Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)

CHEBI ONTOLOGY - ANNOTATIONS

The Chemical Entities of Biological Interest (ChEBI) ontology is downloaded weekly from EMBL-EBI at http://www.ebi.ac.uk/chebi/. The data is made available under the Creative Commons License (CC BY 3.0, http://creativecommons.org/licenses/by/3.0/). For more information see: Degtyarenko et al. (2008) ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res. 36, D344–D350.
Term:spermidine
go back to main search page
Accession:CHEBI:16610 term browser browse the term
Definition:A triamine that is the 1,5,10-triaza derivative of decane.
Synonyms:related_synonym: 1,5,10-triazadecane;   4-azaoctamethylenediamine;   4-azaoctane-1,8-diamine;   Formula=C7H19N3;   InChI=1S/C7H19N3/c8-4-1-2-6-10-7-3-5-9/h10H,1-9H2;   InChIKey=ATHGHQPFGPMSJY-UHFFFAOYSA-N;   N-(3-Aminopropyl)-1,4-butane-diamine;   SMILES=NCCCCNCCCN;   Spermidin
 alt_id: CHEBI:15095;   CHEBI:15097;   CHEBI:26732;   CHEBI:26733;   CHEBI:45647;   CHEBI:9218
 xref: Beilstein:1698591;   CAS:124-20-9;   DrugBank:DB03566;   Gmelin:454510;   HMDB:HMDB0001257;   KEGG:C00315;   KNApSAcK:C00001431;   LINCS:LSM-37075
 xref_mesh: MESH:D013095
 xref: MetaCyc:SPERMIDINE;   PDBeChem:SPD;   PMID:1176793;   PMID:19801973;   PMID:22770225;   PMID:30306826;   PMID:516181;   PMID:6156039;   PMID:7350997;   Reaxys:1698591;   Wikipedia:Spermidine
 cyclic_relationship: is_conjugate_base_of CHEBI:57834


