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.t1 TSS g14171.t1 35215865 35215865
chr_1 g14171 g14171.t1 isoform g14171.t1 35215910 35216738
chr_1 g14171 g14171.t1 exon g14171.t1.exon1 35215910 35215953
chr_1 g14171 g14171.t1 cds g14171.t1.CDS1 35215910 35215953
chr_1 g14171 g14171.t1 exon g14171.t1.exon2 35216042 35216738
chr_1 g14171 g14171.t1 cds g14171.t1.CDS2 35216042 35216738
chr_1 g14171 g14171.t1 TTS g14171.t1 35216778 35216778

Sequences

>g14171.t1 Gene=g14171 Length=741
ATGGAGAAGTGGCAAAATAAAATTGCGGTTGTAACTGGAGCAAGTTCAGGCATTGGTGAG
GCAATTGTTAAAAGTTTAGCCTCATATAGATTGCAAGTTATAGGATTAGCAAGAAAAGTG
GAAAAAATTCCAAGTTGTGAAGGAAGAGTGACAGCAATTAAATGCGATATTAGTGATTTA
GACGAAATCAAAAGAGTTTTTAAAGAAATTGAAGAAAAATTTGGAATAATTCATATTTTG
GTGAATAATGCAGGCGTATCGCTCTATAAAAATATTCTCGATCCATGTGACGAAATTACA
AGACGAATAAATCAAGTTATTGACACAAATTTTAAAGGTTTAGTTCACTGCACTCGCGAG
GGAGTTCAATTAATCAAGAAATCAAATGAAAATGGGGTTGTAATAAATATTGGATCAATT
TTAGACACAATAATTCCCTTTCCTAATCCATCGACAATTTACCCAGCAACAAAACATGCA
GTTCGAGCATTCACTGAAATTGTTAGACAAGAATTAATTCTTACTGGCAATGAAAAAATT
AAGCTTTGCAATATCAGTCCTGGTGTAGTTAAGACAAACATTGCAAAAGCTTGTGGAAGA
GAAAATCCTGAAGAACACTACAATTCTTTACCCCATTTGGAATCTGAAGATATTTCACAA
AGTGTAATTTATGTTCTAAGCACATCACACAATGTTAATGTCACTCAAATAACAATAAAA
CCAGTCGGTGAAAGATTTTAA

>g14171.t1 Gene=g14171 Length=246
MEKWQNKIAVVTGASSGIGEAIVKSLASYRLQVIGLARKVEKIPSCEGRVTAIKCDISDL
DEIKRVFKEIEEKFGIIHILVNNAGVSLYKNILDPCDEITRRINQVIDTNFKGLVHCTRE
GVQLIKKSNENGVVINIGSILDTIIPFPNPSTIYPATKHAVRAFTEIVRQELILTGNEKI
KLCNISPGVVKTNIAKACGRENPEEHYNSLPHLESEDISQSVIYVLSTSHNVNVTQITIK
PVGERF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g14171.t1 Gene3D G3DSA:3.40.50.720 - 2 245 1.7E-50
2 g14171.t1 PANTHER PTHR43115 DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 1 246 1.4E-67
3 g14171.t1 PANTHER PTHR43115:SF4 DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 1 246 1.4E-67
8 g14171.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 8 25 5.3E-23
5 g14171.t1 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 75 86 6.4E-10
10 g14171.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 75 86 5.3E-23
7 g14171.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 126 142 5.3E-23
4 g14171.t1 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 132 140 6.4E-10
6 g14171.t1 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 154 173 6.4E-10
11 g14171.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 154 173 5.3E-23
9 g14171.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 178 195 5.3E-23
1 g14171.t1 Pfam PF00106 short chain dehydrogenase 7 198 5.0E-39
13 g14171.t1 ProSitePatterns PS00061 Short-chain dehydrogenases/reductases family signature. 141 169 -
12 g14171.t1 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 2 238 1.08E-45

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

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