Human Gene SRM (ENST00000376957.7_7) from GENCODE V47lift37
  Description: spermidine synthase (from RefSeq NM_003132.3)
Gencode Transcript: ENST00000376957.7_7
Gencode Gene: ENSG00000116649.10_15
Transcript (Including UTRs)
   Position: hg19 chr1:11,114,646-11,120,075 Size: 5,430 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg19 chr1:11,114,922-11,120,000 Size: 5,079 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:11,114,646-11,120,075)mRNA (may differ from genome)Protein (302 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MalacardsMGIOMIMPubMedReactomeUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SPEE_HUMAN
DESCRIPTION: RecName: Full=Spermidine synthase; Short=SPDSY; EC=2.5.1.16; AltName: Full=Putrescine aminopropyltransferase;
FUNCTION: Catalyzes the production of spermidine from putrescine and decarboxylated S-adenosylmethionine (dcSAM). Has a strong preference for putrescine as substrate, and has very low activity towards 1,3-diaminopropane. Has extremely low activity towards spermidine.
CATALYTIC ACTIVITY: S-adenosylmethioninamine + putrescine = 5'-S- methyl-5'-thioadenosine + spermidine.
ENZYME REGULATION: The activity is thought to be regulated mainly by the availability of decarboxylated S-adenosylmethionine.
BIOPHYSICOCHEMICAL PROPERTIES: Kinetic parameters: KM=20 uM for putrescine; KM=0.9 uM for S-adenosylmethioninamine;
PATHWAY: Amine and polyamine biosynthesis; spermidine biosynthesis; spermidine from putrescine: step 1/1.
SUBUNIT: Homodimer or homotetramer.
SIMILARITY: Belongs to the spermidine/spermine synthase family.

-  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: SRM
Diseases sorted by gene-association score: sleeping sickness (10), leishmaniasis (4), malaria (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  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: 63.22 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 1598.35 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -38.3075-0.511 Picture PostScript Text
3' UTR -86.00276-0.312 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
IPR001045 - Spermidine/spermine_synthase

Pfam Domains:
PF01564 - Spermine/spermidine synthase domain
PF17284 - Spermidine synthase tetramerisation domain

SCOP Domains:
51735 - NAD(P)-binding Rossmann-fold domains
53335 - S-adenosyl-L-methionine-dependent methyltransferases
53448 - Nucleotide-diphospho-sugar transferases

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2O05 - X-ray MuPIT 2O06 - X-ray MuPIT 2O07 - X-ray MuPIT 2O0L - X-ray MuPIT 3RW9 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P19623
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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 orthologGenome Browser
Gene Details  Gene Details Gene Details
Gene Sorter  Gene Sorter Gene Sorter
  Ensembl  SGD
     Protein Sequence
     Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003824 catalytic activity
GO:0004766 spermidine synthase activity
GO:0005515 protein binding
GO:0016740 transferase activity
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity

Biological Process:
GO:0006595 polyamine metabolic process
GO:0006596 polyamine biosynthetic process
GO:0008295 spermidine biosynthetic process
GO:1990830 cellular response to leukemia inhibitory factor

Cellular Component:
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  LF206727 - JP 2014500723-A/14230: Polycomb-Associated Non-Coding RNAs.
BC033106 - Homo sapiens spermidine synthase, mRNA (cDNA clone MGC:45687 IMAGE:5420683), complete cds.
BC000309 - Homo sapiens spermidine synthase, mRNA (cDNA clone MGC:8422 IMAGE:2820975), complete cds.
M34338 - Human spermidine synthase mRNA, complete cds.
JD132140 - Sequence 113164 from Patent EP1572962.
LF357392 - JP 2014500723-A/164895: Polycomb-Associated Non-Coding RNAs.
JD466456 - Sequence 447480 from Patent EP1572962.
JD256474 - Sequence 237498 from Patent EP1572962.
JD218865 - Sequence 199889 from Patent EP1572962.
JD137766 - Sequence 118790 from Patent EP1572962.
LF357391 - JP 2014500723-A/164894: Polycomb-Associated Non-Coding RNAs.
JD478102 - Sequence 459126 from Patent EP1572962.
JD076257 - Sequence 57281 from Patent EP1572962.
JD189304 - Sequence 170328 from Patent EP1572962.
JD276105 - Sequence 257129 from Patent EP1572962.
JD461227 - Sequence 442251 from Patent EP1572962.
JD457294 - Sequence 438318 from Patent EP1572962.
EU831469 - Synthetic construct Homo sapiens clone HAIB:100066498; DKFZo008F1117 spermidine synthase protein (SRM) gene, encodes complete protein.
KJ897602 - Synthetic construct Homo sapiens clone ccsbBroadEn_06996 SRM gene, encodes complete protein.
EU831556 - Synthetic construct Homo sapiens clone HAIB:100066585; DKFZo004F1118 spermidine synthase protein (SRM) gene, encodes complete protein.
LF357390 - JP 2014500723-A/164893: Polycomb-Associated Non-Coding RNAs.
LF357389 - JP 2014500723-A/164892: Polycomb-Associated Non-Coding RNAs.
LF357387 - JP 2014500723-A/164890: Polycomb-Associated Non-Coding RNAs.
LF357384 - JP 2014500723-A/164887: Polycomb-Associated Non-Coding RNAs.
MA442304 - JP 2018138019-A/14230: Polycomb-Associated Non-Coding RNAs.
MA592969 - JP 2018138019-A/164895: Polycomb-Associated Non-Coding RNAs.
MA592968 - JP 2018138019-A/164894: Polycomb-Associated Non-Coding RNAs.
MA592967 - JP 2018138019-A/164893: Polycomb-Associated Non-Coding RNAs.
MA592966 - JP 2018138019-A/164892: Polycomb-Associated Non-Coding RNAs.
MA592964 - JP 2018138019-A/164890: Polycomb-Associated Non-Coding RNAs.
MA592961 - JP 2018138019-A/164887: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  BioCyc Knowledge Library
BSUBPOLYAMSYN-PWY - spermidine biosynthesis
PWY-7527 - L-methionine salvage cycle

Reactome (by CSHL, EBI, and GO)

Protein P19623 (Reactome details) participates in the following event(s):

R-HSA-351215 Putrescine + dc-Adenosyl methionine => Spermidine + 5'-methylthioadenosine
R-HSA-351202 Metabolism of polyamines
R-HSA-71291 Metabolism of nitrogenous molecules
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: B1AKP9, ENST00000376957.1, ENST00000376957.2, ENST00000376957.3, ENST00000376957.4, ENST00000376957.5, ENST00000376957.6, NM_003132, P19623, Q15511, SPEE_HUMAN, SPS1, SRML1, uc318nhg.1, uc318nhg.2
UCSC ID: ENST00000376957.7_7
RefSeq Accession: NM_003132.3
Protein: P19623 (aka SPEE_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.