Human Gene SGPL1 (ENST00000373202.8_5) from GENCODE V47lift37

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Description: sphingosine-1-phosphate lyase 1 (from RefSeq NM_003901.4)
Gencode Transcript: ENST00000373202.8_5
Gencode Gene: ENSG00000166224.19_15
Transcript (Including UTRs)
Position: hg19 chr10:72,575,704-72,640,941 Size: 65,238 Total Exon Count: 15 Strand: +
Coding Region
Position: hg19 chr10:72,576,610-72,637,092 Size: 60,483 Coding Exon Count: 14

Page Index	Sequence and Links	UniProtKB Comments	Primers	MalaCards	CTD
Gene Alleles	RNA-Seq Expression	Microarray Expression	RNA Structure	Protein Structure	Other Species
GO Annotations	mRNA Descriptions	Pathways	Other Names	GeneReviews	Model Information
Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr10:72,575,704-72,640,941)			mRNA (may differ from genome)		Protein (568 aa)
Gene Sorter	Genome Browser	Other Species FASTA	VisiGene	Gene interactions	Table Schema
AlphaFold	BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards
HGNC	Malacards	MGI	OMIM	PubMed	Reactome
UniProtKB	Wikipedia	BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: SGPL1_HUMAN DESCRIPTION: RecName: Full=Sphingosine-1-phosphate lyase 1; Short=S1PL; Short=SP-lyase 1; Short=SPL 1; Short=hSPL; EC=4.1.2.27; AltName: Full=Sphingosine-1-phosphate aldolase; FUNCTION: Cleaves phosphorylated sphingoid bases (PSBs), such as sphingosine-1-phosphate, into fatty aldehydes and phosphoethanolamine. Elevates stress-induced ceramide production and apoptosis. CATALYTIC ACTIVITY: Sphinganine 1-phosphate = phosphoethanolamine + palmitaldehyde. COFACTOR: Pyridoxal phosphate (By similarity). PATHWAY: Lipid metabolism; sphingolipid metabolism. INTERACTION: Q86WV6:TMEM173; NbExp=2; IntAct=EBI-1046170, EBI-2800345; SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Single-pass type III membrane protein. TISSUE SPECIFICITY: Found in liver and kidney. SIMILARITY: Belongs to the group II decarboxylase family. Sphingosine-1-phosphate lyase subfamily. SEQUENCE CAUTION: Sequence=BAA86566.1; Type=Erroneous initiation;

Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

MalaCards Disease Associations


	MalaCards Gene Search: SGPL1 Diseases sorted by gene-association score: nephrotic syndrome 14* (900), adrenal insufficiency, congenital, with 46xy sex reversal, partial or complete (7), image syndrome (6) * = Manually curated disease association

Comparative Toxicogenomics Database (CTD)


	The following chemicals interact with this gene D013749 Tetrachlorodibenzodioxin C028474 1,4-bis(2-(3,5-dichloropyridyloxy))benzene C016403 2,4-dinitrotoluene C023514 2,6-dinitrotoluene C009505 4,4'-diaminodiphenylmethane C027576 4-hydroxy-2-nonenal D000082 Acetaminophen D000643 Ammonium Chloride D001564 Benzo(a)pyrene D004041 Dietary Fats more ... click here to view the complete list

Common Gene Haplotype Alleles


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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 21.60 RPKM in Skin - Sun Exposed (Lower leg) Total median expression: 431.24 RPKM View in GTEx track of Genome Browser View at GTEx portal View GTEx Body Map

Microarray Expression Data


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mRNA Secondary Structure of 3' and 5' UTRs

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-99.40	222	-0.448	Picture	PostScript	Text
3' UTR	-1228.00	3849	-0.319	Picture	PostScript	Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

Protein Domain and Structure Information

InterPro Domains: Graphical view of domain structure
IPR002129 - PyrdxlP-dep_de-COase
IPR015424 - PyrdxlP-dep_Trfase_major_dom
IPR015421 - PyrdxlP-dep_Trfase_major_sub1

Pfam Domains:
PF00155 - Aminotransferase class I and II
PF00266 - Aminotransferase class-V
PF00282 - Pyridoxal-dependent decarboxylase conserved domain

SCOP Domains:
53383 - PLP-dependent transferases

ModBase Predicted Comparative 3D Structure on O95470


Front	Top	Side

The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

Orthologous Genes in Other Species

Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	No ortholog	No ortholog
Gene Details	Gene Details
Gene Sorter	Gene Sorter
	RGD

