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.t4 isoform g1327.t4 9722292 9741000
chr_3 g1327 g1327.t4 exon g1327.t4.exon1 9722292 9722438
chr_3 g1327 g1327.t4 cds g1327.t4.CDS1 9722391 9722438
chr_3 g1327 g1327.t4 exon g1327.t4.exon2 9723774 9723913
chr_3 g1327 g1327.t4 cds g1327.t4.CDS2 9723774 9723913
chr_3 g1327 g1327.t4 exon g1327.t4.exon3 9725154 9725298
chr_3 g1327 g1327.t4 cds g1327.t4.CDS3 9725154 9725298
chr_3 g1327 g1327.t4 exon g1327.t4.exon4 9732616 9732705
chr_3 g1327 g1327.t4 cds g1327.t4.CDS4 9732616 9732705
chr_3 g1327 g1327.t4 exon g1327.t4.exon5 9740612 9740743
chr_3 g1327 g1327.t4 cds g1327.t4.CDS5 9740612 9740743
chr_3 g1327 g1327.t4 exon g1327.t4.exon6 9740806 9741000
chr_3 g1327 g1327.t4 cds g1327.t4.CDS6 9740806 9741000
chr_3 g1327 g1327.t4 TSS g1327.t4 NA NA
chr_3 g1327 g1327.t4 TTS g1327.t4 NA NA

Sequences

>g1327.t4 Gene=g1327 Length=849
GCATCATCAACCTCTATACCACAACACAGTAGAGATTATAGCTCCGTACATACACAACAA
CCAGCCGGTCCAATCAGGGAATATAAAATTGATCCATACATGTTATTAGAAGACGAACTT
AAATATATTTTCGAGGACATTCGACAGGAATTACATCAAGGAACTAATCAAAAGGAACTC
ATACAGATTGCCGAATACTATTTCGATGGTCAAGGTAAAGCACTCCGTCCTATGGTGACA
CTATTGATGGGAAAAGCAATAAATTATCACATGTACAGAGAAAACAATCCACGTACAGTT
GATGCTCAAAGAAAGATTGCCATGATAGCAGAAATGATTCACTCAGCAAGTTTAATTCAC
GATGATGTCATCGATCAATCATTCTCTAGAAGAGGAAAACCAAGCGTGAACGTTCTATGG
AACCATAAAAAAGTAACACAAGCTGGTGATTATGTACTTGCAATTGCATCAATTATGCTT
TCACGTCTGAAACACGATGAAGTCACCTTAATGCTCAGTGCGGTCTTGAATGATTTAGTA
CAAGGAGAATTCATGCAACTGGGTGCTAAAGAAACAGAAAATGAACGCTTCTCGCACTAT
TTTACAAAAACCTACAGAAAAACAGCATCACTTATCGCAAATGCCTGCAAGGGTTCTGCA
ACAATAGCTGGAGCTGATGCACCGATAGTCGAGACTGCTTTCCTTTATGGCAAAAATCTT
GGGTTAGCCTTCCAATTCGTTGATGACTTGTTGGACTTTGTGTCGTCATCTGAAACGATG
GGTAAACCAGCAGCAGCAGATTTAAAACTTGGTCTAGCAACAGCACCTGTTCTATTTGCC
TGCGAAAAG

>g1327.t4 Gene=g1327 Length=250
MLLEDELKYIFEDIRQELHQGTNQKELIQIAEYYFDGQGKALRPMVTLLMGKAINYHMYR
ENNPRTVDAQRKIAMIAEMIHSASLIHDDVIDQSFSRRGKPSVNVLWNHKKVTQAGDYVL
AIASIMLSRLKHDEVTLMLSAVLNDLVQGEFMQLGAKETENERFSHYFTKTYRKTASLIA
NACKGSATIAGADAPIVETAFLYGKNLGLAFQFVDDLLDFVSSSETMGKPAAADLKLGLA
TAPVLFACEK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g1327.t4 CDD cd00685 Trans_IPPS_HT 22 250 5.15214E-75
6 g1327.t4 Gene3D G3DSA:1.10.600.10 Farnesyl Diphosphate Synthase 1 250 1.4E-83
2 g1327.t4 PANTHER PTHR12001:SF69 DECAPRENYL-DIPHOSPHATE SYNTHASE SUBUNIT 1 2 250 2.7E-96
3 g1327.t4 PANTHER PTHR12001 GERANYLGERANYL PYROPHOSPHATE SYNTHASE 2 250 2.7E-96
1 g1327.t4 Pfam PF00348 Polyprenyl synthetase 25 249 1.1E-63
5 g1327.t4 ProSitePatterns PS00723 Polyprenyl synthases signature 1. 85 99 -
8 g1327.t4 SFLD SFLDS00005 Isoprenoid Synthase Type I 32 247 2.3E-35
4 g1327.t4 SUPERFAMILY SSF48576 Terpenoid synthases 5 249 1.5E-63

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

## Warning: Removed 1 row(s) containing missing values (geom_path).

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