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.t5 TTS g14578.t5 1391437 1391437
chr_4 g14578 g14578.t5 isoform g14578.t5 1391621 1393253
chr_4 g14578 g14578.t5 exon g14578.t5.exon1 1391621 1391821
chr_4 g14578 g14578.t5 cds g14578.t5.CDS1 1391621 1391821
chr_4 g14578 g14578.t5 exon g14578.t5.exon2 1392464 1392633
chr_4 g14578 g14578.t5 cds g14578.t5.CDS2 1392464 1392633
chr_4 g14578 g14578.t5 exon g14578.t5.exon3 1392692 1393253
chr_4 g14578 g14578.t5 cds g14578.t5.CDS3 1392692 1392974
chr_4 g14578 g14578.t5 TSS g14578.t5 1393298 1393298

Sequences

>g14578.t5 Gene=g14578 Length=933
ATGAATTCTGTAGTAAAAGGTTGGTTTAGTGAAATTTCAGATGAACTCTGGCCTGGTCAA
TGTTTTTCGTTAAAAGTCACCAAAGTGCTACATGAAGAAAAATCTGAATTTCAAGATATT
AAAATTGTCGAAACGTAAGAAATTTCACCTTTGACCTTGACCTTAGTTTTTTGATTTAAT
CTAAAAATTTTTAGTGAAACATATGGACGAGTTTTATTGCTTGACAATGTGATTCAATGC
ACAGAACGTGATGAATTTGCATATCAAGAATTAATTTCAATGATTCCAATTTGTGCTCAT
CCCAATCCCGAAAAAGTTTTAATAGTAGGTGGGGGTGATGGTGGTGTTGCTCGTGAAGTT
GTCAAACATCCAAAAGTTTGTAAAGTTCATCAAGTTGAAATTGATGGAAGAGTTGTAGAT
TTGTCAAAAGAATTTTTACCATTTATGGCTTGCGGATTTGATTCACCCAAAATGAACTTG
ACAATTGGCGATGGATTTGAATTTATGAAAAATCACAAGGAAGAATTTGATGTCATTATT
ACAGATTCAAGTGATCCAATTGGTCCAGCAGTTTCACTTTTTCAAGAGCCATACTTTCAA
TTAATGAAAAATGCACTTCGACCTGGTGGAATTATTTGCTCTCAAGGTAGTAGCTTTTGG
ATTGATGCACAACATGTTAAAGAAACTATGGATGCATGTGGGCAACATTTTAAAAATGTT
TCTTATGCTATGGCAATGGTACCATCATACCCATGTGGCTCAATTGGTTTTGTAATTGGT
TGTTTAGATAAAAAAAGTAAACTTAGTGAACCAGTTCATAAATTTACAACTGAAGAAGTT
GACAAACTTGGATTCAGATACTACACATCAGATGTTCATAAAGCTGCCTTTGTTTTGCCA
CGATTTGCTGAAAAAGCTCTCGGTTTATGCTGA

>g14578.t5 Gene=g14578 Length=217
MIPICAHPNPEKVLIVGGGDGGVAREVVKHPKVCKVHQVEIDGRVVDLSKEFLPFMACGF
DSPKMNLTIGDGFEFMKNHKEEFDVIITDSSDPIGPAVSLFQEPYFQLMKNALRPGGIIC
SQGSSFWIDAQHVKETMDACGQHFKNVSYAMAMVPSYPCGSIGFVIGCLDKKSKLSEPVH
KFTTEEVDKLGFRYYTSDVHKAAFVLPRFAEKALGLC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g14578.t5 CDD cd02440 AdoMet_MTases 12 122 3.42176E-10
6 g14578.t5 Gene3D G3DSA:3.40.50.150 Vaccinia Virus protein VP39 1 215 1.8E-69
4 g14578.t5 Hamap MF_00198 Polyamine aminopropyltransferase [speE]. 1 215 18.021301
2 g14578.t5 PANTHER PTHR11558 SPERMIDINE/SPERMINE SYNTHASE 2 215 2.8E-86
3 g14578.t5 PANTHER PTHR11558:SF11 SPERMIDINE SYNTHASE 2 215 2.8E-86
1 g14578.t5 Pfam PF01564 Spermine/spermidine synthase domain 2 167 1.2E-56
8 g14578.t5 ProSitePatterns PS01330 Polyamine biosynthesis (PABS) domain signature. 13 26 -
9 g14578.t5 ProSiteProfiles PS51006 Polyamine biosynthesis (PABS) domain profile. 1 169 64.724
5 g14578.t5 SUPERFAMILY SSF53335 S-adenosyl-L-methionine-dependent methyltransferases 2 214 4.44E-62

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