General information for g522.t2
Yuki Yoshida
6/2/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Farnesol dehydrogenase.
Parent gene
- The parent gene g522 is located on chr_3: 3874581..3876334 (+ 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 | g522 | g522.t2 | TSS | g522.t2 | 3874525 | 3874525 |
| chr_3 | g522 | g522.t2 | isoform | g522.t2 | 3874581 | 3875142 |
| chr_3 | g522 | g522.t2 | exon | g522.t2.exon1 | 3874581 | 3874630 |
| chr_3 | g522 | g522.t2 | cds | g522.t2.CDS1 | 3874581 | 3874630 |
| chr_3 | g522 | g522.t2 | exon | g522.t2.exon2 | 3874694 | 3875142 |
| chr_3 | g522 | g522.t2 | cds | g522.t2.CDS2 | 3874694 | 3875141 |
| chr_3 | g522 | g522.t2 | TTS | g522.t2 | 3875552 | 3875552 |
Sequences
>g522.t2 Gene=g522 Length=499
ATGTCAGCTACTCGTTGGGCTGGTCGTGTCGCGGTTGTTACTGGTGCAAGTGCTGGAATC
GGAGCTGCAACTGCTCTTGAATTGTGTAGAAATGGAATAATTACAATTGGATTAGCAAGA
AGAGTTGAAAAAATTGAAGAATTAAAATCACAATTAACGCCTGCACAACAAGCAAATTTT
CATCCTTTAAAGTGTGACATTTCAGTTGAAGCTGAAGTTATTCATATTTTTAATGTAATT
GAAAAAATTTATGGTGGTGTTGATATTTTAGTTAACAATGCGGGTGTAGCACCTACAAAG
ACTTTATTGGATCCTGAAAATTCAACTGATATTCAAAGAGTTATTGACACAAATTTACTT
GGTGTTATCAATTGCACAAGAGAAGCAGTGAAATCTATGCGTGAAAGACATGTTGAAGCT
CATATAATTCTTATGAACAGCATTGCTGGTCATTATATGCCTTTTCAAGCTGGAGTGCCA
TCATCAGGAATTTATTTTG
>g522.t2 Gene=g522 Length=166
MSATRWAGRVAVVTGASAGIGAATALELCRNGIITIGLARRVEKIEELKSQLTPAQQANF
HPLKCDISVEAEVIHIFNVIEKIYGGVDILVNNAGVAPTKTLLDPENSTDIQRVIDTNLL
GVINCTREAVKSMRERHVEAHIILMNSIAGHYMPFQAGVPSSGIYF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g522.t2 | Gene3D | G3DSA:3.40.50.720 | - | 1 | 165 | 4.6E-42 |
| 2 | g522.t2 | PANTHER | PTHR43115 | DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 | 5 | 154 | 2.9E-62 |
| 3 | g522.t2 | PANTHER | PTHR43115:SF4 | DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 | 5 | 154 | 2.9E-62 |
| 4 | g522.t2 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 10 | 27 | 6.7E-13 |
| 6 | g522.t2 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 85 | 96 | 6.7E-13 |
| 5 | g522.t2 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 134 | 150 | 6.7E-13 |
| 1 | g522.t2 | Pfam | PF00106 | short chain dehydrogenase | 10 | 154 | 4.4E-34 |
| 10 | g522.t2 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 25 | - |
| 11 | g522.t2 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 9 | - |
| 12 | g522.t2 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 10 | 20 | - |
| 13 | g522.t2 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 21 | 25 | - |
| 9 | g522.t2 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 26 | 166 | - |
| 7 | g522.t2 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 4 | 154 | 8.57E-40 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g522/g522.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g522.t2.fa.iupred3.txt does not exist
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