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_2 g5156 g5156.t4 isoform g5156.t4 7327604 7328703
chr_2 g5156 g5156.t4 exon g5156.t4.exon1 7327604 7327833
chr_2 g5156 g5156.t4 cds g5156.t4.CDS1 7327604 7327833
chr_2 g5156 g5156.t4 exon g5156.t4.exon2 7328016 7328385
chr_2 g5156 g5156.t4 cds g5156.t4.CDS2 7328016 7328385
chr_2 g5156 g5156.t4 exon g5156.t4.exon3 7328448 7328555
chr_2 g5156 g5156.t4 cds g5156.t4.CDS3 7328448 7328555
chr_2 g5156 g5156.t4 exon g5156.t4.exon4 7328617 7328703
chr_2 g5156 g5156.t4 cds g5156.t4.CDS4 7328617 7328703
chr_2 g5156 g5156.t4 TSS g5156.t4 7328803 7328803
chr_2 g5156 g5156.t4 TTS g5156.t4 NA NA

Sequences

>g5156.t4 Gene=g5156 Length=795
ATGGATGGTGTTGAGAATGAAATTCCAATTCCATGGCAAGAAAAACTTGATAATGGTGTA
AAAAGATGGGAAGGAAGAGTTGCAGTTGTGACAGGAGCAAGCAGTCCAATTGGCAGAGCT
ATTTGTGAAGATTTAGTAAAACATGGATTGATAGTTTGTGGATTAGCAACAAGATCAGGA
AAACATGAACTTGAAGATTTAGGCAAAAAACTCGAACGACAACAAGAAAAAGGAAAATTG
CTGGCTTTTGAATGTGACATCAAAGAAGAAGGTCATATACAACCTATTTTTCGGTACATT
GAAGATCACTACGACGGAATAGATTTACTTGTCAATAATGCAAATGTTATGTGTAAAGGT
CTAATTCTCGATGAAGACAACACACCGCTAATGCGAGACGTTATGGAAACAAATATTATT
GGTATGTGTATTGTCACTCGCGAGGCTGCAAGATTGATGAAAATGAGAAAAGAAGAACGC
AAAAATTTGGGTCATGTTGTCAACATTCTCTCAATCGTCGGACATAAGTTTGGACCTTCA
AATTCACGATCGAAGCCTATTAATGAAATATTTCACAGGCATGCAGCAACAGCAATCACA
GAATGTATTCGTCAAGAATTCCTTTTTCTTTATGAAAACGTAAAAATCACAGCGATCAGT
CCAGGTTTAGTGGAAGGTCAAGATACTGATATTCTCACAGAAGAAGAACGTGCACATGGA
AAAATGCCAGCATTAGAGCCAAAAGATGTTAGTGCTGCTGTATTGTATGCAATATCAGTA
AAAGATACAGTTCAA

>g5156.t4 Gene=g5156 Length=265
MDGVENEIPIPWQEKLDNGVKRWEGRVAVVTGASSPIGRAICEDLVKHGLIVCGLATRSG
KHELEDLGKKLERQQEKGKLLAFECDIKEEGHIQPIFRYIEDHYDGIDLLVNNANVMCKG
LILDEDNTPLMRDVMETNIIGMCIVTREAARLMKMRKEERKNLGHVVNILSIVGHKFGPS
NSRSKPINEIFHRHAATAITECIRQEFLFLYENVKITAISPGLVEGQDTDILTEEERAHG
KMPALEPKDVSAAVLYAISVKDTVQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g5156.t4 Gene3D G3DSA:3.40.50.720 - 23 264 0
2 g5156.t4 PANTHER PTHR43115 DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 22 265 0
4 g5156.t4 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 27 44 0
6 g5156.t4 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 105 116 0
3 g5156.t4 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 158 174 0
5 g5156.t4 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 212 229 0
1 g5156.t4 Pfam PF00106 short chain dehydrogenase 27 227 0
7 g5156.t4 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 21 260 0

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5156/g5156.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5156.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