Gene loci information

Transcript annotation

  • This transcript has been annotated as Decaprenyl-diphosphate synthase subunit 1.

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_3 g1327 g1327.t8 isoform g1327.t8 9725163 9742728
chr_3 g1327 g1327.t8 exon g1327.t8.exon1 9725163 9725298
chr_3 g1327 g1327.t8 cds g1327.t8.CDS1 9725188 9725298
chr_3 g1327 g1327.t8 exon g1327.t8.exon2 9732616 9732705
chr_3 g1327 g1327.t8 cds g1327.t8.CDS2 9732616 9732705
chr_3 g1327 g1327.t8 exon g1327.t8.exon3 9740612 9740743
chr_3 g1327 g1327.t8 cds g1327.t8.CDS3 9740612 9740743
chr_3 g1327 g1327.t8 exon g1327.t8.exon4 9740806 9741000
chr_3 g1327 g1327.t8 cds g1327.t8.CDS4 9740806 9741000
chr_3 g1327 g1327.t8 exon g1327.t8.exon5 9742507 9742728
chr_3 g1327 g1327.t8 cds g1327.t8.CDS5 9742507 9742728
chr_3 g1327 g1327.t8 TTS g1327.t8 9742739 9742739
chr_3 g1327 g1327.t8 TSS g1327.t8 NA NA

Sequences

>g1327.t8 Gene=g1327 Length=775
AGTTGATGCTCAAAGAAAGATTGCCATGATAGCAGAAATGATTCACTCAGCAAGTTTAAT
TCACGATGATGTCATCGATCAATCATTCTCTAGAAGAGGAAAACCAAGCGTGAACGTTCT
ATGGAACCATAAAAAAGTAACACAAGCTGGTGATTATGTACTTGCAATTGCATCAATTAT
GCTTTCACGTCTGAAACACGATGAAGTCACCTTAATGCTCAGTGCGGTCTTGAATGATTT
AGTACAAGGAGAATTCATGCAACTGGGTGCTAAAGAAACAGAAAATGAACGCTTCTCGCA
CTATTTTACAAAAACCTACAGAAAAACAGCATCACTTATCGCAAATGCCTGCAAGGGTTC
TGCAACAATAGCTGGAGCTGATGCACCGATAGTCGAGACTGCTTTCCTTTATGGCAAAAA
TCTTGGGTTAGCCTTCCAATTCGTTGATGACTTGTTGGACTTTGTGTCGTCATCTGAAAC
GATGGGTAAACCAGCAGCAGCAGATTTAAAACTTGGTCTAGCAACAGCACCTGTTCTATT
TGCCTGCGAAAAGTACCCTGAATTGAATCCAATGATCATGAGACGTTTTAAGGAGCCTGG
TGATGTTGAAAAGGCGTTTGAGTTAGTACATAAATCACAAGGACTTGAACAAACACGCTT
TCTGGCCCGAAAACACTGCCTTGAAGCCATTAAATTAGCAAACAAGTTAGCTGAATCACC
ATACCAAAAGGGCCTTACAGATATAATGGATTTGGTACTAAATCGAATGAAATAA

>g1327.t8 Gene=g1327 Length=249
MIAEMIHSASLIHDDVIDQSFSRRGKPSVNVLWNHKKVTQAGDYVLAIASIMLSRLKHDE
VTLMLSAVLNDLVQGEFMQLGAKETENERFSHYFTKTYRKTASLIANACKGSATIAGADA
PIVETAFLYGKNLGLAFQFVDDLLDFVSSSETMGKPAAADLKLGLATAPVLFACEKYPEL
NPMIMRRFKEPGDVEKAFELVHKSQGLEQTRFLARKHCLEAIKLANKLAESPYQKGLTDI
MDLVLNRMK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g1327.t8 CDD cd00685 Trans_IPPS_HT 2 247 7.03864E-68
6 g1327.t8 Gene3D G3DSA:1.10.600.10 Farnesyl Diphosphate Synthase 1 249 8.9E-88
2 g1327.t8 PANTHER PTHR12001:SF69 DECAPRENYL-DIPHOSPHATE SYNTHASE SUBUNIT 1 1 249 9.9E-103
3 g1327.t8 PANTHER PTHR12001 GERANYLGERANYL PYROPHOSPHATE SYNTHASE 1 249 9.9E-103
1 g1327.t8 Pfam PF00348 Polyprenyl synthetase 2 201 1.1E-56
5 g1327.t8 ProSitePatterns PS00723 Polyprenyl synthases signature 1. 11 25 -
8 g1327.t8 SFLD SFLDS00005 Isoprenoid Synthase Type I 3 246 2.2E-34
4 g1327.t8 SUPERFAMILY SSF48576 Terpenoid synthases 2 248 8.02E-65

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:0008299 isoprenoid biosynthetic process BP

KEGG

Orthology

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.

Raw TPM values