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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

Alliance Orthologs

More Info

more info ...

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	6	112,679,623 - 112,762,470 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	6	112,679,623 - 112,762,640 (-)	Ensembl				GRCr8
mRatBN7.2	6	106,948,682 - 107,031,532 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	6	106,950,949 - 107,031,542 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	6	107,116,961 - 107,199,840 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	6	107,415,779 - 107,498,659 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	6	106,785,468 - 106,868,346 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	6	111,334,408 - 111,417,960 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	6	111,339,136 - 111,417,954 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	6	120,616,251 - 120,699,243 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	6	111,546,037 - 111,622,959 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	6	104,771,427 - 104,849,755 (-)	NCBI		Celera
RGSC_v3.1	6	111,245,978 - 111,626,585 (-)	NCBI
Cytogenetic Map	6	q31	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Charcot-Marie-Tooth disease (ISO)

COVID-19 (ISO)

genetic disease (ISO)

hereditary sensory and autonomic neuropathy type 1C (ISO)

psoriasis (ISS)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-schisandrin B (EXP)

(-)-epigallocatechin 3-gallate (ISO)

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

1,2-dimethylhydrazine (ISO)

1-benzylpiperazine (EXP)

17beta-estradiol (ISO)

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

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

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

2-acetamidofluorene (ISO)

2-hydroxypropanoic acid (ISO)

2-palmitoylglycerol (ISO)

3,3',5-triiodo-L-thyronine (ISO)

3,4-methylenedioxymethamphetamine (ISO)

3-chloropropane-1,2-diol (EXP)

3-methylcholanthrene (ISO)

4,4'-diaminodiphenylmethane (ISO)

8'-apo-beta,psi-caroten-8'-al (ISO)

acetamide (EXP)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

amphetamine (EXP)

aristolochic acid A (ISO)

Aroclor 1254 (ISO)

arsenite(3-) (ISO)

arsenous acid (ISO)

benzo[a]pyrene diol epoxide I (ISO)

benzo[e]pyrene (ISO)

beta-carotene (ISO)

butanal (ISO)

Butylbenzyl phthalate (ISO)

calcitriol (ISO)

choline (ISO)

cisplatin (ISO)

cobalt dichloride (ISO)

cyclosporin A (ISO)

deoxynivalenol (ISO)

diarsenic trioxide (ISO)

dibutyl phthalate (EXP)

diethylstilbestrol (ISO)

divanadium pentaoxide (ISO)

dorsomorphin (ISO)

entinostat (ISO)

ethanol (ISO)

flutamide (EXP)

folic acid (ISO)

genistein (ISO)

gentamycin (EXP)

GW 4064 (ISO)

isoprenaline (ISO)

ivermectin (ISO)

L-methionine (ISO)

lithocholic acid (ISO)

methapyrilene (ISO)

methidathion (ISO)

methotrexate (ISO)

methoxychlor (EXP)

nickel atom (ISO)

Nivalenol (ISO)

ozone (ISO)

paracetamol (ISO)

paraquat (ISO)

pentachlorophenol (ISO)

pentanal (ISO)

perfluorooctane-1-sulfonic acid (ISO)

perfluorooctanoic acid (ISO)

phenethyl caffeate (ISO)

phenobarbital (ISO)

pirinixic acid (ISO)

piroxicam (ISO)

potassium chromate (ISO)

rac-lactic acid (ISO)

resveratrol (ISO)

SB 431542 (ISO)

sodium arsenite (ISO)

sodium fluoride (ISO)

tert-butyl hydroperoxide (ISO)

testosterone (ISO)

tetrachloromethane (EXP,ISO)

thioacetamide (EXP)

thiram (ISO)

titanium dioxide (ISO)

triclocarban (EXP)

urethane (ISO)

valproic acid (ISO)

vancomycin (ISO)

zinc atom (ISO)

zinc(0) (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

adipose tissue development (IEA,ISO,ISS)

ceramide biosynthetic process (IBA,ISO)

glycosphingolipid biosynthetic process (IEA,ISO)

lipid metabolic process (IEA)

positive regulation of lipophagy (ISO)

response to immobilization stress (IEP)

sphinganine biosynthetic process (ISO)

sphingolipid biosynthetic process (IEA,ISO,ISS)

sphingolipid metabolic process (IEA)

sphingomyelin biosynthetic process (IEA,ISO)

sphingosine biosynthetic process (IBA,IEA,ISO)

Cellular Component

cytoplasmic side of endoplasmic reticulum membrane (IEA,ISO)

endoplasmic reticulum 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,ISS)

transferase activity (IEA)

Molecular Pathway Annotations Click to see Annotation Detail View

Fabry disease pathway (ISO)

Gaucher's disease pathway (ISO)

Krabbe disease pathway (ISO)

metachromatic leukodystrophy pathway (ISO)

sphingolipid metabolic pathway (IEA,ISO)

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.	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.

