General information for g516.t1
Yuki Yoshida
6/2/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Farnesol dehydrogenase.
Parent gene
- The parent gene g516 is located on chr_3: 3862799..3863811 (+ 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 | g516 | g516.t1 | TSS | g516.t1 | 3862759 | 3862759 |
| chr_3 | g516 | g516.t1 | isoform | g516.t1 | 3862799 | 3863716 |
| chr_3 | g516 | g516.t1 | exon | g516.t1.exon1 | 3862799 | 3862851 |
| chr_3 | g516 | g516.t1 | cds | g516.t1.CDS1 | 3862799 | 3862851 |
| chr_3 | g516 | g516.t1 | exon | g516.t1.exon2 | 3862908 | 3863418 |
| chr_3 | g516 | g516.t1 | cds | g516.t1.CDS2 | 3862908 | 3863418 |
| chr_3 | g516 | g516.t1 | exon | g516.t1.exon3 | 3863537 | 3863716 |
| chr_3 | g516 | g516.t1 | cds | g516.t1.CDS3 | 3863537 | 3863716 |
| chr_3 | g516 | g516.t1 | TTS | g516.t1 | 3863816 | 3863816 |
Sequences
>g516.t1 Gene=g516 Length=744
ATGGAAACAACATCGCGTTGGGTAAATTGTGTTGCGGTTGTGACAGGTGCAAGTGCTGGA
ATTGGTGCAGCAACTTGTATTGAATTAGCTAATAGTGGAATAATTACAATTGGAATAGCA
AGAAGAATTGATAAAGTTCAAGCATTAAGGTTTTGCTTAACAACTGATAAACAACGAAAT
TTTCATGCATACAAATGTGATGTCTCAAATGAAGCTGAAGTTAAACAAGTTTTTAGTGAA
ATTGAAAAGAAATTTAATGGAATTGATATTTTAATTAATAATGCTGGTGTTTTTTCAAAG
TCAACTCTAATTCAAGCTGACAATTCAGAAGATGTTCGGCGAGTTATTAATACAAATGTC
ATTGGTGTTGTGAATTGCACAAGAGAAGCAGTGAAAAGTATGAAAATGAAAAATGAAGCT
CACATAATTCACATTGGCAGCTTTTTTAATCAAAATATATCTCAAAACTTTGGAATTTAT
CAAGCAAGCAAACATGCTGTTGCTGCACTCGCTGAACAGCATCGACAGGAATTTAGTAGG
AAAAAATTGAATATTAAAGTCACTACAATAATTCCAAATGCAGTTGCAACTGAATTATAT
GATAATTCATCATATGAACCACCCAAAAGCGTAGAATTATTAGCAGCAAAAGAAATTGCT
GACGTCATAGTCTTTGCTTTAGAAACACCTCGAAACGTCGTCATTACAGAACTCAAAATT
CGTCCTATGAATGACTTTAATTAA
>g516.t1 Gene=g516 Length=247
METTSRWVNCVAVVTGASAGIGAATCIELANSGIITIGIARRIDKVQALRFCLTTDKQRN
FHAYKCDVSNEAEVKQVFSEIEKKFNGIDILINNAGVFSKSTLIQADNSEDVRRVINTNV
IGVVNCTREAVKSMKMKNEAHIIHIGSFFNQNISQNFGIYQASKHAVAALAEQHRQEFSR
KKLNIKVTTIIPNAVATELYDNSSYEPPKSVELLAAKEIADVIVFALETPRNVVITELKI
RPMNDFN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g516.t1 | Gene3D | G3DSA:3.40.50.720 | - | 3 | 247 | 1.4E-55 |
| 2 | g516.t1 | PANTHER | PTHR43115 | DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 | 5 | 243 | 2.2E-74 |
| 3 | g516.t1 | PANTHER | PTHR43115:SF4 | DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 | 5 | 243 | 2.2E-74 |
| 11 | g516.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 11 | 28 | 1.4E-19 |
| 5 | g516.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 86 | 97 | 2.9E-6 |
| 9 | g516.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 86 | 97 | 1.4E-19 |
| 10 | g516.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 134 | 150 | 1.4E-19 |
| 6 | g516.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 140 | 148 | 2.9E-6 |
| 4 | g516.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 160 | 179 | 2.9E-6 |
| 8 | g516.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 160 | 179 | 1.4E-19 |
| 7 | g516.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 183 | 200 | 1.4E-19 |
| 1 | g516.t1 | Pfam | PF00106 | short chain dehydrogenase | 11 | 203 | 2.5E-45 |
| 13 | g516.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 8 | 235 | 5.46E-53 |
| 12 | g516.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 7 | 29 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g516/g516.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g516.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
## [1] "No matching GO terms"KEGG
Orthology
- This transcript has been annotated with K16066 (3-hydroxy acid dehydrogenase / malonic semialdehyde reductase [EC:1.1.1.381 1.1.1.-])
Pathway
- This transcript belongs to the following pathways
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