The polyamines putrescine, spermine, and spermidine are ubiquitous polycationic mediators of cell growth and differentiation. Spermidine synthase is one of four enzymes in the polyamine-biosynthetic pathway and carries out the final step of spermidine biosynthesis. This enzyme catalyzes the conversion of putrescine to spermidine using decarboxylated S-adenosylmethionine as the ... See more...

Aliases for SRM Gene

Aliases for SRM Gene

  • Spermidine Synthase 2 3 4 5
  • SPS1 2 3 4
  • Putrescine Aminopropyltransferase 3 4
  • EC 2.5.1.16 4 50
  • SPDSY 3 4
  • SRML1 3 4
  • Spermidine Synthase-1 3
  • EC 2.5.1 50
  • PAPT 3
  • SRM 5

External Ids for SRM Gene

Previous HGNC Symbols for SRM Gene

  • SRML1

Previous GeneCards Identifiers for SRM Gene

  • GC01M011075
  • GC01M010958
  • GC01M010719
  • GC01M010824
  • GC01M011048
  • GC01M011037
  • GC01M011114
  • GC01M010266

Summaries for SRM Gene

Entrez Gene Summary for SRM Gene

  • The polyamines putrescine, spermine, and spermidine are ubiquitous polycationic mediators of cell growth and differentiation. Spermidine synthase is one of four enzymes in the polyamine-biosynthetic pathway and carries out the final step of spermidine biosynthesis. This enzyme catalyzes the conversion of putrescine to spermidine using decarboxylated S-adenosylmethionine as the cofactor. [provided by RefSeq, Jul 2008]

GeneCards Summary for SRM Gene

SRM (Spermidine Synthase) is a Protein Coding gene. Diseases associated with SRM include Sleeping Sickness and Chagas Disease. Among its related pathways are Nucleotide Metabolism and Sulfur amino acid metabolism. Gene Ontology (GO) annotations related to this gene include protein homodimerization activity and spermidine synthase activity. An important paralog of this gene is SMS.

UniProtKB/Swiss-Prot Summary for SRM Gene

  • 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.

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SRM Gene

Genomics for SRM Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SRM Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SRM on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SRM

Top Transcription factor binding sites by QIAGEN in the SRM gene promoter:
  • c-Myc
  • Max
  • Max1
  • NRSF form 1
  • NRSF form 2

Genomic Locations for SRM Gene

Latest Assembly
chr1:11,054,584-11,060,053
(GRCh38/hg38)
Size:
5,470 bases
Orientation:
Minus strand

Previous Assembly
chr1:11,114,646-11,120,075
(GRCh37/hg19 by Entrez Gene)
Size:
5,430 bases
Orientation:
Minus strand

chr1:11,114,641-11,120,081
(GRCh37/hg19 by Ensembl)
Size:
5,441 bases
Orientation:
Minus strand

Genomic View for SRM Gene

Genes around SRM on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SRM Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SRM Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SRM Gene

Proteins for SRM Gene

  • Protein details for SRM Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P19623-SPEE_HUMAN
    Recommended name:
    Spermidine synthase
    Protein Accession:
    P19623
    Secondary Accessions:
    • B1AKP9
    • Q15511

    Protein attributes for SRM Gene

    Size:
    302 amino acids
    Molecular mass:
    33825 Da
    Quaternary structure:
    • Homodimer or homotetramer.

    Three dimensional structures from OCA and Proteopedia for SRM Gene

neXtProt entry for SRM Gene

Selected DME Specific Peptides for SRM Gene

P19623:
  • GGGDGGVLREV
  • IGGGDGG
  • VLIIGGGDG
  • IPTYPSG
  • IGFMLCS

Post-translational modifications for SRM Gene

  • Ubiquitination at Lys96, Lys135, and Lys277
  • Modification sites at PhosphoSitePlus

Other Protein References for SRM Gene

Domains & Families for SRM Gene

Gene Families for SRM Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for SRM Gene

Suggested Antigen Peptide Sequences for SRM Gene

GenScript: Design optimal peptide antigens:
  • Putrescine aminopropyltransferase (SPEE_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P19623

UniProtKB/Swiss-Prot:

SPEE_HUMAN :
  • Belongs to the spermidine/spermine synthase family.
Family:
  • Belongs to the spermidine/spermine synthase family.
genes like me logo Genes that share domains with SRM: view

