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 g13462 g13462.t11 TTS g13462.t11 30323599 30323599
chr_1 g13462 g13462.t11 isoform g13462.t11 30323726 30324665
chr_1 g13462 g13462.t11 exon g13462.t11.exon1 30323726 30323754
chr_1 g13462 g13462.t11 exon g13462.t11.exon2 30323815 30323910
chr_1 g13462 g13462.t11 cds g13462.t11.CDS1 30323884 30323910
chr_1 g13462 g13462.t11 exon g13462.t11.exon3 30324132 30324665
chr_1 g13462 g13462.t11 cds g13462.t11.CDS2 30324132 30324665
chr_1 g13462 g13462.t11 TSS g13462.t11 30324729 30324729

Sequences

>g13462.t11 Gene=g13462 Length=659
ATGAATTTCGCCGGAAAAGTAGTTTTAATAACCGGAGCATCAAGTGGAATTGGGGCACAA
GCTGCTATAAAATTTGCACAACATGGTGCTTTATTAAGCATTACCGGCAGAAAATTAGAA
AATCTTGAAAAAGTTGCTAGTGAATGCAAAGGTGAAAAACCTTTGATTGTGAATGGCGAC
ATTACAAATGAGACAGACACAAAAAGAATTTTTGATGAAACAATTAAAAAGTATGGAAAA
CTTGATGTACTTGTGAATTGTGCAGGAATAATTGAAACTGGCACAATTGAAAATACTTCA
TTGGAACAATATGATCGAGTTATGAATATGAACATGCGCTCAATTTATCACTTGACAATG
CTTGCTGTACCATATTTAATCAAAAGTCAAGGAAATGTTGTAAATGTTTCAAGTGTTAAT
GGAGTTAGAAGTTTTCCTGGAGTTTTAGCTTATAATTTGTCAAAAGCGTGTGTCGATCAA
TTTACAAGATGCACTGCTCTTGAATTAGCTGCCAAAAATGTTCGTGTTAATTCAGTCGAC
CAGGAACAGTCGATGAATTAGCAAATGCCATATTATTTTTAGCAAGTGATCAAGCAAGTT
TCATTACTGGTATATCTCTGCCAGTTGATGGTGGACGTCATGCCACATGTTTGCGTTAA

>g13462.t11 Gene=g13462 Length=186
MNFAGKVVLITGASSGIGAQAAIKFAQHGALLSITGRKLENLEKVASECKGEKPLIVNGD
ITNETDTKRIFDETIKKYGKLDVLVNCAGIIETGTIENTSLEQYDRVMNMNMRSIYHLTM
LAVPYLIKSQGNVVNVSSVNGVRSFPGVLAYNLSKACVDQFTRCTALELAAKNVRVNSVD
QEQSMN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g13462.t11 Gene3D G3DSA:3.40.50.720 - 1 182 1.8E-60
2 g13462.t11 PANTHER PTHR43975:SF2 ZGC:101858 1 179 5.0E-73
3 g13462.t11 PANTHER PTHR43975 ZGC:101858 1 179 5.0E-73
11 g13462.t11 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 7 24 1.0E-23
5 g13462.t11 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 79 90 3.5E-11
9 g13462.t11 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 79 90 1.0E-23
8 g13462.t11 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 125 141 1.0E-23
6 g13462.t11 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 131 139 3.5E-11
4 g13462.t11 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 151 170 3.5E-11
7 g13462.t11 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 151 170 1.0E-23
10 g13462.t11 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 172 186 1.0E-23
1 g13462.t11 Pfam PF00106 short chain dehydrogenase 6 179 9.3E-50
16 g13462.t11 Phobius SIGNAL_PEPTIDE Signal peptide region 1 21 -
17 g13462.t11 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 6 -
18 g13462.t11 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 7 17 -
19 g13462.t11 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 18 21 -
15 g13462.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 22 186 -
13 g13462.t11 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. 6 177 0.0023
12 g13462.t11 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 1 179 5.07E-58

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

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