Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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_4 g16453 g16453.t1 TSS g16453.t1 9478377 9478377
chr_4 g16453 g16453.t1 isoform g16453.t1 9478416 9479208
chr_4 g16453 g16453.t1 exon g16453.t1.exon1 9478416 9478453
chr_4 g16453 g16453.t1 cds g16453.t1.CDS1 9478416 9478453
chr_4 g16453 g16453.t1 exon g16453.t1.exon2 9478506 9479208
chr_4 g16453 g16453.t1 cds g16453.t1.CDS2 9478506 9479208
chr_4 g16453 g16453.t1 TTS g16453.t1 9479230 9479230

Sequences

>g16453.t1 Gene=g16453 Length=741
ATGGAAAAGTGGCAAAATAAAATTGCAGTTGTAACTGGAGCTTCTTCTGGAATTGGTGAA
GCAATTGTTAAAGATTTAGCTTCACATGGATTGAAAGTTGTAGGATTAGCACGAAGAGTT
GAAAAAATTCCAACTTGTGATGGAAAAGTGACAGCAATAAAATGTGACGTAGCTAATCTT
GATTCAATAAAATCTGCTTTTAAAGAAATTGAAGAAAAATTTGGAAAAATCAATATTTTA
ATTAATAATGCTGGTGTTGGAATTTATGTGAAAGTCCTTGAAGAAGGCGAAGAAATAACA
AGAAAACTTAATGAGGTCATTGACATAAATTTTAAAGGTTTAGTTCATAGTACTCGTGAA
GCAGCAAAGCTTATGAAAAATTCAAATGAAAATGGAATTATCATCAATATTGGCTCAGTT
TTTGATTCAAATATTGCATTTCCTAATCCATCAAGTCTCTACCCAGCTACAAAATATGCA
GTTCGTGCATTTACTGAAATTGTGAGACAAGAATTTGTCATAAGTGAATGTGATAAAATT
AAAGTTTGTAACATCAGTCCAGGAATTGTTAAGACGAATATTGGACATGCAGGTGGAAGA
AAAAATGCTGATAATCATTATGATGCTGTGCCTCATTTAGTTGCAGAAGATATTTCTCAA
AGTGTTTTATATGTCTTAAGTACACCTGAAAATGTTAATGTTACACAAATTACTATTAAA
CCTGTTGGTGAAAAGTTTTAA

>g16453.t1 Gene=g16453 Length=246
MEKWQNKIAVVTGASSGIGEAIVKDLASHGLKVVGLARRVEKIPTCDGKVTAIKCDVANL
DSIKSAFKEIEEKFGKINILINNAGVGIYVKVLEEGEEITRKLNEVIDINFKGLVHSTRE
AAKLMKNSNENGIIINIGSVFDSNIAFPNPSSLYPATKYAVRAFTEIVRQEFVISECDKI
KVCNISPGIVKTNIGHAGGRKNADNHYDAVPHLVAEDISQSVLYVLSTPENVNVTQITIK
PVGEKF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g16453.t1 Gene3D G3DSA:3.40.50.720 - 1 245 0
2 g16453.t1 PANTHER PTHR43115 DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 1 246 0
7 g16453.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 8 25 0
4 g16453.t1 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 75 86 0
9 g16453.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 75 86 0
6 g16453.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 126 142 0
3 g16453.t1 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 132 140 0
5 g16453.t1 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 154 173 0
10 g16453.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 154 173 0
8 g16453.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 178 195 0
1 g16453.t1 Pfam PF00106 short chain dehydrogenase 7 196 0
11 g16453.t1 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 2 238 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

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