General information for g6774.t16
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 g6774 is located on chr_2: 18561390..18562076 (+ 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 | g6774 | g6774.t16 | TSS | g6774.t16 | 18559579 | 18559579 |
| chr_2 | g6774 | g6774.t16 | isoform | g6774.t16 | 18559627 | 18562076 |
| chr_2 | g6774 | g6774.t16 | exon | g6774.t16.exon1 | 18559627 | 18559697 |
| chr_2 | g6774 | g6774.t16 | exon | g6774.t16.exon2 | 18561587 | 18561754 |
| chr_2 | g6774 | g6774.t16 | cds | g6774.t16.CDS1 | 18561625 | 18561754 |
| chr_2 | g6774 | g6774.t16 | exon | g6774.t16.exon3 | 18561817 | 18562076 |
| chr_2 | g6774 | g6774.t16 | cds | g6774.t16.CDS2 | 18561817 | 18562076 |
| chr_2 | g6774 | g6774.t16 | TTS | g6774.t16 | 18562130 | 18562130 |
Sequences
>g6774.t16 Gene=g6774 Length=499
ATGGAAAACTGTTTTTGTGGAAATAAACTTTTAATTTTAATTGGAGTAGCAAGTTTAATC
TATTTTCTAAACAGCTCACAAGTTTGGTGGTGTAAGCAAAAAAGATTTTATGAGTCAAAA
AAATTATAATAGATGGTTCGCATATGGACAAAGCAAATTGGCGAATATTTTGTTCACACG
TGAATTGGCAAAACGACTAAAAGATTATCCGAATTTAACTGTCAACTCCTGCCACCCTGG
TGCTGTTAATACAGAACTTCAAAGACATATGAATAAATTTCTTTGGGAGTATACATTATT
ACCAATTCTTGGAATATTTTTTAAAACTCCATATGAAGGAGCTCAAACCCAAATTAAGTT
GGCCGTTGATCCTGATTTAGAAGGTGTAACAGGAAAATATTTTGTTGATTGCAAAGAAGC
CAAAACATCAAAAGCAGCTCAAAATGATGATGATGCCGAATGGCTTTATAAAAAAAGTAT
TGAATTAGTAGGACTGTAA
>g6774.t16 Gene=g6774 Length=129
MSQKNYNRWFAYGQSKLANILFTRELAKRLKDYPNLTVNSCHPGAVNTELQRHMNKFLWE
YTLLPILGIFFKTPYEGAQTQIKLAVDPDLEGVTGKYFVDCKEAKTSKAAQNDDDAEWLY
KKSIELVGL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g6774.t16 | Gene3D | G3DSA:3.40.50.720 | - | 1 | 129 | 0e+00 |
| 2 | g6774.t16 | PANTHER | PTHR24320 | RETINOL DEHYDROGENASE | 1 | 128 | 0e+00 |
| 3 | g6774.t16 | PANTHER | PTHR24320:SF142 | GH10714P-RELATED | 1 | 128 | 0e+00 |
| 1 | g6774.t16 | Pfam | PF00106 | short chain dehydrogenase | 3 | 56 | 2e-07 |
| 4 | g6774.t16 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 7 | 104 | 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.