show annotations for term's descendants           Sort by:
spermidine term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Adrb1 adrenoceptor beta 1 affects binding ISO Spermidine binds to ADRB1 protein CTD PMID:20885010 NCBI chr 1:255,771,962...255,774,973
Ensembl chr 1:255,771,597...255,807,259 		JBrowse link
G Adrb2 adrenoceptor beta 2 affects binding ISO Spermidine binds to ADRB2 protein CTD PMID:20885010 NCBI chr18:55,642,459...55,644,501
Ensembl chr18:55,502,903...55,644,512 		JBrowse link
G Aoc1 amine oxidase, copper containing 1 decreases expression EXP Spermidine results in decreased expression of AOC1 protein CTD PMID:1644166 NCBI chr 4:77,812,260...77,831,846
Ensembl chr 4:77,812,260...77,831,840 		JBrowse link
G Casp3 caspase 3 multiple interactions ISO [Naphthalimides co-treated with Spermidine] results in increased activity of CASP3 protein; Acetylcysteine inhibits the reaction [[Naphthalimides co-treated with Spermidine] results in increased activity of CASP3 protein] CTD PMID:21349322 NCBI chr16:45,662,910...45,681,171
Ensembl chr16:45,662,910...45,684,648 		JBrowse link
G Col2a1 collagen type II alpha 1 chain multiple interactions EXP [COL2A1 protein co-treated with Freund's Adjuvant] results in decreased abundance of Spermidine CTD PMID:24709313 NCBI chr 7:129,098,489...129,127,560
Ensembl chr 7:129,098,786...129,127,546 		JBrowse link
G Eif3b eukaryotic translation initiation factor 3, subunit B multiple interactions EXP Spermidine inhibits the reaction [Pentanoic Acids results in increased expression of EIF3B protein] CTD PMID:22555848 NCBI chr12:14,196,403...14,220,865
Ensembl chr12:14,196,403...14,220,886 		JBrowse link
G Fxyd2 FXYD domain-containing ion transport regulator 2 increases transport ISO FXYD2 protein results in increased transport of Spermidine CTD PMID:11533133 NCBI chr 8:45,712,901...45,720,032
Ensembl chr 8:45,712,903...45,720,203 		JBrowse link
G Gast gastrin increases abundance EXP GAST protein results in increased abundance of Spermidine CTD PMID:1644166 NCBI chr10:85,264,832...85,269,393
Ensembl chr10:85,264,832...85,267,496 		JBrowse link
G Gclm glutamate cysteine ligase, modifier subunit multiple interactions
increases expression		 ISO pimagedine inhibits the reaction [Spermidine results in increased expression of GCLM mRNA] CTD PMID:12763045 NCBI chr 2:210,347,482...210,367,537
Ensembl chr 2:210,347,482...210,367,535 		JBrowse link
G Gstm1 glutathione S-transferase mu 1 increases expression
multiple interactions		 ISO Spermidine results in increased expression of GSTM1 mRNA
pimagedine inhibits the reaction [Spermidine results in increased expression of GSTM1 mRNA]		 CTD PMID:12763045 NCBI chr 2:195,649,845...195,655,402
Ensembl chr 2:195,649,845...195,655,411 		JBrowse link
G Nfe2l2 NFE2 like bZIP transcription factor 2 affects localization ISO Spermidine affects the localization of NFE2L2 protein CTD PMID:12763045 NCBI chr 3:60,594,239...60,621,712
Ensembl chr 3:60,594,242...60,621,737 		JBrowse link
G Nqo1 NAD(P)H quinone dehydrogenase 1 multiple interactions
increases activity
increases expression		 ISO pimagedine inhibits the reaction [Spermidine results in increased activity of NQO1 protein]; pimagedine inhibits the reaction [Spermidine results in increased expression of NQO1 mRNA] CTD PMID:12763045 NCBI chr19:35,295,633...35,310,528
Ensembl chr19:35,295,573...35,310,557 		JBrowse link
G Odc1 ornithine decarboxylase 1 multiple interactions
increases abundance		 EXP
ISO		 [[Ornithine Decarboxylase Inhibitors results in decreased activity of ODC1 protein] which results in decreased chemical synthesis of Polyamines] which results in decreased abundance of Spermidine; [ODC1 protein results in increased chemical synthesis of Polyamines] which results in increased abundance of Spermidine; [Pentanoic Acids results in decreased activity of ODC1 protein] which results in decreased abundance of Spermidine
ODC1 protein results in increased abundance of Spermidine		 CTD PMID:20805360 PMID:22555848 NCBI chr 6:40,329,831...40,336,444
Ensembl chr 6:40,329,964...40,336,440 		JBrowse link
G Sat1 spermidine/spermine N1-acetyl transferase 1 increases metabolic processing
increases splicing		 ISO SAT1 protein results in increased metabolism of Spermidine analog
Spermidine analog results in increased splicing of SAT1 mRNA		 CTD PMID:21639123 NCBI chr  X:40,158,354...40,161,641
Ensembl chr  X:40,157,046...40,196,813 		JBrowse link
G Smox spermine oxidase multiple interactions ISO [SMOX protein results in increased oxidation of Spermine] which results in increased abundance of Spermidine CTD PMID:23707493 NCBI chr 3:118,731,814...118,767,242
Ensembl chr 3:118,731,900...118,765,710 		JBrowse link
G Tia1 TIA1 cytotoxic granule-associated RNA binding protein multiple interactions EXP Spermidine inhibits the reaction [Pentanoic Acids affects the localization of TIA1 protein] CTD PMID:22555848 NCBI chr 4:118,852,765...118,883,252
Ensembl chr 4:118,852,837...118,880,586 		JBrowse link
G Ugt1a6 UDP glucuronosyltransferase family 1 member A6 increases expression
multiple interactions		 ISO Spermidine results in increased expression of UGT1A6 mRNA
pimagedine inhibits the reaction [Spermidine results in increased expression of UGT1A6 mRNA]		 CTD PMID:12763045 NCBI chr 9:88,747,213...88,808,465
Ensembl chr 9:88,713,184...88,808,465 		JBrowse link
G Xiap X-linked inhibitor of apoptosis multiple interactions ISO [Naphthalimides co-treated with Spermidine] results in decreased expression of XIAP protein CTD PMID:21349322 NCBI chr  X:120,890,537...120,938,413
Ensembl chr  X:120,897,907...120,934,700 		JBrowse link
trypanothione term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Arg1 arginase 1 decreases activity ISO trypanothione results in decreased activity of ARG1 protein CTD PMID:21232540 NCBI chr 1:20,475,878...20,488,422
Ensembl chr 1:20,475,968...20,488,422 		JBrowse link
trypanothione disulfide term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Arg1 arginase 1 decreases activity ISO trypanothione results in decreased activity of ARG1 protein CTD PMID:21232540 NCBI chr 1:20,475,878...20,488,422
Ensembl chr 1:20,475,968...20,488,422 		JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  CHEBI ontology 19921
    role 19893
      biological role 19891
        biochemical role 19598
          autophagy inducer 2068
            spermidine 19
              N(1),N(8)-bis(caffeoyl)spermidine 0
              N(1),N(8)-bis(coumaroyl)spermidine 0
              N(1),N(8)-bis(sinapoyl)-spermidine 0
              N(1),N(8)-bis-(dihydrocaffeoyl)spermidine 0
              N(4)-aminopropylspermidine 0
              N(4)-bis(aminopropyl)spermidine(1+) 0
              N-(3-aminopropyl)but-2-ene-1,4-diamine + 0
              N-[(E)-4-aminobutylidene]propane-1,3-diamine 0
              N-caffeoylspermidine 0
              acetylspermidine + 0
              carboxyspermidine 0
              glutathionylspermidine 0
              mygalin 0
              spermidine alkaloid + 0
              spermidine hydroxycinnamic acid conjugate + 0
              spermidine-(butyl-(13)C4) 0
              trypanothione + 1
Path 2
Term Annotations click to browse term
  CHEBI ontology 19921
    subatomic particle 19919
      composite particle 19919
        hadron 19919
          baryon 19919
            nucleon 19919
              atomic nucleus 19919
                atom 19919
                  main group element atom 19865
                    main group molecular entity 19865
                      s-block molecular entity 19697
                        hydrogen molecular entity 19678
                          hydrides 19184
                            inorganic hydride 18194
                              pnictogen hydride 18184
                                nitrogen hydride 18096
                                  azane 17900
                                    ammonia 17899
                                      organic amino compound 17899
                                        polyamine 9029
                                          triamine 30
                                            spermidine 19
                                              N(1),N(8)-bis(caffeoyl)spermidine 0
                                              N(1),N(8)-bis(coumaroyl)spermidine 0
                                              N(1),N(8)-bis(sinapoyl)-spermidine 0
                                              N(1),N(8)-bis-(dihydrocaffeoyl)spermidine 0
                                              N(4)-aminopropylspermidine 0
                                              N(4)-bis(aminopropyl)spermidine(1+) 0
                                              N-(3-aminopropyl)but-2-ene-1,4-diamine + 0
                                              N-[(E)-4-aminobutylidene]propane-1,3-diamine 0
                                              N-caffeoylspermidine 0
                                              acetylspermidine + 0
                                              carboxyspermidine 0
                                              glutathionylspermidine 0
                                              mygalin 0
                                              spermidine alkaloid + 0
                                              spermidine hydroxycinnamic acid conjugate + 0
                                              spermidine-(butyl-(13)C4) 0
                                              trypanothione + 1
paths to the root