Human Gene SPNS1 (ENST00000311008.16_6) from GENCODE V47lift37
  Description: sphingolipid transporter 1 (putative), transcript variant 1 (from RefSeq NM_032038.3)
Gencode Transcript: ENST00000311008.16_6
Gencode Gene: ENSG00000169682.18_15
Transcript (Including UTRs)
   Position: hg19 chr16:28,986,099-28,995,864 Size: 9,766 Total Exon Count: 12 Strand: +
Coding Region
   Position: hg19 chr16:28,986,473-28,995,620 Size: 9,148 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:28,986,099-28,995,864)mRNA (may differ from genome)Protein (528 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SPNS1_HUMAN
DESCRIPTION: RecName: Full=Protein spinster homolog 1; AltName: Full=HSpin1; AltName: Full=Spinster-like protein 1;
FUNCTION: Sphingolipid transporter (By similarity). May be involved in necrotic or autophagic cell death.
SUBUNIT: Interacts with BCL2 and BCL2L1.
INTERACTION: Q07817:BCL2L1; NbExp=3; IntAct=EBI-1386527, EBI-78035;
SUBCELLULAR LOCATION: Mitochondrion inner membrane; Multi-pass membrane protein. Note=Colocalizes with SDHB.
SIMILARITY: Belongs to the major facilitator (TC 2.A.1) superfamily. Spinster (TC 2.A.1.49) family.
SEQUENCE CAUTION: Sequence=AAQ15259.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=AAQ15259.1; Type=Frameshift; Positions=97;

-  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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 27.12 RPKM in Spleen
Total median expression: 853.36 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -172.10374-0.460 Picture PostScript Text
3' UTR -116.20244-0.476 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
IPR011701 - MFS
IPR020846 - MFS_dom
IPR016196 - MFS_dom_general_subst_transpt

Pfam Domains:
PF00083 - Sugar (and other) transporter
PF07690 - Major Facilitator Superfamily

SCOP Domains:
103473 - MFS general substrate transporter

ModBase Predicted Comparative 3D Structure on Q9H2V7
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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.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0046624 sphingolipid transporter activity

Biological Process:
GO:0003376 sphingosine-1-phosphate signaling pathway
GO:0006869 lipid transport
GO:0040011 locomotion
GO:0055085 transmembrane transport

Cellular Component:
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0005765 lysosomal membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0031982 vesicle


-  Descriptions from all associated GenBank mRNAs
  BC038961 - Homo sapiens spinster homolog 1 (Drosophila), mRNA (cDNA clone MGC:47562 IMAGE:6053095), complete cds.
AK095677 - Homo sapiens cDNA FLJ38358 fis, clone FEBRA2000210.
AK289787 - Homo sapiens cDNA FLJ78727 complete cds.
BC065235 - Homo sapiens spinster homolog 1 (Drosophila), mRNA (cDNA clone MGC:70841 IMAGE:6161778), complete cds.
AF370423 - Homo sapiens PP2030 mRNA, complete cds.
BC047741 - Homo sapiens spinster homolog 1 (Drosophila), mRNA (cDNA clone MGC:54108 IMAGE:5757339), complete cds.
AB209402 - Homo sapiens mRNA for spinster variant protein.
AL390215 - Homo sapiens mRNA; cDNA DKFZp727E151 (from clone DKFZp727E151).
AF212371 - Homo sapiens spinster-like protein mRNA, complete cds.
BC008325 - Homo sapiens spinster homolog 1 (Drosophila), mRNA (cDNA clone MGC:15767 IMAGE:3501826), complete cds.
AM392778 - Synthetic construct Homo sapiens clone IMAGE:100002393 for hypothetical protein (SPIN1 gene).
AM393748 - Synthetic construct Homo sapiens clone IMAGE:100002431 for hypothetical protein (SPIN1 gene).
AB528362 - Synthetic construct DNA, clone: pF1KB0485, Homo sapiens SPNS1 gene for spinster homolog 1, without stop codon, in Flexi system.
CU678917 - Synthetic construct Homo sapiens gateway clone IMAGE:100017390 5' read SPNS1 mRNA.
KJ899746 - Synthetic construct Homo sapiens clone ccsbBroadEn_09140 SPNS1 gene, encodes complete protein.
BC006156 - Homo sapiens spinster homolog 1 (Drosophila), mRNA (cDNA clone IMAGE:3627317), partial cds.
JD477441 - Sequence 458465 from Patent EP1572962.
JD525102 - Sequence 506126 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B5MDM9, ENST00000311008.1, ENST00000311008.10, ENST00000311008.11, ENST00000311008.12, ENST00000311008.13, ENST00000311008.14, ENST00000311008.15, ENST00000311008.2, ENST00000311008.3, ENST00000311008.4, ENST00000311008.5, ENST00000311008.6, ENST00000311008.7, ENST00000311008.8, ENST00000311008.9, NM_032038, PP20300, Q6P182, Q71RB5, Q7L541, Q86VU7, Q8N953, Q8TCS5, Q9BRN5, Q9H2V7, SPIN1, SPNS1_HUMAN, uc317owr.1, uc317owr.2
UCSC ID: ENST00000311008.16_6
RefSeq Accession: NM_032038.3
Protein: Q9H2V7 (aka SPNS1_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.