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0003824 catalytic activity GO:0005515 protein binding GO:0008117 sphinganine-1-phosphate aldolase activity GO:0016829 lyase activity GO:0016831 carboxy-lyase activity GO:0030170 pyridoxal phosphate binding Biological Process: GO:0001553 luteinization GO:0001570 vasculogenesis GO:0001822 kidney development GO:0006629 lipid metabolic process GO:0006631 fatty acid metabolic process GO:0006665 sphingolipid metabolic process GO:0006672 ceramide metabolic process GO:0006807 nitrogen compound metabolic process GO:0006915 apoptotic process GO:0007283 spermatogenesis GO:0008209 androgen metabolic process GO:0008210 estrogen metabolic process GO:0008585 female gonad development GO:0009791 post-embryonic development GO:0010761 fibroblast migration GO:0019752 carboxylic acid metabolic process GO:0030097 hemopoiesis GO:0030148 sphingolipid biosynthetic process GO:0030149 sphingolipid catabolic process GO:0033327 Leydig cell differentiation GO:0040014 regulation of multicellular organism growth GO:0048008 platelet-derived growth factor receptor signaling pathway GO:0048705 skeletal system morphogenesis GO:0060021 palate development GO:0060325 face morphogenesis GO:0097190 apoptotic signaling pathway Cellular Component: GO:0005783 endoplasmic reticulum GO:0005789 endoplasmic reticulum membrane GO:0016020 membrane GO:0016021 integral component of membrane GO:0030176 integral component of endoplasmic reticulum membrane

Descriptions from all associated GenBank mRNAs


	LF208760 - JP 2014500723-A/16263: Polycomb-Associated Non-Coding RNAs. LF385457 - JP 2014500723-A/192960: Polycomb-Associated Non-Coding RNAs. BC052991 - Homo sapiens sphingosine-1-phosphate lyase 1, mRNA (cDNA clone MGC:60255 IMAGE:6150776), complete cds. AB033078 - Homo sapiens KIAA1252 mRNA for KIAA1252 protein. AJ011304 - Homo sapiens mRNA for sphingosine-1-phosphate lyase. AK314615 - Homo sapiens cDNA, FLJ95456, highly similar to Homo sapiens sphingosine-1-phosphate lyase 1 (SGPL1), mRNA. AB384155 - Synthetic construct DNA, clone: pF1KSDA1252, Homo sapiens SGPL1 gene for sphingosine 1-phosphate lyase 1, complete cds, without stop codon, in Flexi system. KJ897928 - Synthetic construct Homo sapiens clone ccsbBroadEn_07322 SGPL1 gene, encodes complete protein. AF144638 - Homo sapiens sphingosine-1-phosphate lyase (SPL) mRNA, complete cds. MA621034 - JP 2018138019-A/192960: Polycomb-Associated Non-Coding RNAs. MA444337 - JP 2018138019-A/16263: Polycomb-Associated Non-Coding RNAs. BC051238 - Homo sapiens sphingosine-1-phosphate lyase 1, mRNA (cDNA clone IMAGE:6253152), partial cds. BC068061 - Homo sapiens cDNA clone IMAGE:6110411, partial cds. JD140244 - Sequence 121268 from Patent EP1572962. JD441641 - Sequence 422665 from Patent EP1572962. JD339236 - Sequence 320260 from Patent EP1572962. JD151674 - Sequence 132698 from Patent EP1572962. LF322576 - JP 2014500723-A/130079: Polycomb-Associated Non-Coding RNAs. JD470781 - Sequence 451805 from Patent EP1572962. JD336591 - Sequence 317615 from Patent EP1572962. JD445199 - Sequence 426223 from Patent EP1572962. JD539285 - Sequence 520309 from Patent EP1572962. LF322570 - JP 2014500723-A/130073: Polycomb-Associated Non-Coding RNAs. LF322568 - JP 2014500723-A/130071: Polycomb-Associated Non-Coding RNAs. MA558153 - JP 2018138019-A/130079: Polycomb-Associated Non-Coding RNAs. MA558147 - JP 2018138019-A/130073: Polycomb-Associated Non-Coding RNAs. MA558145 - JP 2018138019-A/130071: Polycomb-Associated Non-Coding RNAs. LF322564 - JP 2014500723-A/130067: Polycomb-Associated Non-Coding RNAs. LF322563 - JP 2014500723-A/130066: Polycomb-Associated Non-Coding RNAs. AK308610 - Homo sapiens cDNA, FLJ98651. LF322562 - JP 2014500723-A/130065: Polycomb-Associated Non-Coding RNAs. LF322561 - JP 2014500723-A/130064: Polycomb-Associated Non-Coding RNAs. LF322560 - JP 2014500723-A/130063: Polycomb-Associated Non-Coding RNAs. LF322559 - JP 2014500723-A/130062: Polycomb-Associated Non-Coding RNAs. LF213573 - JP 2014500723-A/21076: Polycomb-Associated Non-Coding RNAs. LF322557 - JP 2014500723-A/130060: Polycomb-Associated Non-Coding RNAs. LF322556 - JP 2014500723-A/130059: Polycomb-Associated Non-Coding RNAs. AK023873 - Homo sapiens cDNA FLJ13811 fis, clone THYRO1000320. JD080119 - Sequence 61143 from Patent EP1572962. DQ572767 - Homo sapiens piRNA piR-40879, complete sequence. JD482450 - Sequence 463474 from Patent EP1572962. JD183542 - Sequence 164566 from Patent EP1572962. LF322555 - JP 2014500723-A/130058: Polycomb-Associated Non-Coding RNAs. JD438187 - Sequence 419211 from Patent EP1572962. JD207879 - Sequence 188903 from Patent EP1572962. LF322554 - JP 2014500723-A/130057: Polycomb-Associated Non-Coding RNAs. LF322553 - JP 2014500723-A/130056: Polycomb-Associated Non-Coding RNAs. LF322552 - JP 2014500723-A/130055: Polycomb-Associated Non-Coding RNAs. JD147306 - Sequence 128330 from Patent EP1572962. JD457720 - Sequence 438744 from Patent EP1572962. JD457721 - Sequence 438745 from Patent EP1572962. LF322551 - JP 2014500723-A/130054: Polycomb-Associated Non-Coding RNAs. LF322550 - JP 2014500723-A/130053: Polycomb-Associated Non-Coding RNAs. LF322549 - JP 2014500723-A/130052: Polycomb-Associated Non-Coding RNAs. BC041567 - Homo sapiens, clone IMAGE:3357509, mRNA. BC031338 - Homo sapiens sphingosine-1-phosphate lyase 1, mRNA (cDNA clone IMAGE:3658802), with apparent retained intron. LF322548 - JP 2014500723-A/130051: Polycomb-Associated Non-Coding RNAs. LF322547 - JP 2014500723-A/130050: Polycomb-Associated Non-Coding RNAs. MA558141 - JP 2018138019-A/130067: Polycomb-Associated Non-Coding RNAs. MA558140 - JP 2018138019-A/130066: Polycomb-Associated Non-Coding RNAs. MA558139 - JP 2018138019-A/130065: Polycomb-Associated Non-Coding RNAs. MA558138 - JP 2018138019-A/130064: Polycomb-Associated Non-Coding RNAs. MA558137 - JP 2018138019-A/130063: Polycomb-Associated Non-Coding RNAs. MA558136 - JP 2018138019-A/130062: Polycomb-Associated Non-Coding RNAs. MA558134 - JP 2018138019-A/130060: Polycomb-Associated Non-Coding RNAs. MA558133 - JP 2018138019-A/130059: Polycomb-Associated Non-Coding RNAs. MA558132 - JP 2018138019-A/130058: Polycomb-Associated Non-Coding RNAs. MA558131 - JP 2018138019-A/130057: Polycomb-Associated Non-Coding RNAs. MA558130 - JP 2018138019-A/130056: Polycomb-Associated Non-Coding RNAs. MA558129 - JP 2018138019-A/130055: Polycomb-Associated Non-Coding RNAs. MA558128 - JP 2018138019-A/130054: Polycomb-Associated Non-Coding RNAs. MA558127 - JP 2018138019-A/130053: Polycomb-Associated Non-Coding RNAs. MA558126 - JP 2018138019-A/130052: Polycomb-Associated Non-Coding RNAs. MA558125 - JP 2018138019-A/130051: Polycomb-Associated Non-Coding RNAs. MA558124 - JP 2018138019-A/130050: Polycomb-Associated Non-Coding RNAs. MA449150 - JP 2018138019-A/21076: Polycomb-Associated Non-Coding RNAs.

