',5,5'-hexachlorobiphenyl (ISO)

2,2',5,5'-tetrachlorobiphenyl (ISO)

2,3,7,8-tetrachlorodibenzodioxine (ISO)

2,4,4'-trichlorobiphenyl (ISO)

2-hydroxypropanoic acid (ISO)

4-hydroxyphenyl retinamide (ISO)

6-propyl-2-thiouracil (ISO)

acrylamide (EXP)

aflatoxin B1 (ISO)

aldehydo-D-glucose (ISO)

Azaspiracid (ISO)

azathioprine (ISO)

benzo[a]pyrene (ISO)

benzo[a]pyrene diol epoxide I (ISO)

benzo[e]pyrene (ISO)

beta-naphthoflavone (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

cadmium atom (ISO)

cadmium dichloride (ISO)

chlordecone (ISO)

chloroprene (ISO)

copper(II) sulfate (ISO)

cyclosporin A (ISO)

cytarabine (ISO)

D-glucose (ISO)

deoxynivalenol (ISO)

diiodine (ISO)

dorsomorphin (ISO)

doxorubicin (ISO)

formaldehyde (ISO)

fructose (ISO)

glucose (ISO)

glyphosate (ISO)

inulin (ISO)

leflunomide (ISO)

mercury dibromide (ISO)

methapyrilene (ISO)

methyl methanesulfonate (ISO)

N,N-diethyl-m-toluamide (EXP)

nickel sulfate (ISO)

nicotine (ISO)

okadaic acid (ISO)

ozone (ISO)

paracetamol (ISO)

PCB138 (ISO)

perfluorononanoic acid (ISO)

perfluorooctane-1-sulfonic acid (ISO)

permethrin (EXP)

phenylmercury acetate (ISO)

pirinixic acid (ISO)

potassium chromate (ISO)

quercetin (ISO)

rac-lactic acid (ISO)

S-nitrosoglutathione (ISO)

SB 431542 (ISO)

silicon dioxide (ISO)

sodium arsenite (ISO)

sulforaphane (ISO)

sunitinib (ISO)

temozolomide (ISO)

testosterone (EXP)

tetracycline (ISO)

thiram (ISO)

trichostatin A (ISO)

urethane (ISO)

valproic acid (ISO)

vinclozolin (EXP)

vitamin E (ISO)

zoledronic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

biological_process (ND)

ceramide biosynthetic process (IBA)

lipid metabolic process (IEA)

sphingoid biosynthetic process (ISO)

sphingolipid metabolic process (IEA)

sphingosine biosynthetic process (IBA,IEA,ISO)

Cellular Component

endoplasmic reticulum (IEA)

membrane (IEA)

serine palmitoyltransferase complex (IBA,IEA,ISO)

Molecular Function

acyltransferase activity (IEA)

protein binding (ISO)

pyridoxal phosphate binding (IEA)

serine C-palmitoyltransferase activity (IBA,IEA,ISO)

transferase activity (IEA)

Molecular Pathway Annotations Click to see Annotation Detail View

sphingolipid metabolic pathway (IEA)

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.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
3.	KEGG Annotation Import Pipeline	Pipeline to import KEGG annotations from KEGG into RGD
4.	GOA pipeline	RGD automated data pipeline
5.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
7.	Comprehensive gene review and curation	RGD comprehensive gene curation

Additional References at PubMed

PMID:17331073	PMID:19416851	PMID:19648650

Genomics

Comparative Map Data

Sptlc3
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	3	147,301,570 - 147,431,696 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	3	147,301,801 - 147,434,044 (+)	Ensembl				GRCr8
mRatBN7.2	3	126,847,878 - 126,978,010 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	126,847,878 - 126,978,010 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	3	130,707,371 - 130,835,985 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	3	139,291,458 - 139,420,089 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	3	136,994,594 - 137,123,206 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	3	132,560,437 - 132,689,313 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	132,560,506 - 132,692,737 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	3	139,023,075 - 139,151,792 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	3	127,691,668 - 127,825,206 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	3	125,501,233 - 125,630,510 (+)	NCBI		Celera
RGSC_v3.1	3	127,597,526 - 127,729,920 (+)	NCBI
Cytogenetic Map	3	q36	NCBI

