General information for g522.t6
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.t6 | TSS | g522.t6 | 3874525 | 3874525 |
| chr_3 | g522 | g522.t6 | isoform | g522.t6 | 3874581 | 3875822 |
| chr_3 | g522 | g522.t6 | exon | g522.t6.exon1 | 3874581 | 3874630 |
| chr_3 | g522 | g522.t6 | exon | g522.t6.exon2 | 3874694 | 3874834 |
| chr_3 | g522 | g522.t6 | exon | g522.t6.exon3 | 3874915 | 3875222 |
| chr_3 | g522 | g522.t6 | cds | g522.t6.CDS1 | 3875040 | 3875222 |
| chr_3 | g522 | g522.t6 | exon | g522.t6.exon4 | 3875281 | 3875822 |
| chr_3 | g522 | g522.t6 | cds | g522.t6.CDS2 | 3875281 | 3875481 |
| chr_3 | g522 | g522.t6 | TTS | g522.t6 | 3875803 | 3875803 |
Sequences
>g522.t6 Gene=g522 Length=1041
ATGTCAGCTACTCGTTGGGCTGGTCGTGTCGCGGTTGTTACTGGTGCAAGTGCTGGAATC
GGAGCTGCAACTGCTCTTGAATTGTGTAGAAATGGAATAATTACAATTGGATTAGCAAGA
AGAGTTGAAAAAATTGAAGAATTAAAATCACAATTAACGCCTGCACAACAAGCAAATTTT
CATCCTTTAAATTAACAATGCGGGTGTAGCACCTACAAAGACTTTATTGGATCCTGAAAA
TTCAACTGATATTCAAAGAGTTATTGACACAAATTTACTTGGTGTTATCAATTGCACAAG
AGAAGCAGTGAAATCTATGCGTGAAAGACATGTTGAAGCTCATATAATTCTTATGAACAG
CATTGCTGGTCATTATATGCCTTTTCAAGCTGGAGTGCCATCATCAGGAATTTATTTTGC
TAGTAAATATGCACTTACAGCATTAGCTGAACAATATCGACAAGAATTTATTAAGGAAAA
ATTGAATATAAAAATTTCGTCTTTAAGCCCAGGTTTTGTAAAAACAGAAATTGTGAGCGC
AAACACAGATTTACCACAAGAAGCCGTCGAAGCAGCAGTAGAAAATTGTCCAGGCTTGGA
GTCAAAAGATATTGCTGATGCTGTAATTTATTTATTGAGCACACCCCCAAATGTTTTGGT
CACAGAGCTCATAATTCGACCCATGAATGAAGTCATTTAAATGCGCAGTTGATTTTGCCT
ACAGCAATTTCTCTAGTTTATTAATAATTGAGTGCATTCATAGGAATCTCGAAAAAAAAA
TTCCATATATTTTAGAATTTTCGAGAAAATGATCAAAAAATGGAAAACAACTATGTTGAT
AATAAGAAGATAATTTTATTAATTGTAAACAAAATATTTATTTATTGTTAAAATGTGACT
TATGAAAAAGTTCAAATATTTTTTTACTGACAAGGGAAGACAACTTTAAAAAAATTTAAA
AAACAAATATTAAGAAATATTATCAAAAATTTCATTCAAATAAATTTTGATACTTTTTTA
AATAAAAACTTAAAGTTCCTT
>g522.t6 Gene=g522 Length=127
MRERHVEAHIILMNSIAGHYMPFQAGVPSSGIYFASKYALTALAEQYRQEFIKEKLNIKI
SSLSPGFVKTEIVSANTDLPQEAVEAAVENCPGLESKDIADAVIYLLSTPPNVLVTELII
RPMNEVI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g522.t6 | Gene3D | G3DSA:3.40.50.720 | - | 1 | 125 | 0e+00 |
| 2 | g522.t6 | PANTHER | PTHR43115 | DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 | 1 | 127 | 0e+00 |
| 3 | g522.t6 | PANTHER | PTHR43115:SF4 | DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 | 1 | 127 | 0e+00 |
| 6 | g522.t6 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 2 | 18 | 4e-07 |
| 5 | g522.t6 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 33 | 52 | 4e-07 |
| 7 | g522.t6 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 56 | 73 | 4e-07 |
| 4 | g522.t6 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 89 | 109 | 4e-07 |
| 1 | g522.t6 | Pfam | PF00106 | short chain dehydrogenase | 6 | 76 | 1e-07 |
| 8 | g522.t6 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 1 | 121 | 0e+00 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g522/g522.t6; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g522.t6.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.