Additional References at PubMed

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

Genomics

Comparative Map Data

Sptlc2
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	6	112,679,623 - 112,762,470 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	6	112,679,623 - 112,762,640 (-)	Ensembl				GRCr8
mRatBN7.2	6	106,948,682 - 107,031,532 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	6	106,950,949 - 107,031,542 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	6	107,116,961 - 107,199,840 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	6	107,415,779 - 107,498,659 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	6	106,785,468 - 106,868,346 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	6	111,334,408 - 111,417,960 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	6	111,339,136 - 111,417,954 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	6	120,616,251 - 120,699,243 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	6	111,546,037 - 111,622,959 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	6	104,771,427 - 104,849,755 (-)	NCBI		Celera
RGSC_v3.1	6	111,245,978 - 111,626,585 (-)	NCBI
Cytogenetic Map	6	q31	NCBI

SPTLC2
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	14	77,505,997 - 77,616,637 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	14	77,505,997 - 77,616,672 (-)	Ensembl			hg38	GRCh38
GRCh37	14	77,972,340 - 78,082,980 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	14	77,043,023 - 77,152,863 (-)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	14	77,043,024 - 77,152,863	NCBI
Celera	14	58,011,851 - 58,121,636 (-)	NCBI		Celera
Cytogenetic Map	14	q24.3	NCBI
HuRef	14	58,138,337 - 58,249,054 (-)	NCBI		HuRef
CHM1_1	14	77,911,814 - 78,022,586 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	14	71,715,382 - 71,825,999 (-)	NCBI		T2T-CHM13v2.0

Sptlc2
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	12	87,351,832 - 87,435,129 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	12	87,351,832 - 87,435,129 (-)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	12	87,305,058 - 87,388,355 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	12	87,305,058 - 87,388,355 (-)	Ensembl			mm10	GRCm38
MGSCv37	12	88,648,839 - 88,729,180 (-)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	12	88,196,992 - 88,277,333 (-)	NCBI		MGSCv36	mm8
Celera	12	88,772,417 - 88,852,773 (-)	NCBI		Celera
Cytogenetic Map	12	D2	NCBI
cM Map	12	41.52	NCBI

Sptlc2
(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_004955438	1,385,431 - 1,491,578 (-)	Ensembl
ChiLan1.0	NW_004955438	1,385,431 - 1,491,534 (-)	NCBI	ChiLan1.0	ChiLan1.0

SPTLC2
(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	15	78,591,247 - 78,702,589 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	14	77,807,751 - 77,918,929 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	14	58,066,123 - 58,170,472 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	14	77,266,545 - 77,370,663 (-)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	14	77,266,545 - 77,370,663 (-)	Ensembl			panPan2	panpan1.1

SPTLC2
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	8	50,291,797 - 50,401,202 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	8	50,271,010 - 50,401,313 (-)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	8	49,979,477 - 50,088,850 (-)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	8	50,525,698 - 50,635,391 (-)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	8	50,530,838 - 50,635,427 (-)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	8	50,188,135 - 50,297,514 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	8	50,211,301 - 50,320,641 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	8	50,609,185 - 50,719,362 (-)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

LOC101967158
(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	25,664,744 - 25,778,794 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936488	6,315,715 - 6,419,882 (-)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0 Ensembl	NW_004936488	6,289,833 - 6,296,849 (-)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936488	6,313,189 - 6,404,425 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SPTLC2
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	7	100,544,478 - 100,638,905 (-)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	7	100,545,360 - 100,638,973 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	7	106,672,604 - 106,730,716 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

SPTLC2
(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	24	54,769,072 - 54,876,963 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
Vero_WHO_p1.0	NW_023666053	42,955,305 - 43,064,586 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Sptlc2
(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 1.0	NW_004624734	24,281,482 - 24,400,870 (+)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Sptlc2
(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	7	101,402,226 - 101,480,631 (-)	NCBI		Rrattus_CSIRO_v1

Variants

Variants in Sptlc2
619 total Variants

miRNA Target Status (No longer updated)

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.