SPTLC3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	20	13,008,972 - 13,169,103 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	20	13,008,972 - 13,169,103 (+)	Ensembl			hg38	GRCh38
GRCh37	20	12,989,620 - 13,149,750 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	20	12,937,627 - 13,095,411 (+)	NCBI	Build 36	Build 36	hg18	NCBI36
Celera	20	13,059,733 - 13,217,481 (+)	NCBI		Celera
Cytogenetic Map	20	p12.1	NCBI
HuRef	20	12,941,029 - 13,101,523 (+)	NCBI		HuRef
CHM1_1	20	12,989,665 - 13,147,485 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	20	13,048,743 - 13,212,449 (+)	NCBI		T2T-CHM13v2.0

Sptlc3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	139,335,833 - 139,478,981 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	2	139,335,833 - 139,479,594 (+)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	2	139,493,913 - 139,637,061 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	139,493,913 - 139,637,674 (+)	Ensembl			mm10	GRCm38
MGSCv37	2	139,319,656 - 139,463,410 (+)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	2	139,185,361 - 139,329,115 (+)	NCBI		MGSCv36	mm8
Celera	2	140,671,316 - 140,814,560 (+)	NCBI		Celera
Cytogenetic Map	2	F3	NCBI
cM Map	2	68.52	NCBI

Sptlc3
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955415	22,531,626 - 22,682,564 (+)	Ensembl
ChiLan1.0	NW_004955415	22,532,193 - 22,686,071 (+)	NCBI	ChiLan1.0	ChiLan1.0

SPTLC3
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	21	13,894,378 - 14,053,615 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	20	13,891,210 - 14,052,725 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	20	12,966,584 - 13,125,802 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	20	12,952,501 - 13,111,347 (+)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	20	12,952,524 - 13,111,347 (+)	Ensembl			panPan2	panpan1.1

SPTLC3
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	24	9,447,575 - 9,597,544 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	24	9,447,859 - 9,595,975 (-)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	24	9,258,320 - 9,409,355 (-)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	24	9,860,196 - 10,010,807 (-)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	24	9,861,421 - 10,011,073 (-)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	24	9,471,327 - 9,619,877 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	24	9,555,159 - 9,706,174 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	24	9,904,468 - 10,055,517 (-)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

Sptlc3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024408640	158,213,063 - 158,353,439 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936485	6,644,188 - 6,784,828 (-)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936485	6,647,930 - 6,784,792 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SPTLC3
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	17	21,769,484 - 21,903,264 (+)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	17	21,769,388 - 21,903,269 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	17	24,339,933 - 24,473,785 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

SPTLC3
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	2	41,900,389 - 42,067,842 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	2	41,900,447 - 42,070,112 (+)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666054	2,190,751 - 2,332,203 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Sptlc3
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624741	13,956,570 - 14,152,600 (+)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624741	13,956,688 - 14,152,127 (+)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Sptlc3
(Rattus rattus - black rat)

Black Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Black Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rrattus_CSIRO_v1	5	118,853,278 - 118,963,997 (+)	NCBI		Rrattus_CSIRO_v1

Variants

Variants in Sptlc3
917 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	416
Count of miRNA genes:	212
Interacting mature miRNAs:	251
Transcripts:	ENSRNOT00000005920
Prediction methods:	Microtar, Miranda, 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.

