General information for g13462.t3
Yuki Yoshida
6/2/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 3-oxoacyl-[acyl-carrier-protein] reductase FabG.
Parent gene
- The parent gene g13462 is located on chr_1: 30324230..30324665 (- strand)
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.t3 | TTS | g13462.t3 | 30323599 | 30323599 |
| chr_1 | g13462 | g13462.t3 | isoform | g13462.t3 | 30323726 | 30324665 |
| chr_1 | g13462 | g13462.t3 | exon | g13462.t3.exon1 | 30323726 | 30323754 |
| chr_1 | g13462 | g13462.t3 | exon | g13462.t3.exon2 | 30323815 | 30324060 |
| chr_1 | g13462 | g13462.t3 | cds | g13462.t3.CDS1 | 30323933 | 30324060 |
| chr_1 | g13462 | g13462.t3 | exon | g13462.t3.exon3 | 30324122 | 30324665 |
| chr_1 | g13462 | g13462.t3 | cds | g13462.t3.CDS2 | 30324122 | 30324665 |
| chr_1 | g13462 | g13462.t3 | TSS | g13462.t3 | 30324729 | 30324729 |
Sequences
>g13462.t3 Gene=g13462 Length=819
ATGAATTTCGCCGGAAAAGTAGTTTTAATAACCGGAGCATCAAGTGGAATTGGGGCACAA
GCTGCTATAAAATTTGCACAACATGGTGCTTTATTAAGCATTACCGGCAGAAAATTAGAA
AATCTTGAAAAAGTTGCTAGTGAATGCAAAGGTGAAAAACCTTTGATTGTGAATGGCGAC
ATTACAAATGAGACAGACACAAAAAGAATTTTTGATGAAACAATTAAAAAGTATGGAAAA
CTTGATGTACTTGTGAATTGTGCAGGAATAATTGAAACTGGCACAATTGAAAATACTTCA
TTGGAACAATATGATCGAGTTATGAATATGAACATGCGCTCAATTTATCACTTGACAATG
CTTGCTGTACCATATTTAATCAAAAGTCAAGGAAATGTTGTAAATGTTTCAAGTGTTAAT
GGAGTTAGAAGTTTTCCTGGAGTTTTAGCTTATAATTTGTCAAAAGCGTGTGTCGATCAA
TTTACAAGATGCACTGCTCTTGAATTAGCTGCCAAAAATGTTCGTGTTAATTCAGTAAAT
CCAGGTGTCACTGTCACAAATCTTCATAAAAGAGGAGGAATGGATGAAACTGCCTATGCC
AAATTCTTAGAACATTCAAAATCAACTCATCCCATTGGTAAAAATCTGAAATCCCAGAAA
ATTACAATCTAAGCTTTAAATTTTTGCTCTTTAGGTCGACCAGGAACAGTCGATGAATTA
GCAAATGCCATATTATTTTTAGCAAGTGATCAAGCAAGTTTCATTACTGGTATATCTCTG
CCAGTTGATGGTGGACGTCATGCCACATGTTTGCGTTAA
>g13462.t3 Gene=g13462 Length=223
MNFAGKVVLITGASSGIGAQAAIKFAQHGALLSITGRKLENLEKVASECKGEKPLIVNGD
ITNETDTKRIFDETIKKYGKLDVLVNCAGIIETGTIENTSLEQYDRVMNMNMRSIYHLTM
LAVPYLIKSQGNVVNVSSVNGVRSFPGVLAYNLSKACVDQFTRCTALELAAKNVRVNSVN
PGVTVTNLHKRGGMDETAYAKFLEHSKSTHPIGKNLKSQKITI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g13462.t3 | Gene3D | G3DSA:3.40.50.720 | - | 1 | 222 | 2.5E-66 |
| 2 | g13462.t3 | PANTHER | PTHR43975 | ZGC:101858 | 1 | 220 | 2.2E-89 |
| 10 | g13462.t3 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 7 | 24 | 7.6E-29 |
| 4 | g13462.t3 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 79 | 90 | 5.3E-11 |
| 9 | g13462.t3 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 79 | 90 | 7.6E-29 |
| 8 | g13462.t3 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 125 | 141 | 7.6E-29 |
| 5 | g13462.t3 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 131 | 139 | 5.3E-11 |
| 3 | g13462.t3 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 151 | 170 | 5.3E-11 |
| 6 | g13462.t3 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 151 | 170 | 7.6E-29 |
| 7 | g13462.t3 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 172 | 189 | 7.6E-29 |
| 1 | g13462.t3 | Pfam | PF00106 | short chain dehydrogenase | 6 | 190 | 9.6E-54 |
| 15 | g13462.t3 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 21 | - |
| 16 | g13462.t3 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 6 | - |
| 17 | g13462.t3 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 7 | 17 | - |
| 18 | g13462.t3 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 18 | 21 | - |
| 14 | g13462.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 22 | 223 | - |
| 12 | g13462.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 | 177 | 0.0023 |
| 11 | g13462.t3 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 5 | 215 | 1.38E-63 |
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 transcript has been annotated with K00059 (3-oxoacyl-[acyl-carrier protein] reductase)
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.
