General information for g8020.t3
Yuki Yoshida
6/2/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Farnesol dehydrogenase.
Parent gene
- The parent gene g8020 is located on chr_2: 27931225..27932100 (- 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_2 | g8020 | g8020.t3 | TTS | g8020.t3 | 27931138 | 27931138 |
| chr_2 | g8020 | g8020.t3 | isoform | g8020.t3 | 27931225 | 27932100 |
| chr_2 | g8020 | g8020.t3 | exon | g8020.t3.exon1 | 27931225 | 27931453 |
| chr_2 | g8020 | g8020.t3 | cds | g8020.t3.CDS1 | 27931451 | 27931453 |
| chr_2 | g8020 | g8020.t3 | exon | g8020.t3.exon2 | 27931563 | 27931752 |
| chr_2 | g8020 | g8020.t3 | cds | g8020.t3.CDS2 | 27931563 | 27931752 |
| chr_2 | g8020 | g8020.t3 | exon | g8020.t3.exon3 | 27931817 | 27932100 |
| chr_2 | g8020 | g8020.t3 | cds | g8020.t3.CDS3 | 27931817 | 27932100 |
| chr_2 | g8020 | g8020.t3 | TSS | g8020.t3 | 27932107 | 27932107 |
Sequences
>g8020.t3 Gene=g8020 Length=703
ATGGAGAAGTGGCGAGGAAAAGTTGCAATTGTCACCGGAGCTTCTTCCGGCATAGGTGCT
GCAATTGTTAGAGATTTAGCAAAGAATGGAATCACAGTGATTGGACTAGCACGACGAGTT
CAGAAAATTAGAGAACAAACTAAAGATTTCCCTGAAAATTATGCAAACGTTCATGCATTT
TATTGTGATGTGTCGAAAATTGAAAGCATAAAAGAAGCATTTAAATTGATTGAGGAGAGA
TTTGGAGTAATTAATATTCTGGTAAATAATGCTGGAATTGGAAAAAAAACTTCAATTTTA
GTCGACGATGAAGAAACAGATGGAAAAATTTCCCAAGTGATTGACACAAATTTCACTGGA
TTGGTGCATGTCACACGTCATGCTTATATGCTAATGAAAAAATCTGAAGATTACGGTATG
GTTGTCAACATAAATTCTGTCGCAGGTCACAAAGTTTCATTTCCATATTATGGTTAAGTT
AGATAAAATAATTAAAAACGGTGAATATATGAAAAATTTCTTTCAATGTTTTAAGTCGGT
TAGTCCTGGAGTTGTTGATACTTCTTTCTTCCATTCATCGCAAATGCTTCCTGATAATAT
TGAAATGAGAGATGTAGCACCAGTATTAAATCCATCTGACATAGCAGATGCAGTAATGTA
TTTACTTCAAGTTCCATATCATGTGAATATTACAGAAATGACA
>g8020.t3 Gene=g8020 Length=158
MEKWRGKVAIVTGASSGIGAAIVRDLAKNGITVIGLARRVQKIREQTKDFPENYANVHAF
YCDVSKIESIKEAFKLIEERFGVINILVNNAGIGKKTSILVDDEETDGKISQVIDTNFTG
LVHVTRHAYMLMKKSEDYGMVVNINSVAGHKVSFPYYG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g8020.t3 | CDD | cd05233 | SDR_c | 9 | 153 | 0e+00 |
| 9 | g8020.t3 | Gene3D | G3DSA:3.40.50.720 | - | 1 | 158 | 0e+00 |
| 2 | g8020.t3 | PANTHER | PTHR43115 | DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 | 1 | 155 | 0e+00 |
| 6 | g8020.t3 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 8 | 25 | 0e+00 |
| 4 | g8020.t3 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 82 | 93 | 4e-05 |
| 7 | g8020.t3 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 82 | 93 | 0e+00 |
| 5 | g8020.t3 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 133 | 149 | 0e+00 |
| 3 | g8020.t3 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 139 | 147 | 4e-05 |
| 1 | g8020.t3 | Pfam | PF00106 | short chain dehydrogenase | 7 | 152 | 0e+00 |
| 8 | g8020.t3 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 2 | 155 | 0e+00 |
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