General information for g514.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 g514 is located on chr_3: 3857463..3858366 (- 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 | g514 | g514.t2 | TTS | g514.t2 | 3857367 | 3857367 |
| chr_3 | g514 | g514.t2 | isoform | g514.t2 | 3857463 | 3858366 |
| chr_3 | g514 | g514.t2 | exon | g514.t2.exon1 | 3857463 | 3857666 |
| chr_3 | g514 | g514.t2 | cds | g514.t2.CDS1 | 3857463 | 3857666 |
| chr_3 | g514 | g514.t2 | exon | g514.t2.exon2 | 3857728 | 3858366 |
| chr_3 | g514 | g514.t2 | cds | g514.t2.CDS2 | 3857728 | 3857949 |
| chr_3 | g514 | g514.t2 | TSS | g514.t2 | 3858387 | 3858387 |
Sequences
>g514.t2 Gene=g514 Length=843
ATGACAATTTCACGTTGGTCTGGTCGTATTGCTGTTGTGACTGGTGCAAGGTAAAAAATT
TTATAAATTAAAAAATGTTATTTTAAATTAAAAATTTTGAAATTATTTAGTGCTGGAATT
GGTGCTGCAACTGCAATTGAATTAGCTAAAAATGATTTAATTACAATTGGATTAGCAAGA
AGAGTCGAAAAAGTTGAAGAACTGAAGTCAAATTTACCAAATGATAAGCAAAGAAATCTT
CACGCCATAAAATGTGATGTTTCAATTGAAGCTGAAGTCATTCGTGCATTTGCCGAAATA
GAAAAAAGATTTGGTGGCGTTGATGTGTTGATTAACAATGCTGGCATAGTGCCACAAACT
TCATTAACAAATATAAACAATTCTGACAACGTTCGTCAAGTAATTGACACTAACGTCATG
GGAGTTGTTTTTTGTACACGCGAGGCTGTTAAGATGATGAGAGAGAGAAAATCTGAGGGT
CATATCATTCATATCAACAGTATTGCTGGTCATTATATGTCATATCACTCTGAATCCACA
ACTATGGGAATTTACTATGCCAGCAAATATGCAGTCACAGCTTTAGCTGAACAACATCGT
CATGAATTCATCAAAGAAAAGTTAAACATTAAAGTCACAAGTCTTAGTCCAGGAGGTGTA
AAGACAGAAATCATGAAAGCAAACCCAGGAGCAATTCCGCTTGATATTATTGAGAAAATG
ATGGAATACGCTCCAATGCTTGAGTCAAAAGATATTGCTGATGCTATAATTTATCTTCTT
AGTACACCACCAAATGTTCTCATCACAGAACTCACAATTCGTCCAATGAATGAAACTTTC
TAA
>g514.t2 Gene=g514 Length=141
MGVVFCTREAVKMMRERKSEGHIIHINSIAGHYMSYHSESTTMGIYYASKYAVTALAEQH
RHEFIKEKLNIKVTSLSPGGVKTEIMKANPGAIPLDIIEKMMEYAPMLESKDIADAIIYL
LSTPPNVLITELTIRPMNETF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g514.t2 | Gene3D | G3DSA:3.40.50.720 | - | 1 | 139 | 0 |
| 2 | g514.t2 | PANTHER | PTHR43115 | DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 | 1 | 141 | 0 |
| 3 | g514.t2 | PANTHER | PTHR43115:SF4 | DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 | 1 | 141 | 0 |
| 5 | g514.t2 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 15 | 31 | 0 |
| 7 | g514.t2 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 46 | 65 | 0 |
| 4 | g514.t2 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 69 | 86 | 0 |
| 6 | g514.t2 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 103 | 123 | 0 |
| 1 | g514.t2 | Pfam | PF00106 | short chain dehydrogenase | 2 | 88 | 0 |
| 8 | g514.t2 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 1 | 127 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g514/g514.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g514.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