Gene loci information

Transcript annotation

  • This transcript has been annotated as 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_4 g14436 g14436.t1 TTS g14436.t1 519453 519453
chr_4 g14436 g14436.t1 isoform g14436.t1 519757 520538
chr_4 g14436 g14436.t1 exon g14436.t1.exon1 519757 520439
chr_4 g14436 g14436.t1 cds g14436.t1.CDS1 519757 520439
chr_4 g14436 g14436.t1 exon g14436.t1.exon2 520490 520538
chr_4 g14436 g14436.t1 cds g14436.t1.CDS2 520490 520538
chr_4 g14436 g14436.t1 TSS g14436.t1 520649 520649

Sequences

>g14436.t1 Gene=g14436 Length=732
ATGTCATCATTGAAAGGAAAAACAATTTTAGTCACTGGTGCTGGACAAGGAATTGGTCGT
GAAATTGTCACAAGTCTCATCAGTCTTAATGCTAAAGTTATTGGTATTTCAAGATCAGAA
ACTCCACTAGAAGAACTCAAAAATGAATTAAATTCACCAAACTTTACTGCAATACAACTT
GATCTTTCAGACTGGTCAAAAACTCGATCAATTTTGAAATCTCTTGATGCAAAACTTGAT
GGAATTGTCAATAATGCTGGAATTGCTTTAATCAAACCATTCAATAAGCTTACTGAAGAA
GATTATGATTCCCAAATGAATGTCAATCTTAAAGCTTGCTTTAATGTCATACAATCACTT
TTAGAGAAATTAAATGTAAATTCTAGCATTGTTAATGTTTCTTCTGTAGCTTCACTTAAA
GCCATTCAAGATCACACAATTTATTGCATGTCCAAAGCAGGCCTAGATGCAATGACAAGA
AATTTAGCTTTAGAACTCGCACCAAAGAAAATTCGAGTAAACTCAATTAATCCAACTGTA
ATATTGACAAGAATGGGAAGAGAAAATTGGAGTGATCCAATAAAAGCTGGATCATTATTA
TCAAGAATTCCACTGGGAAGATTTGGGGAAGTTAAAGAAGTTGTTGATCCAGTTATTTGG
CTTTTGAGTGATGAATCAAGTTATATTAATGGCCATTGTTTACCCATTGAAGGCGGTTTA
ATGAGTGCATGA

>g14436.t1 Gene=g14436 Length=243
MSSLKGKTILVTGAGQGIGREIVTSLISLNAKVIGISRSETPLEELKNELNSPNFTAIQL
DLSDWSKTRSILKSLDAKLDGIVNNAGIALIKPFNKLTEEDYDSQMNVNLKACFNVIQSL
LEKLNVNSSIVNVSSVASLKAIQDHTIYCMSKAGLDAMTRNLALELAPKKIRVNSINPTV
ILTRMGRENWSDPIKAGSLLSRIPLGRFGEVKEVVDPVIWLLSDESSYINGHCLPIEGGL
MSA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g14436.t1 Gene3D G3DSA:3.40.50.720 - 1 242 1.6E-76
2 g14436.t1 PANTHER PTHR44252 D-ERYTHRULOSE REDUCTASE 3 242 3.5E-91
3 g14436.t1 PANTHER PTHR44252:SF3 D-ERYTHRULOSE REDUCTASE 3 242 3.5E-91
9 g14436.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 8 25 2.4E-33
4 g14436.t1 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 77 88 1.7E-10
7 g14436.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 77 88 2.4E-33
8 g14436.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 122 138 2.4E-33
5 g14436.t1 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 128 136 1.7E-10
6 g14436.t1 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 148 167 1.7E-10
12 g14436.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 148 167 2.4E-33
11 g14436.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 169 186 2.4E-33
10 g14436.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 204 224 2.4E-33
1 g14436.t1 Pfam PF13561 Enoyl-(Acyl carrier protein) reductase 13 240 5.2E-53
14 g14436.t1 ProSitePatterns PS00061 Short-chain dehydrogenases/reductases family signature. 135 163 -
13 g14436.t1 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 5 241 1.19E-71

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

Pathway

  • This transcript belongs to the following pathways

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