Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 3-oxoacyl-[acyl-carrier-protein] reductase FabG.

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_1 g13463 g13463.t6 TTS g13463.t6 30324843 30324843
chr_1 g13463 g13463.t6 isoform g13463.t6 30325076 30325774
chr_1 g13463 g13463.t6 exon g13463.t6.exon1 30325076 30325433
chr_1 g13463 g13463.t6 cds g13463.t6.CDS1 30325078 30325433
chr_1 g13463 g13463.t6 exon g13463.t6.exon2 30325492 30325774
chr_1 g13463 g13463.t6 cds g13463.t6.CDS2 30325492 30325774
chr_1 g13463 g13463.t6 TSS g13463.t6 30325862 30325862

Sequences

>g13463.t6 Gene=g13463 Length=641
ATGGAGTTTGAAGGAAAAGTTGTGATTATAACCGGAGCATCAAGTGGAATTGGGGCTCAA
ACTGCAAAGGATTTTTCAAAACTAAATGCAAATGTTGTTCTCGTAGGACGAAATGCAGAA
AATTTAAAGGCGATCGCTGCTGAGTGTACTGCAGCAGATAAAACGCTTATCGTGCAGGCT
GACGTTAATTTGGACGATGATTGTAAAAAGATTATCAATGAAACAATTAATAAGTGGGGC
AGAATTGATGTACTTGTTAATAGTGCTGGAATAATTGAAACAGGTAGCATCGAAAATACA
TCAATTGAGCAGTATGATCGAGTCATGAATACAAATATGAGATCTATTTACTTGCTCACA
ATGCTTGCGGTGCCTTATTTGGTTGCTACACAGGGAAATATCGTCAATGTATCGAGCGTA
AATGGAATTCGAAGCTTCGCTGGCGTGCTCGCATATAATTTGTCAAAAGCGTGTGTCGAT
CAATTTACAAGATGCACTGCACTTGAACTAGCTGCTAAAAATGTTCGTGTCAATTCAGTA
AATCCAGGTGTTATTATCACAAATATCCATAAAAGAGGAGGAATGAATGATGAAACTTAT
GCTGCATTTTTAGAAAGATCTAAAACTACGCATCCATTAGG

>g13463.t6 Gene=g13463 Length=213
MEFEGKVVIITGASSGIGAQTAKDFSKLNANVVLVGRNAENLKAIAAECTAADKTLIVQA
DVNLDDDCKKIINETINKWGRIDVLVNSAGIIETGSIENTSIEQYDRVMNTNMRSIYLLT
MLAVPYLVATQGNIVNVSSVNGIRSFAGVLAYNLSKACVDQFTRCTALELAAKNVRVNSV
NPGVIITNIHKRGGMNDETYAAFLERSKTTHPL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g13463.t6 Gene3D G3DSA:3.40.50.720 - 1 211 0.00000
2 g13463.t6 PANTHER PTHR43975 ZGC:101858 1 213 0.00000
10 g13463.t6 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 7 24 0.00000
3 g13463.t6 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 80 91 0.00000
7 g13463.t6 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 80 91 0.00000
6 g13463.t6 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 126 142 0.00000
4 g13463.t6 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 132 140 0.00000
5 g13463.t6 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 152 171 0.00000
9 g13463.t6 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 152 171 0.00000
8 g13463.t6 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 173 190 0.00000
1 g13463.t6 Pfam PF00106 short chain dehydrogenase 6 191 0.00000
12 g13463.t6 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. 6 188 0.00092
11 g13463.t6 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 4 206 0.00000

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

## [1] "No matching GO terms"

KEGG

Orthology

Pathway

This gene does not belong to any 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