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 g8019 g8019.t1 TTS g8019.t1 27928985 27928985
chr_2 g8019 g8019.t1 isoform g8019.t1 27929052 27929937
chr_2 g8019 g8019.t1 exon g8019.t1.exon1 27929052 27929538
chr_2 g8019 g8019.t1 cds g8019.t1.CDS1 27929052 27929538
chr_2 g8019 g8019.t1 exon g8019.t1.exon2 27929596 27929747
chr_2 g8019 g8019.t1 cds g8019.t1.CDS2 27929596 27929747
chr_2 g8019 g8019.t1 exon g8019.t1.exon3 27929806 27929937
chr_2 g8019 g8019.t1 cds g8019.t1.CDS3 27929806 27929937
chr_2 g8019 g8019.t1 TSS g8019.t1 27929951 27929951

Sequences

>g8019.t1 Gene=g8019 Length=771
ATGGAAAAGTGGAAGGGAAAAATTGCTGTTGTTACTGGTGCTAGTGCAGGAATTGGAATA
TCCATTGTTAAAAGTTTAGTTAGTTATGGTGTTCATGTTATTGGACTAGCACGACGAGTG
GAGAAAGTTGAGGAATTGGTAAATGAACTGCAAAATGCTGATGGAAAAGTTTATGCATAC
AAGTGTGATGTGGCGGATCAACAATCAGTAGCAGCAGCATTTCAATGGATGGAAGAGAAG
TTTGGTGGAGTTGACATATTAATAAATAATGCTGGCGTTTATAAATTTATGAAAATATTG
GACGATGGTGAAACCGTAAATGATGATTTGAAGCAAACAGTTGATGTGAATTTAATGGGC
GTTGTTTACTGCACACGTGCTGCCTTTGCGACAATGAAAAACCGAGAATTCTCGCACATT
ATTCATATGAATTCAATTGGGGGACATTTTGTTCCATTTCCAAGCGATTCTTCACCATTC
TATAATATTTATTGTGCATCAAAATATGGCATTACTGCCACAAATGAAGTTTTGAGACAA
GAACTTGCTCTCTCTGAATATAGTAAAAAGATTCGTGTCACATCTATTTCACCCGGAGAG
GTCAAAACTGAAATGGTTGCAGCTGCTGGCGGTGATGCTGAAAAGTATTACGAAACAATT
CCATTCTTGCTACCTGAAGATGTTGCAGAAAGTGTCATTTATGTGCTCTCAACACCAGCT
CGTGTCAATGTCACTGAAGTCATTATTAGACCAACGGGTGAAAGAATATAG

>g8019.t1 Gene=g8019 Length=256
MEKWKGKIAVVTGASAGIGISIVKSLVSYGVHVIGLARRVEKVEELVNELQNADGKVYAY
KCDVADQQSVAAAFQWMEEKFGGVDILINNAGVYKFMKILDDGETVNDDLKQTVDVNLMG
VVYCTRAAFATMKNREFSHIIHMNSIGGHFVPFPSDSSPFYNIYCASKYGITATNEVLRQ
ELALSEYSKKIRVTSISPGEVKTEMVAAAGGDAEKYYETIPFLLPEDVAESVIYVLSTPA
RVNVTEVIIRPTGERI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g8019.t1 Coils Coil Coil 33 56 -
13 g8019.t1 Gene3D G3DSA:3.40.50.720 - 2 256 3.6E-61
2 g8019.t1 PANTHER PTHR43115 DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 1 256 1.1E-91
8 g8019.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 8 25 6.5E-28
5 g8019.t1 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 82 93 2.8E-8
11 g8019.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 82 93 6.5E-28
9 g8019.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 132 148 6.5E-28
4 g8019.t1 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 138 146 2.8E-8
3 g8019.t1 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 164 183 2.8E-8
10 g8019.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 164 183 6.5E-28
6 g8019.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 189 206 6.5E-28
7 g8019.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 218 238 6.5E-28
1 g8019.t1 Pfam PF00106 short chain dehydrogenase 7 209 2.6E-47
12 g8019.t1 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 2 252 1.17E-61

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

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. There were no conditions that were differentially expressed