Biochemical and Signaling Pathways


	Reactome (by CSHL, EBI, and GO) Protein O95470 (Reactome details) participates in the following event(s): R-HSA-428676 sphingosine 1-phosphate => phosphoethanolamine + hexadec-2-enal R-HSA-428681 sphinganine 1-phosphate => phosphoethanolamine + hexadecanal R-HSA-1660661 Sphingolipid de novo biosynthesis R-HSA-428157 Sphingolipid metabolism R-HSA-556833 Metabolism of lipids R-HSA-1430728 Metabolism

Other Names for This Gene


	Alternate Gene Symbols: B2RBD4, ENST00000373202.1, ENST00000373202.2, ENST00000373202.3, ENST00000373202.4, ENST00000373202.5, ENST00000373202.6, ENST00000373202.7, KIAA1252 , NM_003901, O95470, Q7Z732, Q9ULG8, Q9UN89, SGPL1 , SGPL1_HUMAN, uc318koq.1, uc318koq.2 UCSC ID: ENST00000373202.8_5 RefSeq Accession: NM_003901.4 Protein: O95470 (aka SGPL1_HUMAN or SGP1_HUMAN)

GeneReviews for This Gene


	GeneReviews article(s) related to gene SGPL1: sgpl1 (Sphingosine Phosphate Lyase Insufficiency Syndrome)

Gene Model Information


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Methods, Credits, and Use Restrictions


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