QTLs in Region (GRCr8)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
2301411	Bp320	Blood pressure QTL 320		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	141555229	186555229	Rat
12879876	Bw182	Body weight QTL 182		0.003	body mass (VT:0001259)	body weight (CMO:0000012)	3	141555229	186555229	Rat
1582233	Insul10	Insulin level QTL 10	5.4	0.0015	blood insulin amount (VT:0001560)	serum insulin level times blood glucose level (CMO:0002040)	3	133259579	178259579	Rat
12879872	Cm97	Cardiac mass QTL 97		0.001	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	3	141555229	186555229	Rat
12879873	Cm96	Cardiac mass QTL 96		0.001	heart mass (VT:0007028)	heart wet weight to body weight ratio (CMO:0002408)	3	141555229	186555229	Rat
2302373	Gluco39	Glucose level QTL 39	5.01		blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	3	129154923	182114333	Rat
12879874	Cm98	Cardiac mass QTL 98		0.005	heart right ventricle mass (VT:0007033)	heart right ventricle weight to body weight ratio (CMO:0000914)	3	141555229	186555229	Rat
12879875	Kidm64	Kidney mass QTL 64		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	3	141555229	186555229	Rat
70216	Cm14	Cardiac mass QTL 14	2.1		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	51581665	184004958	Rat
2292591	Esta4	Estrogen-induced thymic atrophy QTL 4			thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	3	67641776	167835660	Rat
1358362	Srcrt2	Stress Responsive Cort QTL 2	2.78		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	3	58601291	153936591	Rat
1578754	Stresp16	Stress response QTL 16	4	0.001	blood renin amount (VT:0003349)	plasma renin activity level (CMO:0000116)	3	133134628	178134628	Rat
7387306	Bw124	Body weight QTL 124	3.2	0.0003	body mass (VT:0001259)	body weight (CMO:0000012)	3	104545086	149545086	Rat
1300173	Rf11	Renal function QTL 11	3.38		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	3	141508991	166376254	Rat
8694437	Bw167	Body weight QTL 167	22.46	0.001	retroperitoneal fat pad mass (VT:0010430)	retroperitoneal fat pad weight to body weight ratio (CMO:0000635)	3	112250810	157250810	Rat
10755461	Coatc16	Coat color QTL 16			coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	3	142898802	187898802	Rat
8662816	Vetf4	Vascular elastic tissue fragility QTL 4	4		renal artery integrity trait (VT:0010642)	number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)	3	79649560	177741895	Rat
1559282	Emca5	Estrogen-induced mammary cancer QTL 5	3.9		mammary gland integrity trait (VT:0010552)	percentage of study population developing mammary tumors during a period of time (CMO:0000948)	3	145335553	189428310	Rat
1354611	Despr2	Despair related QTL 2	3.03	0.0028	locomotor behavior trait (VT:0001392)	amount of time spent in voluntary immobility (CMO:0001043)	3	117537367	162537367	Rat
2303620	Vencon4	Ventilatory control QTL 4	3.9		respiration trait (VT:0001943)	tidal volume (CMO:0000222)	3	125116475	170116475	Rat
631649	Bp123	Blood pressure QTL 123	3.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	110225882	155225882	Rat
1358204	Insglur1	Insulin/glucose ratio QTL 1	3.8		blood glucose amount (VT:0000188)	serum glucose level (CMO:0000543)	3	136091420	155634702	Rat
1576306	Schws3	Schwannoma susceptibility QTL 3		0.001	nervous system integrity trait (VT:0010566)	percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)	3	139299381	184299381	Rat
1300159	Kidm4	Kidney mass QTL 4	3.83		kidney mass (VT:0002707)	right kidney wet weight to body weight ratio (CMO:0001953)	3	141508991	177728348	Rat
5686842	Rf59	Renal function QTL 59			urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	3	122395989	167395989	Rat
631673	Iddm13	Insulin dependent diabetes mellitus QTL 13	1.3	0.663	blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	3	137114333	182114333	Rat
2301971	Cm71	Cardiac mass QTL 71	4.63		heart left ventricle mass (VT:0007031)	heart left ventricle weight (CMO:0000776)	3	131036586	176036586	Rat
2301970	Bw81	Body weight QTL 81	5.19		body mass (VT:0001259)	body weight (CMO:0000012)	3	131036586	176036586	Rat
1581546	Pur13	Proteinuria QTL 13	2.93	0.0335	urine total protein amount (VT:0000032)	urine protein excretion rate (CMO:0000759)	3	98651826	167012663	Rat
1331758	Bp207	Blood pressure QTL 207	2.848		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	110634702	155634702	Rat
12879871	Am7	Aortic mass QTL 7		0.001	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	3	141555229	186555229	Rat
631541	Bp81	Blood pressure QTL 81	4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	144575244	189428310	Rat
724532	Cm17	Cardiac mass QTL 17	2		heart mass (VT:0007028)	calculated heart weight (CMO:0000073)	3	116188400	161188400	Rat

Markers in Region

D3Rat14

Rat Assembly	Chr	Position (strand)	Source	JBrowse
GRCr8	3	147,308,445 - 147,308,590 (+)	Marker Load Pipeline
mRatBN7.2	3	126,854,753 - 126,854,898 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	132,567,313 - 132,567,457	NCBI	Rnor6.0
Rnor_5.0	3	139,029,951 - 139,030,095	UniSTS	Rnor5.0
RGSC_v3.4	3	127,698,349 - 127,698,688	RGD	RGSC3.4
RGSC_v3.4	3	127,698,544 - 127,698,688	UniSTS	RGSC3.4
Celera	3	125,508,109 - 125,508,253	UniSTS
RGSC_v3.1	3	127,604,117 - 127,604,261	RGD
RH 3.4 Map	3	1147.4	UniSTS
RH 3.4 Map	3	1147.4	RGD
RH 2.0 Map	3	749.7	RGD
SHRSP x BN Map	3	62.4899	RGD
Cytogenetic Map	3	q36	UniSTS

