General information for g6775.t3
Yuki Yoshida
6/2/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Retinol dehydrogenase 14.
Parent gene
- The parent gene g6775 is located on chr_2: 18562510..18563461 (+ 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_2 | g6775 | g6775.t3 | TSS | g6775.t3 | 18562263 | 18562263 |
| chr_2 | g6775 | g6775.t3 | isoform | g6775.t3 | 18562371 | 18563461 |
| chr_2 | g6775 | g6775.t3 | exon | g6775.t3.exon1 | 18562371 | 18562444 |
| chr_2 | g6775 | g6775.t3 | exon | g6775.t3.exon2 | 18562521 | 18562785 |
| chr_2 | g6775 | g6775.t3 | exon | g6775.t3.exon3 | 18562840 | 18563461 |
| chr_2 | g6775 | g6775.t3 | cds | g6775.t3.CDS1 | 18562892 | 18563461 |
| chr_2 | g6775 | g6775.t3 | TTS | g6775.t3 | 18563567 | 18563567 |
Sequences
>g6775.t3 Gene=g6775 Length=961
ATGGACTGGTGGCTCATTCTATTAATTATAATTTTAGTGTTATTAGGAATTTTTGCTCTT
TTGTATTTATTAAAATTATACATTAGACGAGCAAGATTCACTAAAACTACTAGAATTACT
GATAAAATTGTAATCATCACTGGTGCAAATACAGGCATCGGAAAAGAGACTGCCATTGAC
TTGGCAAAACGAGGTGGGAAAATTTATATTGTATGTCGCGATCAAAAACGCGGTGAGGAT
GCATTGAAAGAAATAAAAGAAAGAAGTGGCAGTGACAAAGTTCATTTCATGCAACTTGAT
CTGGCTTCTCTAGAATCTGTTCGTAAATTTTCACTAAGGATTTCATGAATTGGAGCATCA
ATTGCACATTCTCATAAATAATGCAGGTGTAATGGCCTGTCCAAAATCATATACAGCTGA
TGGATATGAATTGCAATTTGGAACTAATCATTTAGGGCATTTTCTGCTCACAAATTTATT
GCTTGATTTGTTAAAAGCCGGCGCACCGAGTCGAATAGTAGTTGTGTCTAGTGCTGCATA
TCAAATCGGTAGAATAAATAAAGAAGATTTGATGTATGAAAAGAGTTACAATAAATACAA
AGCTTATGGGCAAAGTAAACTTGCAAACATTCTATTTACACGTGAATTAGCAAAACGACT
TGATGGCACAGGTGTCAATGTCAATAGCTGTCATCCTGGCGTTGTTCAAACTGAATTAGG
AAGATATATGGATGAAAATATTCGAAAGTATTTTATCAAACCTATTTTAGGTCCATTTTT
TAAAATTCCATATGAAGGAGCCCAAACTCAAATTCGATTAGCTGTTGATCCTGATTTAGA
TAAAGTGACAGGAAAATATTTTGCCGATTGCAAAGAACATTCACTAAGAAGTAATGCACA
ATGTGAAGAAATTGCAGAATGGCTGTGGAAAAAAAGTGCTGAATTTGTGGGACCTTGTTA
A
>g6775.t3 Gene=g6775 Length=189
MACPKSYTADGYELQFGTNHLGHFLLTNLLLDLLKAGAPSRIVVVSSAAYQIGRINKEDL
MYEKSYNKYKAYGQSKLANILFTRELAKRLDGTGVNVNSCHPGVVQTELGRYMDENIRKY
FIKPILGPFFKIPYEGAQTQIRLAVDPDLDKVTGKYFADCKEHSLRSNAQCEEIAEWLWK
KSAEFVGPC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g6775.t3 | Gene3D | G3DSA:3.40.50.720 | - | 1 | 188 | 0.0e+00 |
| 2 | g6775.t3 | PANTHER | PTHR24320 | RETINOL DEHYDROGENASE | 1 | 187 | 0.0e+00 |
| 3 | g6775.t3 | PANTHER | PTHR24320:SF142 | GH10714P-RELATED | 1 | 187 | 0.0e+00 |
| 4 | g6775.t3 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 34 | 50 | 5.5e-06 |
| 6 | g6775.t3 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 72 | 91 | 5.5e-06 |
| 5 | g6775.t3 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 93 | 110 | 5.5e-06 |
| 1 | g6775.t3 | Pfam | PF00106 | short chain dehydrogenase | 13 | 115 | 0.0e+00 |
| 7 | g6775.t3 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 6 | 164 | 0.0e+00 |
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