General information for g2254.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 g2254 is located on chr_3: 16308902..16314786 (+ 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 | g2254 | g2254.t3 | TSS | g2254.t3 | 16302050 | 16302050 |
| chr_3 | g2254 | g2254.t3 | isoform | g2254.t3 | 16302197 | 16304255 |
| chr_3 | g2254 | g2254.t3 | exon | g2254.t3.exon1 | 16302197 | 16302328 |
| chr_3 | g2254 | g2254.t3 | cds | g2254.t3.CDS1 | 16302197 | 16302328 |
| chr_3 | g2254 | g2254.t3 | exon | g2254.t3.exon2 | 16302388 | 16302518 |
| chr_3 | g2254 | g2254.t3 | cds | g2254.t3.CDS2 | 16302388 | 16302518 |
| chr_3 | g2254 | g2254.t3 | exon | g2254.t3.exon3 | 16302574 | 16302784 |
| chr_3 | g2254 | g2254.t3 | cds | g2254.t3.CDS3 | 16302574 | 16302784 |
| chr_3 | g2254 | g2254.t3 | exon | g2254.t3.exon4 | 16302898 | 16302934 |
| chr_3 | g2254 | g2254.t3 | cds | g2254.t3.CDS4 | 16302898 | 16302934 |
| chr_3 | g2254 | g2254.t3 | exon | g2254.t3.exon5 | 16303398 | 16303495 |
| chr_3 | g2254 | g2254.t3 | cds | g2254.t3.CDS5 | 16303398 | 16303450 |
| chr_3 | g2254 | g2254.t3 | exon | g2254.t3.exon6 | 16304032 | 16304147 |
| chr_3 | g2254 | g2254.t3 | exon | g2254.t3.exon7 | 16304218 | 16304255 |
| chr_3 | g2254 | g2254.t3 | TTS | g2254.t3 | 16304443 | 16304443 |
Sequences
>g2254.t3 Gene=g2254 Length=763
ATGGAAAAGTGGGAAGGAAAAGTAGCTGTTGTCACTGGTGCTTCTGTTGGAATAGGGGCC
GCTTTGTGTCGTGCACTTGTCGAAGCTGGAATGATCGTTTGTGGATTATCAAAACGCAAG
GATAAAATGGAAGCTATTCGACGAACACTTTTTGGTGTTAAAGGGCAATTTAATTGCGTT
GAATGTGACATTCGTGATGAAAATCAAGTCGCTGCTGCTTTTAGATGGATTGAGGATGTT
TGTGGTGGAGTCGATTTATTGATAAACAATGCTGGTGTTATCACTAAAGGTCTTCTCTTG
GACGCAAAAAATACATCCGAACTCTACAGAACTATGGAGACTAACATCATTGGTCTCTGT
CTCATTACTCGTGAAGCTGTTAAACTTATGAAAAAGCGCGATGAAGAACGAGGAACTGTA
GGACATATTGTGAACATCAATAGCATATTCGGTCACAAGATTCATGCCTGTGTTCCGGGA
ACAAAGCCTCTAAATGGGATGTATCCGGTGAATTCGCTGTCACTGCAATCACAGAATGTG
TCCGTCAAGAATTATTGTATTTAGGAACAAAAATCAAAATCACAAGTATTTCACCGGGAT
TGGTCGAAGGTGACATTGGTACTTTAAACACTTCTCATGACATGATCAAATTGATGCCAA
AGCTTAATCCACAAGATGTTGCAGATGCAGTTCTTTATGCTATTTCTACACCAGAAAATG
TTTTGATTCACGAATTGATAATCAAACCAGTCGGAGAATTTCT
>g2254.t3 Gene=g2254 Length=187
MEKWEGKVAVVTGASVGIGAALCRALVEAGMIVCGLSKRKDKMEAIRRTLFGVKGQFNCV
ECDIRDENQVAAAFRWIEDVCGGVDLLINNAGVITKGLLLDAKNTSELYRTMETNIIGLC
LITREAVKLMKKRDEERGTVGHIVNINSIFGHKIHACVPGTKPLNGMYPVNSLSLQSQNV
SVKNYCI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g2254.t3 | Gene3D | G3DSA:3.40.50.720 | - | 1 | 173 | 2.3E-38 |
| 2 | g2254.t3 | PANTHER | PTHR43115 | DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 | 1 | 156 | 1.2E-58 |
| 3 | g2254.t3 | PANTHER | PTHR43115:SF4 | DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 | 1 | 156 | 1.2E-58 |
| 6 | g2254.t3 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 8 | 25 | 1.7E-14 |
| 4 | g2254.t3 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 82 | 93 | 1.4E-5 |
| 8 | g2254.t3 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 82 | 93 | 1.7E-14 |
| 7 | g2254.t3 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 135 | 151 | 1.7E-14 |
| 5 | g2254.t3 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 141 | 149 | 1.4E-5 |
| 1 | g2254.t3 | Pfam | PF00106 | short chain dehydrogenase | 7 | 155 | 3.4E-31 |
| 13 | g2254.t3 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 25 | - |
| 14 | g2254.t3 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 7 | - |
| 15 | g2254.t3 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 8 | 18 | - |
| 16 | g2254.t3 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 19 | 25 | - |
| 12 | g2254.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 26 | 187 | - |
| 10 | g2254.t3 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 3 | 154 | 4.33E-37 |
| 9 | g2254.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 15 | 37 | - |
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