Gene loci information

Transcript annotation

  • This transcript has been annotated as Decaprenyl-diphosphate synthase subunit 2.

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_2 g8536 g8536.t1 isoform g8536.t1 31149955 31151334
chr_2 g8536 g8536.t1 exon g8536.t1.exon1 31149955 31150232
chr_2 g8536 g8536.t1 cds g8536.t1.CDS1 31149955 31150232
chr_2 g8536 g8536.t1 exon g8536.t1.exon2 31150292 31150621
chr_2 g8536 g8536.t1 cds g8536.t1.CDS2 31150292 31150621
chr_2 g8536 g8536.t1 exon g8536.t1.exon3 31150674 31151334
chr_2 g8536 g8536.t1 cds g8536.t1.CDS3 31150674 31151334
chr_2 g8536 g8536.t1 TSS g8536.t1 NA NA
chr_2 g8536 g8536.t1 TTS g8536.t1 NA NA

Sequences

>g8536.t1 Gene=g8536 Length=1269
ATGTTTCTCATTGTTAAAAATTTCAGTAAAAATTCGATAAAATTAAATTCAATTCGAAGA
ATAACTTCAAGTTCATTATCAAAAGGAGTTGCAAACACAAATCAACAAAAACAGCATCAG
CATGACTGGAATAGAGCTGTTAGTGAAGCTGAGAAAATTGTTGGCTATCCAAATTCATTT
TTTGGTCTTCGATGTTTGTTAAGTGATGAAATCGGGAATATTGCATTACATTTAAGAAAA
CTCGTTGGCAGTAATCATCCATTATTAAAAACCGCCAAAAATTTAATTTATGACAGAAAG
TCAAATATGCAAGCATGGGGATTGATAGTTCTACTTTTATCAAAAGCAGCTGGACAATCA
AATGATTTGTTAGAATTAGAACAGGATAAAAGTGCAGGAGTTTTACATTCACAAAGAACA
TTAGCGGAAATAACAGAAATGATTCGAACTTCACATTTGGTTCATGAAGGAATGGTTAAT
TTGCAAAAGCTTAAAAAATCTGGAAATGAATTGGCATCTGATTCTGAGCTCATTTTTGGC
AATAAAATTGCCCTTTTGGGTGGTGATTATTTACTTGGGACAGCTTGCTTAAAACTTGCA
GAATTGAGAAATCAAGAAGTGGGGGAATTGATTTCATTGGCTCTACGAGATCTTACGGAA
TCAAATTTTATCGGTGATAGAGATGATGAAAATGTTGCCCTTCCATCAGATCCAAAGTGC
AAAATTCACATTGAAGATGAAAGTCCGTTAGAACATTTTGAAAGTACAAAAGATATTGAT
ATGAGTCTTATTTTGGGACATCCAGAAAGAGAATGGTCATTTCGTCATACTCTTGCATCA
GGATCACTTTTAGGCAAGAGTTGTCAAGGAACATTGAAGCTTGCAGAACAATCGGAAGAA
CTTCAAAGACATGGATATTTATTTGGAAAGCACTTGGCTCTTGCATGGCAAGCGAGTATG
GATTTAGAGCCATTTAGAATGCAAGAATTACCTTATAATACTTCATTTAGTCTCATAAGT
GCTCCAGTTCTCTTTCAACTTGACCATGATCCATCATTATATGAAGAAATCAAAAAAGGA
CGAAAATCTGTTGAAGAAATCAATTACAGAAAAATTCATGAAGCTGTCTTAAGTGGTCCA
GGAATTGAACAAACCAAAGAATTGTTAATCAAACATGGACAAGGTGCATTAGATGAGCTT
GACTATTTTCCTGATTGTGAATCTAAAAGCGCTCTACAAAATATTATTTTAGCTGTATGT
TGGTTTTAA

>g8536.t1 Gene=g8536 Length=422
MFLIVKNFSKNSIKLNSIRRITSSSLSKGVANTNQQKQHQHDWNRAVSEAEKIVGYPNSF
FGLRCLLSDEIGNIALHLRKLVGSNHPLLKTAKNLIYDRKSNMQAWGLIVLLLSKAAGQS
NDLLELEQDKSAGVLHSQRTLAEITEMIRTSHLVHEGMVNLQKLKKSGNELASDSELIFG
NKIALLGGDYLLGTACLKLAELRNQEVGELISLALRDLTESNFIGDRDDENVALPSDPKC
KIHIEDESPLEHFESTKDIDMSLILGHPEREWSFRHTLASGSLLGKSCQGTLKLAEQSEE
LQRHGYLFGKHLALAWQASMDLEPFRMQELPYNTSFSLISAPVLFQLDHDPSLYEEIKKG
RKSVEEINYRKIHEAVLSGPGIEQTKELLIKHGQGALDELDYFPDCESKSALQNIILAVC
WF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g8536.t1 Gene3D G3DSA:1.10.600.10 Farnesyl Diphosphate Synthase 61 420 0e+00
2 g8536.t1 PANTHER PTHR12001:SF55 DECAPRENYL-DIPHOSPHATE SYNTHASE SUBUNIT 2 22 417 0e+00
3 g8536.t1 PANTHER PTHR12001 GERANYLGERANYL PYROPHOSPHATE SYNTHASE 22 417 0e+00
1 g8536.t1 Pfam PF00348 Polyprenyl synthetase 107 317 5e-07
4 g8536.t1 SUPERFAMILY SSF48576 Terpenoid synthases 52 418 0e+00

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