Function for SRM Gene

Molecular function for SRM Gene

UniProtKB/Swiss-Prot 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.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=putrescine + S-adenosyl 3-(methylsulfanyl)propylamine = H(+) + S-methyl-5'-thioadenosine + spermidine; Xref=Rhea:RHEA:12721, ChEBI:CHEBI:15378, ChEBI:CHEBI:17509, ChEBI:CHEBI:57443, ChEBI:CHEBI:57834, ChEBI:CHEBI:326268; EC=2.5.1.16; Evidence={ECO:0000269|PubMed:17585781};.
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=20 uM for putrescine {ECO:0000269|PubMed:17585781}; KM=0.9 uM for S-adenosylmethioninamine {ECO:0000269|PubMed:17585781};
UniProtKB/Swiss-Prot EnzymeRegulation:
The activity is thought to be regulated mainly by the availability of decarboxylated S-adenosylmethionine.
GENATLAS Biochemistry:
spermidine synthetase,polyamine biosynthesis

Enzyme Numbers (IUBMB) for SRM Gene

Phenotypes From GWAS Catalog for SRM Gene

Gene Ontology (GO) - Molecular Function for SRM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003824 catalytic activity IEA --
GO:0004766 spermidine synthase activity IBA,TAS --
GO:0005515 protein binding IPI 21044950
GO:0016740 transferase activity IEA --
GO:0042802 identical protein binding IPI 17585781
genes like me logo Genes that share ontologies with SRM: view
genes like me logo Genes that share phenotypes with SRM: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SRM

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SRM Gene

Localization for SRM Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SRM gene
Compartment Confidence
cytosol 5
nucleus 3
extracellular 2
peroxisome 2
plasma membrane 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SRM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with SRM: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for SRM Gene

Pathways & Interactions for SRM Gene

genes like me logo Genes that share pathways with SRM: view

UniProtKB/Swiss-Prot P19623-SPEE_HUMAN

  • Pathway: Amine and polyamine biosynthesis; spermidine biosynthesis; spermidine from putrescine: step 1/1.

Gene Ontology (GO) - Biological Process for SRM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006595 polyamine metabolic process TAS --
GO:0006596 polyamine biosynthetic process IEA,IBA 21873635
GO:0008295 spermidine biosynthetic process IBA,IEA --
GO:1990830 cellular response to leukemia inhibitory factor IEA --
genes like me logo Genes that share ontologies with SRM: view

No data available for SIGNOR curated interactions for SRM Gene

Drugs & Compounds for SRM Gene

(9) Drugs for SRM Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Ademetionine Approved, Investigational Nutra Enzyme, substrate 0
putrescine Experimental Pharma 0
spermidine Experimental Pharma 0
spermine Experimental Nutra 0
5'-Methylthioadenosine Experimental Pharma 0

(9) Additional Compounds for SRM Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Aminopropylcadaverine
  • 3-Apcad
  • N-(3-Aminopropyl)-1,5-pentanediamine
  • N-(3-Aminopropyl)cadaverine
  • N-3-Aminopropyl-1,5-diaminopentane
56-19-9
S-Adenosylmethioninamine
  • (5-Deoxy-5-adenosyl)(3-aminopropyl)methylsulfonium
  • (5-Deoxy-5-adenosyl)(3-aminopropyl)methylsulfonium cation
  • (5-Deoxy-5-adenosyl)(3-aminopropyl)methylsulfonium salt
  • [1-(Adenin-9-yl)-1,5-dideoxy-beta-D-ribofuranos-5-yl](3-aminopropyl)(methyl)sulfonium
  • S--Adenosylmethioninamine
22365-13-5
genes like me logo Genes that share compounds with SRM: view

Transcripts for SRM Gene

mRNA/cDNA for SRM Gene

1 REFSEQ mRNAs :
3 NCBI additional mRNA sequence :
6 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SRM

Alternative Splicing Database (ASD) splice patterns (SP) for SRM Gene

ExUns: 1 ^ 2a · 2b ^ 3a · 3b · 3c · 3d ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8a · 8b · 8c · 8d
SP1: - - - -
SP2: - -
SP3: - - - -
SP4: -
SP5:
SP6:

Relevant External Links for SRM Gene

GeneLoc Exon Structure for
SRM

Expression for SRM Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SRM Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SRM Gene

This gene is overexpressed in Bone marrow stromal cell (8.2), Oral epithelium (7.4), and Lymph node (7.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SRM Gene



Protein tissue co-expression partners for SRM Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SRM

SOURCE GeneReport for Unigene cluster for SRM Gene:

Hs.76244

Evidence on tissue expression from TISSUES for SRM Gene

  • Skin(4.7)
  • Nervous system(4.7)
  • Lung(4.5)
  • Muscle(3)
  • Intestine(2.4)
  • Stomach(2.3)
  • Heart(2.3)
  • Liver(2.2)
  • Pancreas(2.1)
  • Spleen(2.1)
genes like me logo Genes that share expression patterns with SRM: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SRM Gene

