General information for g14578.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Spermidine synthase.
Parent gene
- The parent gene g14578 is located on chr_4: 1392469..1393253 (- strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_4 | g14578 | g14578.t4 | TTS | g14578.t4 | 1390544 | 1390544 |
| chr_4 | g14578 | g14578.t4 | isoform | g14578.t4 | 1391170 | 1393253 |
| chr_4 | g14578 | g14578.t4 | exon | g14578.t4.exon1 | 1391170 | 1391524 |
| chr_4 | g14578 | g14578.t4 | exon | g14578.t4.exon2 | 1391598 | 1391821 |
| chr_4 | g14578 | g14578.t4 | cds | g14578.t4.CDS1 | 1391621 | 1391821 |
| chr_4 | g14578 | g14578.t4 | exon | g14578.t4.exon3 | 1392464 | 1392633 |
| chr_4 | g14578 | g14578.t4 | cds | g14578.t4.CDS2 | 1392464 | 1392633 |
| chr_4 | g14578 | g14578.t4 | exon | g14578.t4.exon4 | 1392692 | 1393059 |
| chr_4 | g14578 | g14578.t4 | cds | g14578.t4.CDS3 | 1392692 | 1393059 |
| chr_4 | g14578 | g14578.t4 | exon | g14578.t4.exon5 | 1393120 | 1393253 |
| chr_4 | g14578 | g14578.t4 | cds | g14578.t4.CDS4 | 1393120 | 1393253 |
| chr_4 | g14578 | g14578.t4 | TSS | g14578.t4 | 1393298 | 1393298 |
Sequences
>g14578.t4 Gene=g14578 Length=1251
ATGAATTCTGTAGTAAAAGGTTGGTTTAGTGAAATTTCAGATGAACTCTGGCCTGGTCAA
TGTTTTTCGTTAAAAGTCACCAAAGTGCTACATGAAGAAAAATCTGAATTTCAAGATATT
AAAATTGTCGAAACTGAAACATATGGACGAGTTTTATTGCTTGACAATGTGATTCAATGC
ACAGAACGTGATGAATTTGCATATCAAGAATTAATTTCAATGATTCCAATTTGTGCTCAT
CCCAATCCCGAAAAAGTTTTAATAGTAGGTGGGGGTGATGGTGGTGTTGCTCGTGAAGTT
GTCAAACATCCAAAAGTTTGTAAAGTTCATCAAGTTGAAATTGATGGAAGAGTTGTAGAT
TTGTCAAAAGAATTTTTACCATTTATGGCTTGCGGATTTGATTCACCCAAAATGAACTTG
ACAATTGGCGATGGATTTGAATTTATGAAAAATCACAAGGAAGAATTTGATGTCATTATT
ACAGATTCAAGTGATCCAATTGGTCCAGCAGTTTCACTTTTTCAAGAGCCATACTTTCAA
TTAATGAAAAATGCACTTCGACCTGGTGGAATTATTTGCTCTCAAGGTAGTAGCTTTTGG
ATTGATGCACAACATGTTAAAGAAACTATGGATGCATGTGGGCAACATTTTAAAAATGTT
TCTTATGCTATGGCAATGGTACCATCATACCCATGTGGCTCAATTGGTTTTGTAATTGGT
TGTTTAGATAAAAAAAGTAAACTTAGTGAACCAGTTCATAAATTTACAACTGAAGAAGTT
GACAAACTTGGATTCAGATACTACACATCAGATGTTCATAAAGCTGCCTTTGTTTTGCCA
CGATTTGCTGAAAAAGCTCTCGGTTTATGCTGATTAATGAAAACTTTTTTAATTTTATGC
TAATAATTAAAAATTTAAAGGCTGAAATCATACACATACTCTTGTTAGCCTATTAATAAT
AAAAATTCTTTTATACTTCCAATTTCATTCCAAAGTATATAGAAACGTGAATAATCAAGT
CCTCAGCCATTATGCAAATTTGTGCTTATGAAGTTCATTTCATCTATTTCCTTGTTCATA
ATAACTTTGTTATATTTGCGTTATATTTTTTAAATGTCTTCCTAATATTAATGGAAGTTC
AATATTTTTCTCAACGTTCGTAAAAAATACAAATCCTTTATTGTTTTCATTTTATTTCAC
CGGTATAAAAACATCTGTTCATTCATGCGACTTGTCTCAACACATTCCTCA
>g14578.t4 Gene=g14578 Length=290
MNSVVKGWFSEISDELWPGQCFSLKVTKVLHEEKSEFQDIKIVETETYGRVLLLDNVIQC
TERDEFAYQELISMIPICAHPNPEKVLIVGGGDGGVAREVVKHPKVCKVHQVEIDGRVVD
LSKEFLPFMACGFDSPKMNLTIGDGFEFMKNHKEEFDVIITDSSDPIGPAVSLFQEPYFQ
LMKNALRPGGIICSQGSSFWIDAQHVKETMDACGQHFKNVSYAMAMVPSYPCGSIGFVIG
CLDKKSKLSEPVHKFTTEEVDKLGFRYYTSDVHKAAFVLPRFAEKALGLC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g14578.t4 | CDD | cd02440 | AdoMet_MTases | 85 | 195 | 4.17474E-10 |
| 7 | g14578.t4 | Gene3D | G3DSA:2.30.140.10 | - | 4 | 63 | 2.0E-27 |
| 8 | g14578.t4 | Gene3D | G3DSA:3.40.50.150 | Vaccinia Virus protein VP39 | 64 | 288 | 1.2E-73 |
| 5 | g14578.t4 | Hamap | MF_00198 | Polyamine aminopropyltransferase [speE]. | 7 | 288 | 34.428085 |
| 3 | g14578.t4 | PANTHER | PTHR11558 | SPERMIDINE/SPERMINE SYNTHASE | 1 | 287 | 6.1E-123 |
| 4 | g14578.t4 | PANTHER | PTHR11558:SF11 | SPERMIDINE SYNTHASE | 1 | 287 | 6.1E-123 |
| 9 | g14578.t4 | PIRSF | PIRSF000502 | Spermidine_synth | 1 | 290 | 7.8E-136 |
| 1 | g14578.t4 | Pfam | PF17284 | Spermidine synthase tetramerisation domain | 7 | 62 | 5.1E-23 |
| 2 | g14578.t4 | Pfam | PF01564 | Spermine/spermidine synthase domain | 65 | 240 | 6.6E-60 |
| 11 | g14578.t4 | ProSitePatterns | PS01330 | Polyamine biosynthesis (PABS) domain signature. | 86 | 99 | - |
| 13 | g14578.t4 | ProSiteProfiles | PS51006 | Polyamine biosynthesis (PABS) domain profile. | 6 | 242 | 93.571 |
| 6 | g14578.t4 | SUPERFAMILY | SSF53335 | S-adenosyl-L-methionine-dependent methyltransferases | 11 | 287 | 1.66E-85 |
| 12 | g14578.t4 | TIGRFAM | TIGR00417 | speE: spermidine synthase | 8 | 282 | 1.6E-103 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0006595 | polyamine metabolic process | BP |
| GO:0003824 | catalytic activity | MF |
KEGG
Orthology
- This transcript has been annotated with K00797 (spermidine synthase)
Pathway
- This transcript belongs to the following pathways
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.
