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_4 g14436 g14436.t2 TTS g14436.t2 519453 519453
chr_4 g14436 g14436.t2 isoform g14436.t2 519455 520424
chr_4 g14436 g14436.t2 exon g14436.t2.exon1 519455 520424
chr_4 g14436 g14436.t2 cds g14436.t2.CDS1 519757 520173
chr_4 g14436 g14436.t2 TSS g14436.t2 520649 520649

Sequences

>g14436.t2 Gene=g14436 Length=970
TTGTCACAAGTCTCATCAGTCTTAATGCTAAAGTTATTGGTATTTCAAGATCAGAAACTC
CACTAGAAGAACTCAAAAATGAATTAAATTCACCAAACTTTACTGCAATACAACTTGATC
TTTCAGACTGGTCAAAAACTCGATCAATTTTGAAATCTCTTGATGCAAAACTTGATGGAA
TTGTCAATAATGCTGGAATTGCTTTAATCAAACCATTCAATAAGCTTACTGAAGAAGATT
ATGATTCCCAAATGAATGTCAATCTTAAAGCTTGCTTTAATGTCATACAATCACTTTTAG
AGAAATTAAATGTAAATTCTAGCATTGTTAATGTTTCTTCTGTAGCTTCACTTAAAGCCA
TTCAAGATCACACAATTTATTGCATGTCCAAAGCAGGCCTAGATGCAATGACAAGAAATT
TAGCTTTAGAACTCGCACCAAAGAAAATTCGAGTAAACTCAATTAATCCAACTGTAATAT
TGACAAGAATGGGAAGAGAAAATTGGAGTGATCCAATAAAAGCTGGATCATTATTATCAA
GAATTCCACTGGGAAGATTTGGGGAAGTTAAAGAAGTTGTTGATCCAGTTATTTGGCTTT
TGAGTGATGAATCAAGTTATATTAATGGCCATTGTTTACCCATTGAAGGCGGTTTAATGA
GTGCATGAAAAATTTATGAGATTGGTTTAACTAAAAATTTTAAAAAACATGAAATGAATA
TTTTGAATCGAAATGATTTATTAAAGAAATATTTGTAAAAAATTTTCAAGTTTCAAAAGA
TAGAAACAGCTGTTTACGAATAGTTGATTGAAAAAATATACTTTATTTTCATCCCTTTAA
ATTTTTAAAAAAAAATTATCTTTACCGGTTTTTCAAAATATAACATTATTAATAAAATTT
TTAAATTTATTTCAAAAACAATTTACATAATAAAAATTCGAAATAAAAGTTTCATGTTCA
TATTTTAAAA

>g14436.t2 Gene=g14436 Length=138
MNVNLKACFNVIQSLLEKLNVNSSIVNVSSVASLKAIQDHTIYCMSKAGLDAMTRNLALE
LAPKKIRVNSINPTVILTRMGRENWSDPIKAGSLLSRIPLGRFGEVKEVVDPVIWLLSDE
SSYINGHCLPIEGGLMSA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g14436.t2 Gene3D G3DSA:3.40.50.720 - 1 137 1.5E-44
2 g14436.t2 PANTHER PTHR44252 D-ERYTHRULOSE REDUCTASE 1 137 5.8E-56
3 g14436.t2 PANTHER PTHR44252:SF3 D-ERYTHRULOSE REDUCTASE 1 137 5.8E-56
7 g14436.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 17 33 1.0E-20
4 g14436.t2 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 23 31 2.1E-5
5 g14436.t2 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 43 62 2.1E-5
8 g14436.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 43 62 1.0E-20
6 g14436.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 64 81 1.0E-20
9 g14436.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 99 119 1.0E-20
1 g14436.t2 Pfam PF13561 Enoyl-(Acyl carrier protein) reductase 1 135 6.0E-37
11 g14436.t2 ProSitePatterns PS00061 Short-chain dehydrogenases/reductases family signature. 30 58 -
10 g14436.t2 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 1 136 2.02E-42

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