Orthologs for SRM Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SRM Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SRM 29 30
  • 99.23 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SRM 29 30
  • 90.73 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SRM 29 30
  • 90.55 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Srm 29
  • 89.18 (n)
Mouse
(Mus musculus)
Mammalia Srm 29 16 30
  • 88.85 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SRM 30
  • 76 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SRM 30
  • 61 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SRM 29 30
  • 80.95 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SRM 30
  • 86 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia srm 29
  • 74.86 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.25559 29
Zebrafish
(Danio rerio)
Actinopterygii srm 29 30
  • 72.16 (n)
OneToOne
zgc63600 29
Fruit Fly
(Drosophila melanogaster)
Insecta SpdS 29 30
  • 62.86 (n)
OneToOne
CG8327 31
  • 55 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011126 29
  • 62.49 (n)
Worm
(Caenorhabditis elegans)
Secernentea spds-1 29 30
  • 58.7 (n)
OneToOne
Y46G5A.19 31
  • 48 (a)
A. gosspyii yeast
(Eremothecium gossypii)
Saccharomycetes AGOS_ADL340W 29
  • 62.44 (n)
K. Lactis Yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0B09372g 29
  • 58.57 (n)
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SPE3 29 30 32
  • 57.28 (n)
OneToOne
Thale Cress
(Arabidopsis thaliana)
eudicotyledons SPDS1 29
  • 55.48 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.2088 29
Soybean
(Glycine max)
eudicotyledons Gma.2891 29
Rice
(Oryza sativa)
Liliopsida Os07g0408700 29
  • 54.44 (n)
Os.4599 29
Barley
(Hordeum vulgare)
Liliopsida Hv.6371 29
Wheat
(Triticum aestivum)
Liliopsida Ta.24743 29
Corn
(Zea mays)
Liliopsida Zm.16536 29
Bread mold
(Neurospora crassa)
Ascomycetes NCU06727 29
  • 66.55 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 58 (a)
OneToOne
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPBC12C2.07c 29
  • 57.93 (n)
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.2167 29
Species where no ortholog for SRM was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for SRM Gene

ENSEMBL:
Gene Tree for SRM (if available)
TreeFam:
Gene Tree for SRM (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SRM: view image
Alliance of Genome Resources:
Additional Orthologs for SRM

Paralogs for SRM Gene

Paralogs for SRM Gene

Pseudogenes.org Pseudogenes for SRM Gene

genes like me logo Genes that share paralogs with SRM: view

Variants for SRM Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SRM Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
rs1049932 -- p.Leu149Val

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SRM Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for SRM Gene

Variant ID Type Subtype PubMed ID
nsv474577 CNV novel sequence insertion 20440878
nsv545407 CNV gain 21841781
nsv832425 CNV loss 17160897
nsv953456 CNV deletion 24416366

Variation tolerance for SRM Gene

Residual Variation Intolerance Score: 32.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.49; 10.73% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SRM Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SRM
Leiden Open Variation Database (LOVD)
SRM

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SRM Gene

Disorders for SRM Gene

MalaCards: The human disease database

(6) MalaCards diseases for SRM Gene - From: COP and GCD

Disorder Aliases PubMed IDs
sleeping sickness
  • african sleeping sickness
chagas disease
  • american trypanosomiasis
leishmaniasis
  • post kala-azar dermal leishmaniasis
syndromic x-linked intellectual disability snyder type
  • mental retardation, x-linked, snyder-robinson type
thymus lymphoma
  • thymic lymphoma
- elite association - COSMIC cancer census association via MalaCards
Search SRM in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SRM

genes like me logo Genes that share disorders with SRM: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SRM Gene

Publications for SRM Gene

  1. Human spermidine synthase: cloning and primary structure. (PMID: 2344393) Wahlfors J … Eloranta TO (DNA and cell biology 1990) 2 3 4 22
  2. Structure and mechanism of spermidine synthases. (PMID: 17585781) Wu H … Plotnikov AN (Biochemistry 2007) 3 4 22
  3. Human spermidine synthase gene: structure and chromosomal localization. (PMID: 2069720) Myöhänen S … Jänne J (DNA and cell biology 1991) 3 4 22
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  5. Inhibition of spermidine synthase gene expression by transforming growth factor-beta 1 in hepatoma cells. (PMID: 9020892) Nishikawa Y … Carr BI (The Biochemical journal 1997) 3 22

Products for SRM Gene

Sources for SRM Gene