D3Got236

Rat Assembly	Chr	Position (strand)	Source	JBrowse
GRCr8	3	147,413,227 - 147,413,514 (+)	Marker Load Pipeline
mRatBN7.2	3	126,959,541 - 126,959,828 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	132,670,849 - 132,671,135	NCBI	Rnor6.0
Rnor_5.0	3	139,133,328 - 139,133,614	UniSTS	Rnor5.0
RGSC_v3.4	3	127,806,792 - 127,807,078	UniSTS	RGSC3.4
Celera	3	125,612,038 - 125,612,324	UniSTS
Cytogenetic Map	3	q36	UniSTS

Genetic Models

This gene Sptlc3 is modified in the following models/strains:

F344-Sptlc3^{Tn(sb-T2/Bart3)2.147Mcwi}

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Download All Expressed Objects for this Gene

alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	sensory system	visual system
13	4	4	95	29	28	1	7	1	6	112	35	10	67	60	74	27	5	5

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001106517	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH473949	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000003	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000005920 ⟹ ENSRNOP00000005920

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	3	147,301,801 - 147,434,044 (+)	Ensembl
mRatBN7.2 Ensembl	3	126,847,878 - 126,978,010 (+)	Ensembl
Rnor_6.0 Ensembl	3	132,560,506 - 132,692,737 (+)	Ensembl

RefSeq Acc Id:

NM_001106517 ⟹ NP_001099987

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	3	147,301,570 - 147,431,696 (+)	NCBI
mRatBN7.2	3	126,847,878 - 126,978,010 (+)	NCBI
Rnor_6.0	3	132,560,437 - 132,689,313 (+)	NCBI
Rnor_5.0	3	139,023,075 - 139,151,792 (+)	NCBI
RGSC_v3.4	3	127,691,668 - 127,825,206 (+)	RGD
Celera	3	125,501,233 - 125,630,510 (+)	RGD

Sequence:

