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_3 g1902 g1902.t1 TTS g1902.t1 13775495 13775495
chr_3 g1902 g1902.t1 isoform g1902.t1 13775614 13776384
chr_3 g1902 g1902.t1 exon g1902.t1.exon1 13775614 13776384
chr_3 g1902 g1902.t1 cds g1902.t1.CDS1 13775614 13776384
chr_3 g1902 g1902.t1 TSS g1902.t1 13776391 13776391

Sequences

>g1902.t1 Gene=g1902 Length=771
ATGGACAAGTGGAAGGGAAAGACAGCGATTGTAACCGGAGCGAGCTCGGGGATTGGAAAA
GCTGTTTCACTTGAGCTGCTTAACCATGGAATGACCGTAATCAACCTAGATCGTAACGTT
GATGAAACGAGTGTCAAGGAGTTTGAGAAAATTGCTAAACAAAAAGGAGATGGCGAGTAC
TTCGCTCGCAAATGTGAAATAACTGATATGAAAGCTCTCAAGGAAACCTTTCAATGGATT
GAAGAAAATTTCTCGAATGTAAGAGTTCATGTAAATTGTGCTGGTGTTGCTCACAATCTC
AATCTATTAAGCGAGCAAGATGATGCAACTGAGAGAATAAATAACACAATTGATGTAAAT
TTTAAGGCAGCAGTGAATGTAACACGTGAAGCATTTCGGTTGATTAAAAAGTCAGAAGAT
TATGGAATGATTATCAACGTTGCTTCACTTTTTGGACACATTATTCCATATCCCATTGTT
GGAAATGTTTATGCAGCCACAAAATTTGCTATGAGAGCTTTCTCGGAAATAGTAAGACAG
GAGTTAGTAGCAAGTGGATGTGAAAAAATTAGAGTTTCAAATGTTTCACCAGGGACGATT
AAAACAAATGTTCGAGTGACAGGAGGTTGGGATAACATGGAAGAATTTTATGAGCAACGA
CCATTCTTAGAACCAAAAGAAATTGGTGATGCAATCATTTACTTACTTAGTACTCCATAT
AATGTAAATGTTACTGAATTAACTATAAGACCTGTGGGAGAAAAATTCTAA

>g1902.t1 Gene=g1902 Length=256
MDKWKGKTAIVTGASSGIGKAVSLELLNHGMTVINLDRNVDETSVKEFEKIAKQKGDGEY
FARKCEITDMKALKETFQWIEENFSNVRVHVNCAGVAHNLNLLSEQDDATERINNTIDVN
FKAAVNVTREAFRLIKKSEDYGMIINVASLFGHIIPYPIVGNVYAATKFAMRAFSEIVRQ
ELVASGCEKIRVSNVSPGTIKTNVRVTGGWDNMEEFYEQRPFLEPKEIGDAIIYLLSTPY
NVNVTELTIRPVGEKF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g1902.t1 Gene3D G3DSA:3.40.50.720 - 1 253 5.5E-49
2 g1902.t1 PANTHER PTHR43115 DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 1 256 5.0E-59
7 g1902.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 8 25 8.1E-24
3 g1902.t1 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 85 96 2.3E-6
9 g1902.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 85 96 8.1E-24
8 g1902.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 136 152 8.1E-24
5 g1902.t1 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 142 150 2.3E-6
4 g1902.t1 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 164 183 2.3E-6
10 g1902.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 164 183 8.1E-24
11 g1902.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 188 205 8.1E-24
6 g1902.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 218 238 8.1E-24
1 g1902.t1 Pfam PF00106 short chain dehydrogenase 7 205 3.7E-39
13 g1902.t1 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 2 247 1.71E-48
12 g1902.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 143 165 -

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