Gene loci information

Transcript annotation

  • This transcript has been annotated as Spermidine synthase.

Parent gene

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.t6 TTS g14578.t6 1391437 1391437
chr_4 g14578 g14578.t6 isoform g14578.t6 1391621 1393253
chr_4 g14578 g14578.t6 exon g14578.t6.exon1 1391621 1391821
chr_4 g14578 g14578.t6 exon g14578.t6.exon2 1392464 1393059
chr_4 g14578 g14578.t6 cds g14578.t6.CDS1 1392546 1393059
chr_4 g14578 g14578.t6 exon g14578.t6.exon3 1393120 1393253
chr_4 g14578 g14578.t6 cds g14578.t6.CDS2 1393120 1393253
chr_4 g14578 g14578.t6 TSS g14578.t6 1393298 1393298

Sequences

>g14578.t6 Gene=g14578 Length=931
ATGAATTCTGTAGTAAAAGGTTGGTTTAGTGAAATTTCAGATGAACTCTGGCCTGGTCAA
TGTTTTTCGTTAAAAGTCACCAAAGTGCTACATGAAGAAAAATCTGAATTTCAAGATATT
AAAATTGTCGAAACTGAAACATATGGACGAGTTTTATTGCTTGACAATGTGATTCAATGC
ACAGAACGTGATGAATTTGCATATCAAGAATTAATTTCAATGATTCCAATTTGTGCTCAT
CCCAATCCCGAAAAAGTTTTAATAGTAGGTGGGGGTGATGGTGGTGTTGCTCGTGAAGTT
GTCAAACATCCAAAAGTTTGTAAAGTTCATCAAGTTGAAATTGATGGAAGAGTTGTAGAT
TTGTCAAAAGAATTTTTACCATTTATGGCTTGCGGATTTGATTCACCCAAAATGAACTTG
ACAATTGGCGATGGATTTGAATTTATGAAAAATCACAAGGAAGAATTTGATGTCATTATT
ACAGATTCAAGTGATCCAATTGGTAAAATTTTTAAGCATGTTTTTAATTTTTTTCAATTA
TTATTTTTTTTATCTTTCAGGTCCAGCAGTTTCACTTTTTCAAGAGCCATACTTTCAATT
AATGAAAAATGCACTTCGACCTGGTGGAATTATTTGCTCTCAAGGTAGTAGCTTTTGGAT
TGATGCACAACATGTTAAAGAAACTATGGATGCATGTGGGCAACATTTTAAAAATGTTTC
TTATGCTATGGCAATGGTACCATCATACCCATGTGGCTCAATTGGTTTTGTAATTGGTTG
TTTAGATAAAAAAAGTAAACTTAGTGAACCAGTTCATAAATTTACAACTGAAGAAGTTGA
CAAACTTGGATTCAGATACTACACATCAGATGTTCATAAAGCTGCCTTTGTTTTGCCACG
ATTTGCTGAAAAAGCTCTCGGTTTATGCTGA

>g14578.t6 Gene=g14578 Length=215
MNSVVKGWFSEISDELWPGQCFSLKVTKVLHEEKSEFQDIKIVETETYGRVLLLDNVIQC
TERDEFAYQELISMIPICAHPNPEKVLIVGGGDGGVAREVVKHPKVCKVHQVEIDGRVVD
LSKEFLPFMACGFDSPKMNLTIGDGFEFMKNHKEEFDVIITDSSDPIGKIFKHVFNFFQL
LFFLSFRSSSFTFSRAILSINEKCTSTWWNYLLSR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g14578.t6 CDD cd02440 AdoMet_MTases 85 164 1.01345E-6
7 g14578.t6 Gene3D G3DSA:2.30.140.10 - 4 61 1.2E-27
8 g14578.t6 Gene3D G3DSA:3.40.50.150 Vaccinia Virus protein VP39 62 188 1.3E-43
5 g14578.t6 Hamap MF_00198 Polyamine aminopropyltransferase [speE]. 7 215 21.496349
3 g14578.t6 PANTHER PTHR11558 SPERMIDINE/SPERMINE SYNTHASE 1 169 1.4E-78
4 g14578.t6 PANTHER PTHR11558:SF11 SPERMIDINE SYNTHASE 1 169 1.4E-78
1 g14578.t6 Pfam PF17284 Spermidine synthase tetramerisation domain 7 62 3.1E-23
2 g14578.t6 Pfam PF01564 Spermine/spermidine synthase domain 65 177 9.9E-41
10 g14578.t6 ProSitePatterns PS01330 Polyamine biosynthesis (PABS) domain signature. 86 99 -
11 g14578.t6 ProSiteProfiles PS51006 Polyamine biosynthesis (PABS) domain profile. 6 215 72.063
6 g14578.t6 SUPERFAMILY SSF53335 S-adenosyl-L-methionine-dependent methyltransferases 11 170 2.33E-57

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.

Raw TPM values