General information for g2253.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 g2253 is located on chr_3: 16295325..16297144 (- 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_3 | g2253 | g2253.t1 | TTS | g2253.t1 | 16295137 | 16295137 |
| chr_3 | g2253 | g2253.t1 | isoform | g2253.t1 | 16295325 | 16296829 |
| chr_3 | g2253 | g2253.t1 | exon | g2253.t1.exon1 | 16295325 | 16295366 |
| chr_3 | g2253 | g2253.t1 | cds | g2253.t1.CDS1 | 16295325 | 16295366 |
| chr_3 | g2253 | g2253.t1 | exon | g2253.t1.exon2 | 16295474 | 16295575 |
| chr_3 | g2253 | g2253.t1 | cds | g2253.t1.CDS2 | 16295474 | 16295575 |
| chr_3 | g2253 | g2253.t1 | exon | g2253.t1.exon3 | 16295727 | 16295838 |
| chr_3 | g2253 | g2253.t1 | cds | g2253.t1.CDS3 | 16295727 | 16295838 |
| chr_3 | g2253 | g2253.t1 | exon | g2253.t1.exon4 | 16295926 | 16295933 |
| chr_3 | g2253 | g2253.t1 | cds | g2253.t1.CDS4 | 16295926 | 16295933 |
| chr_3 | g2253 | g2253.t1 | exon | g2253.t1.exon5 | 16296063 | 16296095 |
| chr_3 | g2253 | g2253.t1 | cds | g2253.t1.CDS5 | 16296063 | 16296095 |
| chr_3 | g2253 | g2253.t1 | exon | g2253.t1.exon6 | 16296184 | 16296525 |
| chr_3 | g2253 | g2253.t1 | cds | g2253.t1.CDS6 | 16296184 | 16296525 |
| chr_3 | g2253 | g2253.t1 | exon | g2253.t1.exon7 | 16296631 | 16296737 |
| chr_3 | g2253 | g2253.t1 | cds | g2253.t1.CDS7 | 16296631 | 16296737 |
| chr_3 | g2253 | g2253.t1 | exon | g2253.t1.exon8 | 16296799 | 16296829 |
| chr_3 | g2253 | g2253.t1 | cds | g2253.t1.CDS8 | 16296799 | 16296829 |
| chr_3 | g2253 | g2253.t1 | TSS | g2253.t1 | 16297144 | 16297144 |
Sequences
>g2253.t1 Gene=g2253 Length=777
ATGTATAAATGGAATGGTCGCGTGGCAATAGTCACCGGAGCATCAACTCCAATTGGAATG
GCAATTTGTAAAGCTCTTGTAACACATGGACTTAAAGTATGTGCGATAGCAAAGAAATCA
GGAGTTGCTAAATTAGATGCATTAAACACGACATTTTTTGATGTCAAAGGAAAGATGCTC
ACATATGAGTGTGATTTAACGGATGAAGAGCAAGTTAAGGCAGTTTTTAGACATATTGGT
GAAAAATATGATGGAATCGATTTACTTGTAAATAATGCCAATGTGATGAAAAAAGGACTT
TTATTAGATCAAAATAACACCAATGATATGCATTATATAATGAACACAAATGTTCTCGCT
CTATGCATTGTCACGAGAGAGGCAGTAAAATTAATGCGACAGCGAACGATGGAGAGAAAA
GATGTAGCTCATATAGTGAACATAAATTCGATTTTCGGACACAAAATTATGGCCACTGTG
CCTGGTACCACTCCAATGAACGGTCTATATCCTGCGTCAAAATATGCTTCAACTGCAATA
ACTGAATGTGTGCGACAAGAACTTTTATTTTTGGACGAAACTGTCAAAGTAACAAGTATC
TCACCAGGATTAGTTGAGAGCGATATAATTCATGCAAATGCACATGACGAAATTTTAAAA
TTGATGCCTGCACTTAAACCGGATGATGTTGCAGGTGCAGTGATTTTTGCACTTGGCGCA
AAAGAAGGTGTTGAGGTTCATGAGATTGTAATTAAGCCAGTTGGTGAATATCTGTAA
>g2253.t1 Gene=g2253 Length=258
MYKWNGRVAIVTGASTPIGMAICKALVTHGLKVCAIAKKSGVAKLDALNTTFFDVKGKML
TYECDLTDEEQVKAVFRHIGEKYDGIDLLVNNANVMKKGLLLDQNNTNDMHYIMNTNVLA
LCIVTREAVKLMRQRTMERKDVAHIVNINSIFGHKIMATVPGTTPMNGLYPASKYASTAI
TECVRQELLFLDETVKVTSISPGLVESDIIHANAHDEILKLMPALKPDDVAGAVIFALGA
KEGVEVHEIVIKPVGEYL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g2253.t1 | Gene3D | G3DSA:3.40.50.720 | - | 2 | 256 | 0e+00 |
| 2 | g2253.t1 | PANTHER | PTHR43115 | DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 | 1 | 258 | 0e+00 |
| 3 | g2253.t1 | PANTHER | PTHR43115:SF4 | DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 | 1 | 258 | 0e+00 |
| 9 | g2253.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 8 | 25 | 0e+00 |
| 6 | g2253.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 84 | 95 | 8e-07 |
| 10 | g2253.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 84 | 95 | 0e+00 |
| 12 | g2253.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 137 | 153 | 0e+00 |
| 5 | g2253.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 143 | 151 | 8e-07 |
| 4 | g2253.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 170 | 189 | 8e-07 |
| 7 | g2253.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 170 | 189 | 0e+00 |
| 8 | g2253.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 193 | 210 | 0e+00 |
| 11 | g2253.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 220 | 240 | 0e+00 |
| 1 | g2253.t1 | Pfam | PF00106 | short chain dehydrogenase | 8 | 214 | 0e+00 |
| 13 | g2253.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 1 | 250 | 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