show sequence

CCTCAGCCTCAAAAGGCAGCTAGCAAGGCAAATTCTCTTTGTAGTTTCAGAACAGGTTTGTTGC
CATGGATCCCACAACGCGACTGGAGTAAACTAGTAAAAGGTAACAACTAAAGATCTAGTCAATA
GATAGGCTGTGGTTCTTCTTCTGGAAAATCCTGACTGGTAGGATTCCTTTAAAGGCTCTGCCGC
AAAGTGCTTTATGTTATTACTTCAGCTGCTTGAAAAGTGAAGTTCCAGGAGACCGCAGAAAGAG
AACCTGCCTTGGCCAAAGCACTTCCCACTAATGGCCAACCCGAGGGACAGTGCTGTTACTAATG
GGACTCTACGCAATCCCAAGACCCAGCCGGGAAAAAGACAGAGCACTGATTGTGTGAAAAATGG
AATCTCGAAAGAAGCCCAGCAAAATAGGAAGGCAGAGGAGGACGATAAACTTGTCTTTAAGCCC
TACCCAGAGCCACCACTTTATGTCTTCGTTTTCACATACATGGGATATGGAATTGGCATGCTGT
TCGGCTATCTCAGAGACTTCATGAGAAACTGGGGAATAGAAAAATGCAACGCAGCTGTAGAGCG
AGAAGAACAAAAAGATTTTGTGCCGCTGTATCAGGACTTTGAGAACTTTTATACAAGAAACCTT
TACATGAGAATCAGAGACAGCTGGAGTCACACCGTCTGCAGTGTCCCAGTACCTAACTTTGACA
TAATGGAAAAAGTGACAGATGACTATAACTGGACATTCAGGCATACTGGAAAAGTTATCAAAAA
TGTTATCAACATGGCCTCCTACAACTACCTTGGCCTTGCATCAAAATACAATGAGTCAATGGAG
AAAGTTAAAGACACTATAGAAAAGTATGGCGTAGGTGTGGCCAGCACCAGAAATGAAATGGGTT
CCTTGGATATACACAACGAGCTGGAGGATCTCATGGCTAAGTTCTTGAATGTGGAAGCAGTGAT
GGTTTTTGGGATGGGATTCGCAACCAACTCGACGAATATCCCTATATTTGTTGGAAAGGGATGC
CTCATTTTAAGTGACGAGTTCAACCACACTTCAGTCATCCTGGGGTCTCGACTCTCAGGCGCAG
TCATAAGACCCTTCAAACACAATAATATACAAAACCTAGAGAAGCTCCTGAGAGAAGCTATCAT
CCGTGGCCAGCCTCGCACGGGAAGAGCTTGGAAAAAGATTCTCATCCTGGTAGAGGGAGTCTAC
AGCATGGAAGGTTCCATTGTGAACCTTCCCCAGATAGTGGCTCTAAAGAAGAAATACAAGGCTT
ACCTCTACATGGATGAAGCTCACAGTATTGGCTGTACAGGTACCATGGGCCAAGGCATCCGAGA
GTTGTTTGGACTGGCCCCTGAAGATATCGACATATACATGGGTACATTCACCAAAAGCTTCGCG
GCTTCTGGAGGCTATATAGCTGGTAAAAAGGAAATTGTGGATTATGTACGGGTTCAGTCGCATA
GTGCTACATATGCTACATCCATGAGTCCTGTAGTAGCAGCGCAAATCATCAGATCATTGAAGAT
AATGATGGGATATGAAGGAAACTTTGGAGGTGTGCAGAGAATACAGCAACTTAGAGAAAACATA
AAATATTTCCGACGGCGACTTATAGAGATGGGATTCATCATCTATGGCAATGACTACTCTCCCG
TGGTCCCCGTCCTCCTCTACATGCCTGCTAAAGTGTCTGCTTTTGGAAGACTTTTGCTTAAGAA
AAAGATTGCGGTGGTGGTCGTTGGATTTCCAGCTACTTCTCTGCCAGAAGGTCGGGCTAGGTTC
AGCCTTTCCTCAGCTCATACTCGGGAGATGTTAGACACAGTTTTGGAAGTTGTTGATAAAATCG
GTGATCTCCTGAATGTGAAATATTTCCCATACAAGAAGTCAGGACGGGCTGTACTCTACAATAA
GGAGAATTTTGACAATGAAGCAAGCTTTGAAGAGAAGAGCTCTGAACCAGAAGCCTAAGTTTCC
TGGCTCTAAATAGAACATAAAGACTACCAGAAAGACCTCCCTCCCTCTTTATCTCAAAAGTAAT
ATAATTGTATTTTACCCCTTCTAAGAACAATTTTATTTTTCAAACAAACTTAATTGAAGAAGGG
AAATAATCATTTATTTAATGTCTCAAACTTGCTGCTACAAAGTGAAAGAATATAATTCTAGATT
TAAGTTTTCCCTCTTCTTTGCTGTAAATACACACATACGTGCAAATGGTAGTAAGCCTATGTTT
TAGCTGCTTTTGGGTCAGGCCTTATCAAGGGCTACAACTAAAATGAAAGGATTTTGATTTTTTA
CTTGATAATCTTCCTGTGTACCATCTGCACACAAGAAAAAGTGTCAGAGAGGAGCTGGGTCCCT
CGTTCCACCTGAAACAGTTCATATGTGTCGTGGGAAGCTCCAGAAAAGGAGAAGACAATGTTGC
TTCTGTTTGTCACATTTGGACTTTATCCAAGGACAGGTGTCAAAAGACACAGTTAATGCTTGGG
AGAGAATACAGAACTGGCTGGTGGTGAGCAGAGACGTCTTTGAAGTGAGCCTCCTTTTTCCTCT
TGATGTTCTCCTACAGCTTTATTGTTAAGCTCTAAGGACTGGAAAGTTCATGTCTCTTGTTTTC
TAAAGAGGAGGAAGAAAAGCAATCACAAGCCAGTTTTGGACCTAGACTAAAACTATAAAATTAA
AACAACCCAAATGATGCTGGTGCCATGCAGAGGGAGCCTAAAAACGCTTGGCCTTTATTGCTTT
AAGGAACATCTTCCCATTTTTCTATTGAATTCTGAGTACATAGTGAAACTCAATTTCCCTTACA
ACACATTCCCAAATTGCACTT

hide sequence

Protein Sequences


Protein RefSeqs	NP_001099987	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDL80317	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000005920
	ENSRNOP00000005920.4