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
4145119	Mcs25	Mammary carcinoma susceptibility QTL 25		0.0001	mammary gland integrity trait (VT:0010552)	ratio of deaths to total study population during a period of time (CMO:0001023)	6	71278722	116278722	Rat
4145118	Mcs26	Mammary carcinoma susceptibility QTL 26		0.0001	mammary gland integrity trait (VT:0010552)	post-insult time to mammary tumor formation (CMO:0000345)	6	112483610	147156653	Rat
2293088	Iddm28	Insulin dependent diabetes mellitus QTL 28	5.21		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	6	68767270	135411972	Rat
1331799	Bp211	Blood pressure QTL 211	3.66407		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	6	88019181	136741135	Rat
1581563	Uae33	Urinary albumin excretion QTL 33			urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	6	93560258	136550638	Rat
10054138	Gmadr3	Adrenal mass QTL 3	3.68	0.00045	adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	6	90871046	135871046	Rat
1641917	Colcr5	Colorectal carcinoma resistance QTL 5	3.18	0.0009	intestine integrity trait (VT:0010554)	benign colorectal tumor number (CMO:0001795)	6	98944780	143944780	Rat
71111	Iddm8	Insulin dependent diabetes mellitus QTL 8	1.9	0.002	blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	6	110921244	147156653	Rat
61414	Pia3	Pristane induced arthritis QTL 3	4.5		joint integrity trait (VT:0010548)	post-insult time to onset of experimental arthritis (CMO:0001450)	6	100704576	136029228	Rat
724524	Uae2	Urinary albumin excretion QTL 2	2.7	0.0005	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	6	79198463	144254945	Rat
1358355	Srcrt4	Stress Responsive Cort QTL 4	6.39		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	6	106095977	147156653	Rat
737827	Hcar11	Hepatocarcinoma resistance QTL 11	4.4		liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	6	46050607	116278722	Rat
2303624	Vencon5	Ventilatory control QTL 5	4.45		respiration trait (VT:0001943)	minute ventilation (CMO:0000132)	6	93778632	138778632	Rat
1576309	Emca7	Estrogen-induced mammary cancer QTL 7	4		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	6	20859430	113082285	Rat
61329	Eae9	Experimental allergic encephalomyelitis QTL 9	3.7		body mass (VT:0001259)	change in body weight (CMO:0002045)	6	84490437	129490437	Rat
10054123	Srcrt6	Stress Responsive Cort QTL 6	2.5	0.0043	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	6	90871046	135871046	Rat
724536	Uae7	Urinary albumin excretion QTL 7	3.5		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	6	93560258	136550638	Rat
2313399	Anxrr28	Anxiety related response QTL 28			aggression-related behavior trait (VT:0015014)	tameness/aggressiveness composite score (CMO:0002136)	6	101593607	138161926	Rat
1576302	Schws4	Schwannoma susceptibility QTL 4		0.0078	nervous system integrity trait (VT:0010566)	percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)	6	78204640	123204640	Rat
1581550	Pur8	Proteinuria QTL 8			urine total protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	6	93560258	136550638	Rat
1300075	Glom7	Glomerulus QTL 7	5.6	0.0000002	kidney glomerulus morphology trait (VT:0005325)	count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)	6	76937178	121937178	Rat
1331725	Bp212	Blood pressure QTL 212	3.52475		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	6	99437079	125323237	Rat
12801471	Schws9	Schwannoma susceptibility QTL 9			nervous system integrity trait (VT:0010566)	percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)	6	101593607	146593607	Rat

Markers in Region

D19271

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	6	106,953,252 - 106,953,411 (+)	MAPPER	mRatBN7.2
Rnor_6.0	6	111,338,980 - 111,339,138	NCBI	Rnor6.0
Rnor_5.0	6	120,620,823 - 120,620,981	UniSTS	Rnor5.0
Celera	6	104,773,271 - 104,773,429	UniSTS
Cytogenetic Map	6	q31	UniSTS

RH138750

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	6	107,008,557 - 107,008,777 (+)	MAPPER	mRatBN7.2
Rnor_6.0	6	111,394,494 - 111,394,713	NCBI	Rnor6.0
Rnor_5.0	6	120,675,810 - 120,676,029	UniSTS	Rnor5.0
RGSC_v3.4	6	111,599,983 - 111,600,202	UniSTS	RGSC3.4
Celera	6	104,827,505 - 104,827,724	UniSTS
RH 3.4 Map	6	748.9	UniSTS
Cytogenetic Map	6	q31	UniSTS

