General information for g16406.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Farnesol dehydrogenase.
Parent gene
- The parent gene g16406 is located on chr_4: 9358457..9359197 (- 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 | g16406 | g16406.t1 | isoform | g16406.t1 | 9358457 | 9359197 |
| chr_4 | g16406 | g16406.t1 | exon | g16406.t1.exon1 | 9358457 | 9359197 |
| chr_4 | g16406 | g16406.t1 | cds | g16406.t1.CDS1 | 9358457 | 9359197 |
| chr_4 | g16406 | g16406.t1 | TSS | g16406.t1 | NA | NA |
| chr_4 | g16406 | g16406.t1 | TTS | g16406.t1 | NA | NA |
Sequences
>g16406.t1 Gene=g16406 Length=741
ATGGACAAGTGGAAGACTAAAATTGCTGTCATTACTGGAGCTTCTTCGGGTATTGGTGCA
GCAATTACACTTTCTTTAGCATCTCATGGTTTGACTGTCATTGGTTTAGCACGTCGTAGT
GAAAATGTTGAAGAACTTTCAAAAAAACTTGAAAATTCTGAAGGAAAAATTATAGCTATA
AAGTGTGATGTTGCTGATTTAAATTCAATTAAAAATGCTTTTAAAGAAATTGAAGAAAAT
TTTGGAAAAGTTCATATCTTAATTAATAATGCTGGAATGAGTTCAAAAGTGACAATTTTA
GATGAGAGTGATTATGCAACAGAGAGAATAAATTCGACAATTGATGTCAATTTTAAAGCT
TATGTTCATTGTGTTCGTGAGTGTATAAAACTCATGAAAAAAATTGAAAATGAGCACGCA
ATGATTATCAATGTTGGATCAATTTTAGATAGTGTCATTCCTTATCCACATCGAACTATT
TATCCAACAACAAAACATGCAGTTCGAGCATTATCTGAAATTATTAGACAAGAATTAATC
GTAAGTGAATGTGATAAGATAAAAGTGACAAATTTGAGTCCGGGTGCTGTAAAAACTGAA
ATAGCTAGCGAAGATTATTTTAATAGTATACCACATTTGACACCTAATGACATTGCAGAA
TCTGTTATTTATTTATTAAGTACTCCATGGAATGTTAATGTAACACAATTAACCATTAAA
CCTGTTGGAGAGAAATTTTAA
>g16406.t1 Gene=g16406 Length=246
MDKWKTKIAVITGASSGIGAAITLSLASHGLTVIGLARRSENVEELSKKLENSEGKIIAI
KCDVADLNSIKNAFKEIEENFGKVHILINNAGMSSKVTILDESDYATERINSTIDVNFKA
YVHCVRECIKLMKKIENEHAMIINVGSILDSVIPYPHRTIYPTTKHAVRALSEIIRQELI
VSECDKIKVTNLSPGAVKTEIASEDYFNSIPHLTPNDIAESVIYLLSTPWNVNVTQLTIK
PVGEKF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g16406.t1 | Coils | Coil | Coil | 36 | 63 | - |
| 13 | g16406.t1 | Gene3D | G3DSA:3.40.50.720 | - | 2 | 245 | 5.1E-57 |
| 2 | g16406.t1 | PANTHER | PTHR43115 | DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 | 1 | 246 | 1.8E-73 |
| 7 | g16406.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 8 | 25 | 2.9E-23 |
| 4 | g16406.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 82 | 93 | 6.3E-7 |
| 10 | g16406.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 82 | 93 | 2.9E-23 |
| 9 | g16406.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 134 | 150 | 2.9E-23 |
| 3 | g16406.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 140 | 148 | 6.3E-7 |
| 5 | g16406.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 161 | 180 | 6.3E-7 |
| 11 | g16406.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 161 | 180 | 2.9E-23 |
| 6 | g16406.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 185 | 202 | 2.9E-23 |
| 8 | g16406.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 208 | 228 | 2.9E-23 |
| 1 | g16406.t1 | Pfam | PF00106 | short chain dehydrogenase | 7 | 204 | 1.6E-48 |
| 16 | g16406.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 27 | - |
| 17 | g16406.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 7 | - |
| 18 | g16406.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 8 | 19 | - |
| 19 | g16406.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 20 | 27 | - |
| 15 | g16406.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 28 | 246 | - |
| 21 | g16406.t1 | ProSitePatterns | PS00061 | Short-chain dehydrogenases/reductases family signature. | 148 | 176 | - |
| 12 | g16406.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 1 | 235 | 2.73E-54 |
| 20 | g16406.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 7 | 29 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0055114 | NA | NA |
| GO:0016491 | oxidoreductase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K06123 (1-acylglycerone phosphate 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. There were no conditions that were differentially expressed