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_1 g14171 g14171.t4 TSS g14171.t4 35215865 35215865
chr_1 g14171 g14171.t4 isoform g14171.t4 35215910 35216738
chr_1 g14171 g14171.t4 exon g14171.t4.exon1 35215910 35215917
chr_1 g14171 g14171.t4 cds g14171.t4.CDS1 35215911 35215917
chr_1 g14171 g14171.t4 exon g14171.t4.exon2 35216179 35216738
chr_1 g14171 g14171.t4 cds g14171.t4.CDS2 35216179 35216738
chr_1 g14171 g14171.t4 TTS g14171.t4 35216778 35216778

Sequences

>g14171.t4 Gene=g14171 Length=568
ATGGAGAAACGAAATCAAAAGAGTTTTTAAAGAAATTGAAGAAAAATTTGGAATAATTCA
TATTTTGGTGAATAATGCAGGCGTATCGCTCTATAAAAATATTCTCGATCCATGTGACGA
AATTACAAGACGAATAAATCAAGTTATTGACACAAATTTTAAAGGTTTAGTTCACTGCAC
TCGCGAGGGAGTTCAATTAATCAAGAAATCAAATGAAAATGGGGTTGTAATAAATATTGG
ATCAATTTTAGACACAATAATTCCCTTTCCTAATCCATCGACAATTTACCCAGCAACAAA
ACATGCAGTTCGAGCATTCACTGAAATTGTTAGACAAGAATTAATTCTTACTGGCAATGA
AAAAATTAAGCTTTGCAATATCAGTCCTGGTGTAGTTAAGACAAACATTGCAAAAGCTTG
TGGAAGAGAAAATCCTGAAGAACACTACAATTCTTTACCCCATTTGGAATCTGAAGATAT
TTCACAAAGTGTAATTTATGTTCTAAGCACATCACACAATGTTAATGTCACTCAAATAAC
AATAAAACCAGTCGGTGAAAGATTTTAA

>g14171.t4 Gene=g14171 Length=188
WRNEIKRVFKEIEEKFGIIHILVNNAGVSLYKNILDPCDEITRRINQVIDTNFKGLVHCT
REGVQLIKKSNENGVVINIGSILDTIIPFPNPSTIYPATKHAVRAFTEIVRQELILTGNE
KIKLCNISPGVVKTNIAKACGRENPEEHYNSLPHLESEDISQSVIYVLSTSHNVNVTQIT
IKPVGERF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g14171.t4 Gene3D G3DSA:3.40.50.720 - 2 188 5.9E-32
2 g14171.t4 PANTHER PTHR43115 DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 4 188 9.3E-42
5 g14171.t4 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 17 28 3.5E-10
9 g14171.t4 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 17 28 2.1E-13
6 g14171.t4 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 68 84 2.1E-13
3 g14171.t4 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 74 82 3.5E-10
4 g14171.t4 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 96 115 3.5E-10
7 g14171.t4 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 96 115 2.1E-13
8 g14171.t4 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 120 137 2.1E-13
1 g14171.t4 Pfam PF00106 short chain dehydrogenase 2 140 8.3E-25
11 g14171.t4 ProSitePatterns PS00061 Short-chain dehydrogenases/reductases family signature. 83 111 -
10 g14171.t4 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 3 181 4.32E-27

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:0055114 NA NA
GO:0016491 oxidoreductase activity MF

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