RH131889

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	6	106,952,847 - 106,953,045 (+)	MAPPER	mRatBN7.2
Rnor_6.0	6	111,338,575 - 111,338,772	NCBI	Rnor6.0
Rnor_5.0	6	120,620,418 - 120,620,615	UniSTS	Rnor5.0
Celera	6	104,772,866 - 104,773,063	UniSTS
RH 3.4 Map	6	748.9	UniSTS
Cytogenetic Map	6	q31	UniSTS

RH134867

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	6	106,951,098 - 106,951,279 (+)	MAPPER	mRatBN7.2
Rnor_6.0	6	111,336,826 - 111,337,006	NCBI	Rnor6.0
Rnor_5.0	6	120,618,669 - 120,618,849	UniSTS	Rnor5.0
Celera	6	104,771,117 - 104,771,297	UniSTS
RH 3.4 Map	6	744.1	UniSTS
Cytogenetic Map	6	q31	UniSTS

BE115266

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	6	106,957,199 - 106,957,394 (+)	MAPPER	mRatBN7.2
Rnor_6.0	6	111,342,663 - 111,342,857	NCBI	Rnor6.0
Rnor_5.0	6	120,624,089 - 120,624,283	UniSTS	Rnor5.0
RGSC_v3.4	6	111,546,617 - 111,546,811	UniSTS	RGSC3.4
Celera	6	104,776,449 - 104,776,643	UniSTS
RH 3.4 Map	6	743.6	UniSTS
Cytogenetic Map	6	q31	UniSTS

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
23	13	81	214	91	90	59	157	59	6	485	281	21	192	114	124	31	34	34

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001037097	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_008764823	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC107662	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473982	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000006	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000016324 ⟹ ENSRNOP00000016324

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	6	111,339,136 - 111,417,813 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000085458 ⟹ ENSRNOP00000071651

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	6	112,679,623 - 112,762,640 (-)	Ensembl
mRatBN7.2 Ensembl	6	106,950,949 - 107,031,542 (-)	Ensembl
Rnor_6.0 Ensembl	6	111,342,024 - 111,417,954 (-)	Ensembl

RefSeq Acc Id:

NM_001037097 ⟹ NP_001032174

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	6	112,679,623 - 112,762,470 (-)	NCBI
mRatBN7.2	6	106,948,682 - 107,031,532 (-)	NCBI
Rnor_6.0	6	111,337,136 - 111,417,913 (-)	NCBI
Rnor_5.0	6	120,616,251 - 120,699,243 (-)	NCBI
RGSC_v3.4	6	111,546,037 - 111,622,959 (-)	RGD
Celera	6	104,771,427 - 104,849,755 (-)	RGD

Sequence:

