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 g519 g519.t2 TSS g519.t2 3869009 3869009
chr_3 g519 g519.t2 isoform g519.t2 3869122 3870018
chr_3 g519 g519.t2 exon g519.t2.exon1 3869122 3869171
chr_3 g519 g519.t2 cds g519.t2.CDS1 3869136 3869171
chr_3 g519 g519.t2 exon g519.t2.exon2 3869243 3869764
chr_3 g519 g519.t2 cds g519.t2.CDS2 3869243 3869764
chr_3 g519 g519.t2 exon g519.t2.exon3 3869818 3870018
chr_3 g519 g519.t2 cds g519.t2.CDS3 3869818 3870018
chr_3 g519 g519.t2 TTS g519.t2 3870053 3870053

Sequences

>g519.t2 Gene=g519 Length=773
ATGACAATTTCACGATGGTCTGGTCGTGTTGCGGTTGTGACGGGAGCAAGATTGGTGCTG
CAACTGCAATAGAATTAGCTAAAAATGGTTTGATCACAATCGGATTAGCGAGAAGAGTCG
AAAAAATTGAAGAACTTCGATCACAATTGACATCAGATCAACAGAAAAATTTTCATGCCA
TGAAATGTGATGTTTCAGTTGAAGCTGAAATTGTTAGAACTTTTTCTGACATTGTTAAGA
AATTTGGTGGAATTGATGTCTTAATTAATAACGCTGCTTTTATGACGCTAACAAAATTGA
TTGATTTGGAAAATTCAAGTGAATTTCAAAAAGTTTTCGAAGTTAATGTATTCGGTGTCA
TAAATTGTACAAGAGAATTTGTGAAGTCAATTCGTGAAAGAAATGCTGAAGGTCATGTAA
TTCATATTAATAGCATCCTTGGTCATGTTATGCCTTTTTATCTTGAACATCCTACTTTTG
GAGTCTATAGTGCAAGTAAATTTGCAGTCACAGCTTTGGCAGAGCAACATCGACAAGAAT
TTATTAAAGAAAAACTGAACATTAAAGTCACATCTTTAAGTCCAGGATTTGTTGCAACCG
AAATGCTAGGGAATATTATGAAATTGTCTAAAGAACAAATTGAAAAATACTTAGAAAAAT
ATCCACATTTGCTGCCTAAAGATATTGCTGATGCCATTATTTATTTATTGAGCACACCAC
AAAATGTTTTAGTTACAGAGCTCACAATTAGACCAATGAATGAAAGTTCTTAA

>g519.t2 Gene=g519 Length=252
MVWSCCGCDGSKIGAATAIELAKNGLITIGLARRVEKIEELRSQLTSDQQKNFHAMKCDV
SVEAEIVRTFSDIVKKFGGIDVLINNAAFMTLTKLIDLENSSEFQKVFEVNVFGVINCTR
EFVKSIRERNAEGHVIHINSILGHVMPFYLEHPTFGVYSASKFAVTALAEQHRQEFIKEK
LNIKVTSLSPGFVATEMLGNIMKLSKEQIEKYLEKYPHLLPKDIADAIIYLLSTPQNVLV
TELTIRPMNESS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g519.t2 Gene3D G3DSA:3.40.50.720 - 6 250 3.7E-55
2 g519.t2 PANTHER PTHR43115 DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 13 250 2.3E-83
3 g519.t2 PANTHER PTHR43115:SF4 DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 13 250 2.3E-83
5 g519.t2 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 78 89 4.4E-7
9 g519.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 78 89 1.7E-16
11 g519.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 127 143 1.7E-16
6 g519.t2 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 133 141 4.4E-7
4 g519.t2 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 158 177 4.4E-7
8 g519.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 158 177 1.7E-16
10 g519.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 181 198 1.7E-16
7 g519.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 214 234 1.7E-16
1 g519.t2 Pfam PF00106 short chain dehydrogenase 12 201 5.9E-41
13 g519.t2 ProSitePatterns PS00061 Short-chain dehydrogenases/reductases family signature. 145 173 -
12 g519.t2 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 10 239 2.45E-50

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g519/g519.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g519.t2.fa.iupred3.txt does not exist

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.

Raw TPM values