Sptlc3 MGI Mouse Gene Detail - MGI:2444678 - serine palmitoyltransferase, long chain base subunit 3

Symbol

Sptlc3
Name

serine palmitoyltransferase, long chain base subunit 3
Synonyms

C130053K05Rik

Feature Type

protein coding gene
IDs

MGI:2444678
NCBI Gene: 228677
Alliance

gene page
Transcription Start Sites

11 TSS

Sequence Map

Chr2:139335833-139478981 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 2, 68.52 cM
Mapping Data

1 experiment

SNPs within 2kb

3349 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_2444678	protein coding gene	Chr2:139335833-139479594 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0026564	protein coding gene	Chr2:143380135-143539731 (+)
A/J	MGP_AJ_G0026528	protein coding gene	Chr2:137600395-137740575 (+)
AKR/J	MGP_AKRJ_G0026502	protein coding gene	Chr2:141525124-141674881 (+)
BALB/cJ	MGP_BALBcJ_G0026540	protein coding gene	Chr2:137978654-138125475 (+)
C3H/HeJ	MGP_C3HHeJ_G0026283	protein coding gene	Chr2:142008345-142179717 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0026985	protein coding gene	Chr2:147692204-147846492 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0024362	protein coding gene	Chr2:131930493-132057482 (+)
CAST/EiJ	MGP_CASTEiJ_G0025744	protein coding gene	Chr2:142332773-142477792 (+)
CBA/J	MGP_CBAJ_G0026263	protein coding gene	Chr2:153100496-153263577 (+)
DBA/2J	MGP_DBA2J_G0026397	protein coding gene	Chr2:136917762-137066409 (+)
FVB/NJ	MGP_FVBNJ_G0026361	protein coding gene	Chr2:135493032-135628714 (+)
LP/J	MGP_LPJ_G0026501	protein coding gene	Chr2:143529928-143672406 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0026381	protein coding gene	Chr2:157088138-157261112 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0027040	protein coding gene	Chr2:141499613-141641014 (+)
PWK/PhJ	MGP_PWKPhJ_G0025480	protein coding gene	Chr2:136501941-136647021 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0025282	protein coding gene	Chr2:140563395-140715325 (+)
WSB/EiJ	MGP_WSBEiJ_G0025818	protein coding gene	Chr2:142463722-142615301 (+)

Human Ortholog

SPTLC3, serine palmitoyltransferase long chain base subunit 3

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

SPTLC3, serine palmitoyltransferase long chain base subunit 3
Synonyms

C20orf38, dJ718P11, dJ718P11.1, hLCB2b, LCB2B, LCB 3, LCB3, SPT 3, SPT3, SPTLC2L
Links

HGNC:16253

NCBI Gene ID: 55304

neXtProt AC: NX_Q9NUV7

UniProt: Q9NUV7
Chr Location

chr20:13008972-13169103 (+) GRCh38

MGI Vertebrate Homology

Sptlc3 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: SPTLC3
Gene Tree

Sptlc3

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Phenotype Summary

4 phenotypes from 1 allele in 1 genetic background
9 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

5
Chemically induced (other)

1
Endonuclease-mediated

2
Radiation induced

1
Targeted

1
Genomic Mutations

2 involving Sptlc3
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

30 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

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All GO Annotations

12
GO References

7

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

906
Tissues

114
cDNA Data

9
Literature Summary

6

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase sptlc3

ZFIN sptlc3

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All Sequences

37
RefSeq

4
UniProt

1
CCDS

CCDS16800.1

Ensembl

ENSMUSG00000039092 (Evidence)
NCBI Gene

228677

			Length	Strain/Species	Flank
genomic	228677	NCBI Gene Model \| MGI Sequence Detail	143149	C57BL/6J	± kb
transcript	NM_001356507	RefSeq \| MGI Sequence Detail	2232	C57BL/6
polypeptide	Q8BG54	UniProt \| EBI \| MGI Sequence Detail	563	Not Applicable

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UniProt

1 Sequence
Protein Ontology

PR:000015598 serine palmitoyltransferase 3

(term hierarchy)
EC

2.3.1.50
InterPro Domains

IPR050087 8-amino-7-oxononanoate synthase class-II

IPR004839 Aminotransferase, class I/classII

IPR001917 Aminotransferase, class-II, pyridoxal-phosphate binding site

IPR015424 Pyridoxal phosphate-dependent transferase

IPR015421 Pyridoxal phosphate-dependent transferase, major domain

IPR015422 Pyridoxal phosphate-dependent transferase, small domain

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All nucleic 10

cDNA 9

Primer pair 1

Microarray probesets 4

Summaries

All 38

Developmental Gene Expression 6

Gene Ontology 7

Phenotypes 9
Earliest

J:109968 Roderick TH, et al., Nineteen paracentric chromosomal inversions in mice. Genetics. 1974 Jan;76(1):109-17
Latest

J:345621 Adams DJ, et al., Genetic determinants of micronucleus formation in vivo. Nature. 2024 Mar;627(8002):130-136

TSS for Sptlc3:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr20462	Chr2:139335834-139335843 (+)	6 bp
Tssr20463	Chr2:139335852-139335857 (+)	22 bp
Tssr20464	Chr2:139335874-139335892 (+)	50 bp
Tssr20465	Chr2:139335896-139335935 (+)	83 bp
Tssr20466	Chr2:139335958-139335970 (+)	131 bp
Tssr20467	Chr2:139335973-139335983 (+)	145 bp
Tssr20468	Chr2:139336038-139336095 (+)	234 bp
Tssr20469	Chr2:139336112-139336117 (+)	282 bp
Tssr20470	Chr2:139387937-139387940 (+)	52,106 bp
Tssr20471	Chr2:139421388-139421398 (+)	85,560 bp
Tssr20472	Chr2:139443138-139443141 (+)	107,307 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
Citing These Resources Funding Information Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 12/10/2024 MGI 6.24