show sequence

CAGCCATTTCCGGTTTCGGAGAGGTGGGTGCGGTGCGGAGCGGGAGTTGGCGCCGCCGCCGCCT
CCAGAGCCTGTCTTGCTGCCGGGTGCTGCCGGGAGGATGCGGCCGGAGCCAGGAGGCTGCTGCT
GCCGCCGCCCGATGCGGGCGAACGGCTGCGTGAAAAACGGGGAAGTGAGGAACGGGTACTTGAG
GAGCAGCACCGCCACCATCGCGGCTGCGGGCCAGATTCATCATATTACAGAAAATGGAGGACTG
TACAAAAGACCGTTTAATGAAGCTTTTGAAGAAACACCCATGCTAGTTGCTGTGCTCACATACG
TGGGCTATGGTGTACTCACCCTCTTTGGATATCTTCGAGATTTCTTGAGGCATTGGAGAATTGA
AAAGTGCCACCATGCAACAGAAAGAGAAGAACAAAAGGACTTTGTGTCCTTGTATCAGGATTTT
GAAAACTTCTATACAAGGAACCTCTACATGAGGATCAGAGACAACTGGAATCGACCCATCTGTA
GTGTGCCTGGAGCCAAGGTGGATATCATGGAGAGACAGTCTCATGACTACAACTGGTCATTCAA
GTACACAGGGAATATAATTAAAGGTGTAATAAACATGGGTTCCTACAACTATCTTGGATTTGCG
AGGAACACTGGATCATGTCAGGAAGCAGCTGCTGAAGTTCTCAAGACATATGGAGCAGGGGTGT
GCAGCACTCGCCAGGAAATTGGGAACCTGGACAAGCACGAGGAACTAGAGAAACTGGTAGCAAG
GTTCTTGGGTGTGGAAGCTGCTTTGACCTATGGCATGGGATTTGCGACAAATTCAATGAACATT
CCTGCTCTTGTTGGCAAAGGTTGCCTGATTCTGAGTGATGAGCTGAACCATGCATCCTTGGTTC
TAGGAGCCAGACTGTCGGGAGCAACCATTCGAATCTTCAAACACAACAATATGCAAAGCTTGGA
GAAGCTTTTAAAAGATGCCATTGTTTATGGTCAGCCTCGGACAAGAAGGCCCTGGAAGAAAATC
CTAATCCTCGTGGAAGGCATATATAGCATGGAAGGGTCTATTGTTCGCCTTCCTGAAGTGATTG
CTCTCAAGAAGAAATACAAGGCATACTTGTATCTGGATGAGGCTCACAGCATTGGGGCTCTTGG
CCCTTCAGGGCGTGGTGTAGTAGACTACTTTGGCCTGGATCCTGAGGATGTAGATGTTATGATG
GGAACATTCACAAAGAGCTTCGGTGCTTCAGGAGGATACATTGGCGGCAAGAAGGAGCTGATAG
ACTACCTACGCACACATTCTCACAGTGCTGTGTACGCCACGTCAATGTCACCACCTGTGATGGA
GCAGATCATCACCTCCATGAAGTGCATCATGGGGCAGGATGGCACCAGTCTTGGCAAAGAATGT
ATCCAGCAGTTGGCTGAGAACACCAGGTATTTCAGGAGACGCCTGAAGGAAATGGGGTTCATCA
TCTATGGCAATGAAGACTCCCCGGTGGTGCCTTTGATGCTCTACATGCCGGCCAAAATTGGCGC
CTTTGGGAGAGAGATGCTGAAGCGGAACATTGGTGTAGTTGTGGTGGGATTTCCTGCTACCCCA
ATCATTGAGTCCAGAGCCAGATTTTGCCTGTCAGCGGCTCATACCAAAGAAATACTTGACACGG
CTTTGAAGGAAATAGATGAAGTTGGGGATCTGCTGCAACTGAAGTACTCCCGCCACCGGCCGCT
GCCTCTGCTGGACAGGCCCTTTGACGAGACTACCTATGAGGAGACAGAAGACTGAGCCTTTCTG
GTGCTCCCTAGAGGGGGATGCTTCCTCCCAGGACAGTGTGTGGCCTTTCTGAGCCAATCCCAGG
AGCCACACTTCAGTGACCACTTCATGTGAAAGACATTTCCCAAGTTACTGAAGATGGCCACCTC
CACTCCAAATGGCATTTTGTAAATAGTAAAAAAACAAACTGCTTCACATTCTTCCTTTGTTTGC
TAAGTCTCACACACATACACACACACACATATATATATGATTACTTTGTCCATTAAAAATGTTT
TATTTTATAACTATTCTACTTGTGAAATCACGCTGACCCTTGCCTGTGGCTTCTGGAACAGGCA
TTCCCCACTGCAGTCACCTCATAGGCTTGGATGCATCAAGACCTACTTCAGGCCCTGGCTCTCC
AGCCTTGAGACTCACTGGCCCTCTCCCTAGGGAGCAAGTGCCTTCTGCTGACTTCCCGCCCGGG
TCTCAGAGGTTGTCCCCCTTGTAATCCCTTTTTAACCAGTCGAGTTAACCAACCAAAGCATTCT
GTCTTTAGTCTTAAGGTAAACGTAACCAAGACCCAATGGCTTATGTGACTCCTCCTGGCCAAGG
ACTTCCTAAAACTGGTCTCTTTTTGTTGTTGTTCTGTTCATCAAATATTTATTCACTATCAGAT
CTTTCTTCATATGATCTCTGAAGATGTATCTCATGATTTAGTTCTCCCTGAGATCTAACCCTAA
TGCTTCCCACCTCCAAAGTTACAACCCCCTCTGGCTCATTCAGGGTCCAGATTAAGATTTGACC
AGTAAAGGCAAGTGTTGGTCAGTCCTTTGCTCATGTCCCACTTCACCATTAGTGGGGTAAGCTT
TCTGTGTCACTGACCCACTTGAACAATGCTCTTCCAAAGGCCAGCTCTTCTACTCCTCCTGTGC
TAACAAGAATTTACCCAGCATCTGGGCTGGCTTCTCTTGTGCTTCCATTGTATTTCCCCCCTTT
GAGGAATTCGTCAAATACCTCTTTCTTAGACTGGAATAGCCTGTTTTCCTGTCTCCACTGGGTG
AGGGGCTTCATCCAGAGCTTTGTGCTGCTTGACCAAAGAACACATCCGAGGAGCACCGTTTTGA
AGTTAATTTTTTTTCTTTTGACCAAAGCATAATTGAAGAGAACTTTTGACTTTATTGTACTGAA
GATGAATTTGTCTTTTAGTACTGATCAAGTGTTATAAGGAAGGATTGAGAACAGAATGAGGAAA
AACTGTTTAGAAGTCATTTTGTATGTCATTCTTTAAAGTTATTATTATTACTGATAAAGATGCT
CAAACCAAGTTCTTCTGGGGACCGTCAGCTGCAGGTACATGGAAGAGAAGCAGTATCATTTGTG
AAGCTGTTTTCATGCCTTGGATCTTTGGCCCTCTTGGCATCTGTGAGCTTTCAGCCCTTGAGAT
ATTGTAAGGTTGTATGTGGAGGTTTTAAAGAATAGACATGGGTGAACAGGCTGGGTGTGGTAAC
CTTTGCCTTTAATCCCAGATCTCAGAAGGCAGAGGCAAGCTAATCTCCTGCCGGTTTGAGGTCA
GCCTGGTATACATAGAGTTCCGGGATAGCCTGGGTTGCATAGTGAAACCTGGAGAGAGAGAGAG
AGAGAACACACACCATAGAAAGAAGCAAGAACTTCATGTATAAAAAGATTCCATAACTAAATCC
TATAAAGCTCAAACACCTTCCTCCCTTCCCCTGTAGAAGCCCACGGGAATACCAAGTATTTTGC
ACAGCACTATTTGATAGTGCAGCATAGGGCTTGCAAAAGTAACAAACCTTAAGCAATGAACATG
CCCACTAGCCTCTGAGCTTACATGAAATCACTTCAAATTAAAATGCTACTCCAGGCATTTAAAT
ATTTCTGTATGTATCTTGGTTGGTGCAAAGTTTATTTCGGGCTAAATGTAATTAAGTTAAAGTT
TTTTATTGTTAAAAAAAAAAAAAAAAAAAA

