Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative L-xylulose reductase.

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 g7622 g7622.t3 TSS g7622.t3 24976537 24976537
chr_2 g7622 g7622.t3 isoform g7622.t3 24976580 24977338
chr_2 g7622 g7622.t3 exon g7622.t3.exon1 24976580 24977213
chr_2 g7622 g7622.t3 cds g7622.t3.CDS1 24976580 24977213
chr_2 g7622 g7622.t3 exon g7622.t3.exon2 24977301 24977338
chr_2 g7622 g7622.t3 cds g7622.t3.CDS2 24977301 24977338
chr_2 g7622 g7622.t3 TTS g7622.t3 24977415 24977415

Sequences

>g7622.t3 Gene=g7622 Length=672
ATGGATTTTACTGACAAAGTTATTATCATCACTGGAGCTTCTTCCGGAATTGGACAAGGA
GCTGCGTTATATCTTTCAAAACTCGGCGCTAAATTAGTTTTGACAGGTCGTAATGAAAGT
AATTTGAAAGAGACAGCTAAGAATTGTGTGGGTGAAACAATTACCGTCATTGGTGATGTT
AATGATGAAGCGCATCGAAAGCAAATTATTGATGAGACTATCAGCAAATATGGCAAAATA
AATGTTCTTGTCAATAATTCAGGACGTGGATTAGCGGGCGATGCTGAGAGTACAAAATTA
GAAGATTTTGATTTAATTATGAATACTAATGTTCGATCGGTGTTTCATCTTACACAACTT
GCTATTCCTCATTTGATTAAAACTGAAGGAAATATAGTAAATATCTCGTCGGTCGCAGGT
CTTCGAGCTTTTGCAAATGCTTCTGTATATTGCATGAGCAAAGCGGCAATTGATCAATTC
ACAAGATGTCTCGCTCTTGATTTGGCGCCGAAAAAAGTTAGATGTAATGCAGTAAATCCA
GCAGTTATTGTAACTAATTTTCATCGTGCAGTAGGAATGGATGAAGAGGCTTACAAAGCA
TTTCTTGAACATTGTAAAACAACACATCCATTAGCAGTTGATGGAGGCAAAGCAGTATTA
TGCCCACGTTAA

>g7622.t3 Gene=g7622 Length=223
MDFTDKVIIITGASSGIGQGAALYLSKLGAKLVLTGRNESNLKETAKNCVGETITVIGDV
NDEAHRKQIIDETISKYGKINVLVNNSGRGLAGDAESTKLEDFDLIMNTNVRSVFHLTQL
AIPHLIKTEGNIVNISSVAGLRAFANASVYCMSKAAIDQFTRCLALDLAPKKVRCNAVNP
AVIVTNFHRAVGMDEEAYKAFLEHCKTTHPLAVDGGKAVLCPR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g7622.t3 Gene3D G3DSA:3.40.50.720 - 1 214 4.6E-66
2 g7622.t3 PANTHER PTHR43975 ZGC:101858 1 212 1.3E-84
10 g7622.t3 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 7 24 3.9E-27
4 g7622.t3 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 78 89 9.4E-12
6 g7622.t3 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 78 89 3.9E-27
8 g7622.t3 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 124 140 3.9E-27
3 g7622.t3 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 130 138 9.4E-12
5 g7622.t3 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 150 169 9.4E-12
7 g7622.t3 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 150 169 3.9E-27
9 g7622.t3 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 171 188 3.9E-27
1 g7622.t3 Pfam PF00106 short chain dehydrogenase 6 191 1.2E-52
13 g7622.t3 ProSitePatterns PS00061 Short-chain dehydrogenases/reductases family signature. 137 165 -
12 g7622.t3 SMART SM00822 This enzymatic domain is part of bacterial polyketide synthases and catalyses the first step in the reductive modification of the beta-carbonyl centres in the growing polyketide chain. It uses NADPH to reduce the keto group to a hydroxy group. 6 183 0.0057
11 g7622.t3 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 5 216 8.39E-65

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

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