General information for g14578.t3
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.t3 | TTS | g14578.t3 | 1390544 | 1390544 |
| chr_4 | g14578 | g14578.t3 | isoform | g14578.t3 | 1391089 | 1393253 |
| chr_4 | g14578 | g14578.t3 | exon | g14578.t3.exon1 | 1391089 | 1391524 |
| chr_4 | g14578 | g14578.t3 | exon | g14578.t3.exon2 | 1391598 | 1391821 |
| chr_4 | g14578 | g14578.t3 | cds | g14578.t3.CDS1 | 1391621 | 1391821 |
| chr_4 | g14578 | g14578.t3 | exon | g14578.t3.exon3 | 1392464 | 1392627 |
| chr_4 | g14578 | g14578.t3 | cds | g14578.t3.CDS2 | 1392464 | 1392627 |
| chr_4 | g14578 | g14578.t3 | exon | g14578.t3.exon4 | 1392692 | 1393253 |
| chr_4 | g14578 | g14578.t3 | cds | g14578.t3.CDS3 | 1392692 | 1392974 |
| chr_4 | g14578 | g14578.t3 | TSS | g14578.t3 | 1393298 | 1393298 |
Sequences
>g14578.t3 Gene=g14578 Length=1386
ATGAATTCTGTAGTAAAAGGTTGGTTTAGTGAAATTTCAGATGAACTCTGGCCTGGTCAA
TGTTTTTCGTTAAAAGTCACCAAAGTGCTACATGAAGAAAAATCTGAATTTCAAGATATT
AAAATTGTCGAAACGTAAGAAATTTCACCTTTGACCTTGACCTTAGTTTTTTGATTTAAT
CTAAAAATTTTTAGTGAAACATATGGACGAGTTTTATTGCTTGACAATGTGATTCAATGC
ACAGAACGTGATGAATTTGCATATCAAGAATTAATTTCAATGATTCCAATTTGTGCTCAT
CCCAATCCCGAAAAAGTTTTAATAGTAGGTGGGGGTGATGGTGGTGTTGCTCGTGAAGTT
GTCAAACATCCAAAAGTTTGTAAAGTTCATCAAGTTGAAATTGATGGAAGAGTTGTAGAT
TTGTCAAAAGAATTTTTACCATTTATGGCTTGCGGATTTGATTCACCCAAAATGAACTTG
ACAATTGGCGATGGATTTGAATTTATGAAAAATCACAAGGAAGAATTTGATGTCATTATT
ACAGATTCAAGTGATCCAATTGCAGTTTCACTTTTTCAAGAGCCATACTTTCAATTAATG
AAAAATGCACTTCGACCTGGTGGAATTATTTGCTCTCAAGGTAGTAGCTTTTGGATTGAT
GCACAACATGTTAAAGAAACTATGGATGCATGTGGGCAACATTTTAAAAATGTTTCTTAT
GCTATGGCAATGGTACCATCATACCCATGTGGCTCAATTGGTTTTGTAATTGGTTGTTTA
GATAAAAAAAGTAAACTTAGTGAACCAGTTCATAAATTTACAACTGAAGAAGTTGACAAA
CTTGGATTCAGATACTACACATCAGATGTTCATAAAGCTGCCTTTGTTTTGCCACGATTT
GCTGAAAAAGCTCTCGGTTTATGCTGATTAATGAAAACTTTTTTAATTTTATGCTAATAA
TTAAAAATTTAAAGGCTGAAATCATACACATACTCTTGTTAGCCTATTAATAATAAAAAT
TCTTTTATACTTCCAATTTCATTCCAAAGTATATAGAAACGTGAATAATCAAGTCCTCAG
CCATTATGCAAATTTGTGCTTATGAAGTTCATTTCATCTATTTCCTTGTTCATAATAACT
TTGTTATATTTGCGTTATATTTTTTAAATGTCTTCCTAATATTAATGGAAGTTCAATATT
TTTCTCAACGTTCGTAAAAAATACAAATCCTTTATTGTTTTCATTTTATTTCACCGGTAT
AAAAACATCTGTTCATTCATGCGACTTGTCTCAACACATTCCTCAGTCTTCGAAGAAATT
TTGAGAAGAGAACACAGTGAAAATCTAGAAAAAAGTAAATAATTATAAAATTTTCTAATT
TTTACT
>g14578.t3 Gene=g14578 Length=215
MIPICAHPNPEKVLIVGGGDGGVAREVVKHPKVCKVHQVEIDGRVVDLSKEFLPFMACGF
DSPKMNLTIGDGFEFMKNHKEEFDVIITDSSDPIAVSLFQEPYFQLMKNALRPGGIICSQ
GSSFWIDAQHVKETMDACGQHFKNVSYAMAMVPSYPCGSIGFVIGCLDKKSKLSEPVHKF
TTEEVDKLGFRYYTSDVHKAAFVLPRFAEKALGLC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g14578.t3 | CDD | cd02440 | AdoMet_MTases | 12 | 120 | 1.85684E-10 |
| 6 | g14578.t3 | Gene3D | G3DSA:3.40.50.150 | Vaccinia Virus protein VP39 | 1 | 213 | 1.1E-66 |
| 4 | g14578.t3 | Hamap | MF_00198 | Polyamine aminopropyltransferase [speE]. | 1 | 213 | 17.223747 |
| 2 | g14578.t3 | PANTHER | PTHR11558 | SPERMIDINE/SPERMINE SYNTHASE | 2 | 213 | 9.3E-83 |
| 3 | g14578.t3 | PANTHER | PTHR11558:SF11 | SPERMIDINE SYNTHASE | 2 | 213 | 9.3E-83 |
| 1 | g14578.t3 | Pfam | PF01564 | Spermine/spermidine synthase domain | 2 | 165 | 3.0E-53 |
| 8 | g14578.t3 | ProSitePatterns | PS01330 | Polyamine biosynthesis (PABS) domain signature. | 13 | 26 | - |
| 9 | g14578.t3 | ProSiteProfiles | PS51006 | Polyamine biosynthesis (PABS) domain profile. | 1 | 167 | 58.299 |
| 5 | g14578.t3 | SUPERFAMILY | SSF53335 | S-adenosyl-L-methionine-dependent methyltransferases | 2 | 212 | 7.13E-59 |
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:0003824 | catalytic activity | MF |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
