Gene loci information

Transcript annotation

  • This transcript has been annotated as 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 g514 g514.t4 TTS g514.t4 3857367 3857367
chr_3 g514 g514.t4 isoform g514.t4 3857463 3858366
chr_3 g514 g514.t4 exon g514.t4.exon1 3857463 3857658
chr_3 g514 g514.t4 cds g514.t4.CDS1 3857463 3857658
chr_3 g514 g514.t4 exon g514.t4.exon2 3857747 3858256
chr_3 g514 g514.t4 cds g514.t4.CDS2 3857747 3858256
chr_3 g514 g514.t4 exon g514.t4.exon3 3858317 3858366
chr_3 g514 g514.t4 cds g514.t4.CDS3 3858317 3858366
chr_3 g514 g514.t4 TSS g514.t4 3858387 3858387

Sequences

>g514.t4 Gene=g514 Length=756
ATGACAATTTCACGTTGGTCTGGTCGTATTGCTGTTGTGACTGGTGCAAGTGCTGGAATT
GGTGCTGCAACTGCAATTGAATTAGCTAAAAATGATTTAATTACAATTGGATTAGCAAGA
AGAGTCGAAAAAGTTGAAGAACTGAAGTCAAATTTACCAAATGATAAGCAAAGAAATCTT
CACGCCATAAAATGTGATGTTTCAATTGAAGCTGAAGTCATTCGTGCATTTGCCGAAATA
GAAAAAAGATTTGGTGGCGTTGATGTGTTGATTAACAATGCTGGCATAGTGCCACAAACT
TCATTAACAAATATAAACAATTCTGACAACGTTCGTCAAGTAATTGACACTAACGTCATG
GGAGTTGTTTTTTGTACACGCGAGGCTGTTAAGATGATGAGAGAGAGAAAATCTGAGGGT
CATATCATTCATATCAACAGTATTGCTGGTCATTATATGTCATATCACTCTGAATCCACA
ACTATGGGAATTTACTATGCCAGCAAATATGCAGTCACAGCTTTAGCTGAACAACATCGT
CATGAATTCATCAAAGAAAATCCAGGAGGTGTAAAGACAGAAATCATGAAAGCAAACCCA
GGAGCAATTCCGCTTGATATTATTGAGAAAATGATGGAATACGCTCCAATGCTTGAGTCA
AAAGATATTGCTGATGCTATAATTTATCTTCTTAGTACACCACCAAATGTTCTCATCACA
GAACTCACAATTCGTCCAATGAATGAAACTTTCTAA

>g514.t4 Gene=g514 Length=251
MTISRWSGRIAVVTGASAGIGAATAIELAKNDLITIGLARRVEKVEELKSNLPNDKQRNL
HAIKCDVSIEAEVIRAFAEIEKRFGGVDVLINNAGIVPQTSLTNINNSDNVRQVIDTNVM
GVVFCTREAVKMMRERKSEGHIIHINSIAGHYMSYHSESTTMGIYYASKYAVTALAEQHR
HEFIKENPGGVKTEIMKANPGAIPLDIIEKMMEYAPMLESKDIADAIIYLLSTPPNVLIT
ELTIRPMNETF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g514.t4 Gene3D G3DSA:3.40.50.720 - 2 250 2.5E-55
2 g514.t4 PANTHER PTHR43115 DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 4 251 5.0E-96
8 g514.t4 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 10 27 1.6E-22
4 g514.t4 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 85 96 1.1E-7
10 g514.t4 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 85 96 1.6E-22
9 g514.t4 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 134 150 1.6E-22
5 g514.t4 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 140 148 1.1E-7
3 g514.t4 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 165 184 1.1E-7
7 g514.t4 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 165 184 1.6E-22
6 g514.t4 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 213 233 1.6E-22
1 g514.t4 Pfam PF00106 short chain dehydrogenase 10 197 3.0E-43
14 g514.t4 Phobius SIGNAL_PEPTIDE Signal peptide region 1 25 -
15 g514.t4 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 9 -
16 g514.t4 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 10 20 -
17 g514.t4 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 21 25 -
13 g514.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 26 251 -
11 g514.t4 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 5 235 4.13E-52

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g514/g514.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g514.t4.fa.iupred3.txt does not exist

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