RefSeq Acc Id:

NP_001099987 ⟸ NM_001106517

- UniProtKB:

D4A9V0 (UniProtKB/TrEMBL), A6HQL6 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MANPRDSAVTNGTLRNPKTQPGKRQSTDCVKNGISKEAQQNRKAEEDDKLVFKPYPEPPLYVFV
FTYMGYGIGMLFGYLRDFMRNWGIEKCNAAVEREEQKDFVPLYQDFENFYTRNLYMRIRDSWSH
TVCSVPVPNFDIMEKVTDDYNWTFRHTGKVIKNVINMASYNYLGLASKYNESMEKVKDTIEKYG
VGVASTRNEMGSLDIHNELEDLMAKFLNVEAVMVFGMGFATNSTNIPIFVGKGCLILSDEFNHT
SVILGSRLSGAVIRPFKHNNIQNLEKLLREAIIRGQPRTGRAWKKILILVEGVYSMEGSIVNLP
QIVALKKKYKAYLYMDEAHSIGCTGTMGQGIRELFGLAPEDIDIYMGTFTKSFAASGGYIAGKK
EIVDYVRVQSHSATYATSMSPVVAAQIIRSLKIMMGYEGNFGGVQRIQQLRENIKYFRRRLIEM
GFIIYGNDYSPVVPVLLYMPAKVSAFGRLLLKKKIAVVVVGFPATSLPEGRARFSLSSAHTREM
LDTVLEVVDKIGDLLNVKYFPYKKSGRAVLYNKENFDNEASFEEKSSEPEA

hide sequence

Ensembl Acc Id:

ENSRNOP00000005920 ⟸ ENSRNOT00000005920

Protein Domains

Aminotransferase class I/classII large

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-D4A9V0-F1-model_v2	AlphaFold	D4A9V0	1-563	view protein structure

Transcriptome

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1310030	AgrOrtholog
BioCyc Gene	G2FUF-47670	BioCyc
Ensembl Genes	ENSRNOG00000004443	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000005920	ENTREZGENE
	ENSRNOT00000005920.7	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
	AON_synthase_class-II	UniProtKB/TrEMBL
	PyrdxlP-dep_Trfase_major_dom	UniProtKB/TrEMBL
	PyrdxlP-dep_Trfase_major_sub1	UniProtKB/TrEMBL
	PyrdxlP-dep_Trfase_major_sub2	UniProtKB/TrEMBL
KEGG Report	rno:296188	UniProtKB/TrEMBL
NCBI Gene	296188	ENTREZGENE
PANTHER	CLASS II AMINOTRANSFERASE/8-AMINO-7-OXONONANOATE SYNTHASE	UniProtKB/TrEMBL
	SERINE PALMITOYLTRANSFERASE 3	UniProtKB/TrEMBL
Pfam	Aminotran_1_2	UniProtKB/TrEMBL
PhenoGen	Sptlc3	PhenoGen
PROSITE	AA_TRANSFER_CLASS_2	UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000004443	RatGTEx
Superfamily-SCOP	PyrdxlP-dep_Trfase_major	UniProtKB/TrEMBL
UniProt	A6HQL6	ENTREZGENE, UniProtKB/TrEMBL
	D4A9V0	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-02-27	Sptlc3	serine palmitoyltransferase, long chain base subunit 3	RGD1310030_predicted	similar to RIKEN cDNA C130053K05 gene; similar to dJ718P11.1.1 (novel class II aminotransferase similar to serine palmotyltransferase (isoform 1)) (predicted)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-01-20	RGD1310030_predicted	similar to RIKEN cDNA C130053K05 gene; similar to dJ718P11.1.1 (novel class II aminotransferase similar to serine palmotyltransferase (isoform 1)) (predicted)	LOC296188_predicted		Symbol and Name status set to approved	1331353	APPROVED
2005-01-12	LOC296188_predicted	similar to RIKEN cDNA C130053K05 gene; similar to dJ718P11.1.1 (novel class II aminotransferase similar to serine palmotyltransferase (isoform 1)) (predicted)			Symbol and Name status set to provisional	70820	PROVISIONAL

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - ClinVar

Imported Annotations - KEGG (archival)