General information for g16443.t1
Yuki Yoshida
6/2/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Farnesol dehydrogenase.
Parent gene
- The parent gene g16443 is located on chr_4: 9451445..9452191 (+ 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_4 | g16443 | g16443.t1 | isoform | g16443.t1 | 9451445 | 9452191 |
| chr_4 | g16443 | g16443.t1 | exon | g16443.t1.exon1 | 9451445 | 9452191 |
| chr_4 | g16443 | g16443.t1 | cds | g16443.t1.CDS1 | 9451445 | 9452191 |
| chr_4 | g16443 | g16443.t1 | TTS | g16443.t1 | 9452560 | 9452560 |
| chr_4 | g16443 | g16443.t1 | TSS | g16443.t1 | NA | NA |
Sequences
>g16443.t1 Gene=g16443 Length=747
ATGGAAAAGTGGACAGGAAAGACAGCAGTGATCACAGGAGGAAATTCAGGCATTGGTGCA
GCAATTCTTTCACAGTTTATTAAACATGGTTTAAAAGTCATCAATTTAGACATAAATGTC
ACTGAAAAAGACTCAAATTTTGACGAGAATTCAAATATTTTCAATCGCAAATGTGATGTT
GCAAATTTGGATTCAATCAAGGAAAATTTCAAATGGATTGAAGAAAATTTTGGTGTTGTT
CATATTTTGGTTAATTGTGCTGGAATTGCAAGTTTAACAAAATTAATTGATGGAAATGAT
GAAAATACAAAACTCATTGACAAAACAATTGATATTAACTTTCGTGGTGCAGTTCATTGT
GCTCGTGAGGCAATGAAGTTAATGATAAAGTCAGATGACTACTGCATGATCATCAATATT
TGTTCACTTTATGGTCATGTTATTCCATACACAGACAGCTCAGTGTCAGTTTATAGCTGT
ACCAAATATGCAATCAGAGCACTTTCAGAAGTCATCAGGCAAGAACTTGTGATGAGTGAA
AACAAGAAAATTCGAATCAGCAATCTCAGTCCGAGCAGTGTCAACTCAAACTTATGGACT
GCATTTGGATTGACAAAAGAATATATGGAAAGTGTAAACTTTATGAAAACTGACGATGTT
GCTGATGCTGTTGTTTATTTACTTAGCACACCTTACAATGTCAATGTCACTGAAATGATT
ATTAGACCTGTTGGTGAAAAATTTTAA
>g16443.t1 Gene=g16443 Length=248
MEKWTGKTAVITGGNSGIGAAILSQFIKHGLKVINLDINVTEKDSNFDENSNIFNRKCDV
ANLDSIKENFKWIEENFGVVHILVNCAGIASLTKLIDGNDENTKLIDKTIDINFRGAVHC
AREAMKLMIKSDDYCMIINICSLYGHVIPYTDSSVSVYSCTKYAIRALSEVIRQELVMSE
NKKIRISNLSPSSVNSNLWTAFGLTKEYMESVNFMKTDDVADAVVYLLSTPYNVNVTEMI
IRPVGEKF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g16443.t1 | Gene3D | G3DSA:3.40.50.720 | - | 1 | 239 | 0.0e+00 |
| 2 | g16443.t1 | PANTHER | PTHR43115 | DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 | 1 | 248 | 0.0e+00 |
| 3 | g16443.t1 | PANTHER | PTHR43115:SF4 | DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 | 1 | 248 | 0.0e+00 |
| 10 | g16443.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 8 | 25 | 0.0e+00 |
| 6 | g16443.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 78 | 89 | 1.1e-05 |
| 8 | g16443.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 78 | 89 | 0.0e+00 |
| 9 | g16443.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 129 | 145 | 0.0e+00 |
| 5 | g16443.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 135 | 143 | 1.1e-05 |
| 4 | g16443.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 158 | 177 | 1.1e-05 |
| 7 | g16443.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 158 | 177 | 0.0e+00 |
| 12 | g16443.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 182 | 199 | 0.0e+00 |
| 11 | g16443.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 210 | 230 | 0.0e+00 |
| 1 | g16443.t1 | Pfam | PF00106 | short chain dehydrogenase | 7 | 200 | 0.0e+00 |
| 13 | g16443.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 5 | 231 | 0.0e+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.
