Gene loci information

Transcript annotation

  • This transcript has been annotated as Farnesol dehydrogenase.

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 g8020 g8020.t2 TTS g8020.t2 27931138 27931138
chr_2 g8020 g8020.t2 isoform g8020.t2 27931225 27932100
chr_2 g8020 g8020.t2 exon g8020.t2.exon1 27931225 27931392
chr_2 g8020 g8020.t2 cds g8020.t2.CDS1 27931225 27931392
chr_2 g8020 g8020.t2 exon g8020.t2.exon2 27931455 27931752
chr_2 g8020 g8020.t2 cds g8020.t2.CDS2 27931455 27931752
chr_2 g8020 g8020.t2 exon g8020.t2.exon3 27931817 27932100
chr_2 g8020 g8020.t2 cds g8020.t2.CDS3 27931817 27932100
chr_2 g8020 g8020.t2 TSS g8020.t2 27932107 27932107

Sequences

>g8020.t2 Gene=g8020 Length=750
ATGGAGAAGTGGCGAGGAAAAGTTGCAATTGTCACCGGAGCTTCTTCCGGCATAGGTGCT
GCAATTGTTAGAGATTTAGCAAAGAATGGAATCACAGTGATTGGACTAGCACGACGAGTT
CAGAAAATTAGAGAACAAACTAAAGATTTCCCTGAAAATTATGCAAACGTTCATGCATTT
TATTGTGATGTGTCGAAAATTGAAAGCATAAAAGAAGCATTTAAATTGATTGAGGAGAGA
TTTGGAGTAATTAATATTCTGGTAAATAATGCTGGAATTGGAAAAAAAACTTCAATTTTA
GTCGACGATGAAGAAACAGATGGAAAAATTTCCCAAGTGATTGACACAAATTTCACTGGA
TTGGTGCATGTCACACGTCATGCTTATATGCTAATGAAAAAATCTGAAGATTACGGTATG
GTTGTCAACATAAATTCTGTCGCAGGTCACAAAGTTTCATTTCCATATTATGGTGTGCCT
GAAACAAATGTCTACAATGGATCTAAATTTGCTGTTACTGCAACTACTGAATATTTGAGG
CACGAATTGATTCAAATGAAAGATAAGAAAGTTCGAGTTTCATCGGTTAGTCCTGGAGTT
GTTGATACTTCTTTCTTCCATTCATCGCAAATGCTTCCTGATAATATTGAAATGAGAGAT
GTAGCACCAGTATTAAATCCATCTGACATAGCAGATGCAGTAATGTATTTACTTCAAGTT
CCATATCATGTGAATATTACAGAAATGACA

>g8020.t2 Gene=g8020 Length=250
MEKWRGKVAIVTGASSGIGAAIVRDLAKNGITVIGLARRVQKIREQTKDFPENYANVHAF
YCDVSKIESIKEAFKLIEERFGVINILVNNAGIGKKTSILVDDEETDGKISQVIDTNFTG
LVHVTRHAYMLMKKSEDYGMVVNINSVAGHKVSFPYYGVPETNVYNGSKFAVTATTEYLR
HELIQMKDKKVRVSSVSPGVVDTSFFHSSQMLPDNIEMRDVAPVLNPSDIADAVMYLLQV
PYHVNITEMT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g8020.t2 Gene3D G3DSA:3.40.50.720 - 1 249 0
2 g8020.t2 PANTHER PTHR43115 DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 1 249 0
3 g8020.t2 PANTHER PTHR43115:SF4 DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 1 249 0
10 g8020.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 8 25 0
6 g8020.t2 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 82 93 0
12 g8020.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 82 93 0
9 g8020.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 133 149 0
5 g8020.t2 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 139 147 0
4 g8020.t2 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 165 184 0
8 g8020.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 165 184 0
7 g8020.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 189 206 0
11 g8020.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 220 240 0
1 g8020.t2 Pfam PF00106 short chain dehydrogenase 7 208 0
13 g8020.t2 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 2 239 0

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

## [1] "No matching GO terms"

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. There were no conditions that were differentially expressed