hide sequence

Protein Sequences


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:

show sequence

MRPEPGGCCCRRPMRANGCVKNGEVRNGYLRSSTATIAAAGQIHHITENGGLYKRPFNEAFEET
PMLVAVLTYVGYGVLTLFGYLRDFLRHWRIEKCHHATEREEQKDFVSLYQDFENFYTRNLYMRI
RDNWNRPICSVPGAKVDIMERQSHDYNWSFKYTGNIIKGVINMGSYNYLGFARNTGSCQEAAAE
VLKTYGAGVCSTRQEIGNLDKHEELEKLVARFLGVEAALTYGMGFATNSMNIPALVGKGCLILS
DELNHASLVLGARLSGATIRIFKHNNMQSLEKLLKDAIVYGQPRTRRPWKKILILVEGIYSMEG
SIVRLPEVIALKKKYKAYLYLDEAHSIGALGPSGRGVVDYFGLDPEDVDVMMGTFTKSFGASGG
YIGGKKELIDYLRTHSHSAVYATSMSPPVMEQIITSMKCIMGQDGTSLGKECIQQLAENTRYFR
RRLKEMGFIIYGNEDSPVVPLMLYMPAKIGAFGREMLKRNIGVVVVGFPATPIIESRARFCLSA
AHTKEILDTALKEIDEVGDLLQLKYSRHRPLPLLDRPFDETTYEETED

hide sequence

Ensembl Acc Id:

ENSRNOP00000071651 ⟸ ENSRNOT00000085458

Ensembl Acc Id:

ENSRNOP00000016324 ⟸ ENSRNOT00000016324

Protein Domains

Aminotransferase class I/classII large

Protein Structures

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

Transcriptome

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

Promoters

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 Assembly	Chr	Position (strand)	Source
Rnor_6.0	6	111,417,840 - 111,417,900	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1305447	AgrOrtholog
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

Nomenclature History

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

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 Disease Annotations - MGI

Imported Disease Annotations - OMIM

Imported Annotations - SMPDB

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - MGI

Imported Disease Annotations - OMIM

Imported Annotations - SMPDB

Imported Annotations - KEGG (archival)