General information for g6798.t1
Yuki Yoshida
6/2/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Retinol dehydrogenase 12.
Parent gene
- The parent gene g6798 is located on chr_2: 18778162..18779297 (+ 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 | g6798 | g6798.t1 | TSS | g6798.t1 | 18778133 | 18778133 |
| chr_2 | g6798 | g6798.t1 | isoform | g6798.t1 | 18778162 | 18779297 |
| chr_2 | g6798 | g6798.t1 | exon | g6798.t1.exon1 | 18778162 | 18778226 |
| chr_2 | g6798 | g6798.t1 | cds | g6798.t1.CDS1 | 18778162 | 18778226 |
| chr_2 | g6798 | g6798.t1 | exon | g6798.t1.exon2 | 18778282 | 18778545 |
| chr_2 | g6798 | g6798.t1 | cds | g6798.t1.CDS2 | 18778282 | 18778545 |
| chr_2 | g6798 | g6798.t1 | exon | g6798.t1.exon3 | 18778617 | 18778975 |
| chr_2 | g6798 | g6798.t1 | cds | g6798.t1.CDS3 | 18778617 | 18778975 |
| chr_2 | g6798 | g6798.t1 | exon | g6798.t1.exon4 | 18779044 | 18779297 |
| chr_2 | g6798 | g6798.t1 | cds | g6798.t1.CDS4 | 18779044 | 18779297 |
| chr_2 | g6798 | g6798.t1 | TTS | g6798.t1 | 18779449 | 18779449 |
Sequences
>g6798.t1 Gene=g6798 Length=942
ATGACTTTCTGCGTTTGCTTGAAATATACTTTACTTGGTATTGTTATTCTTTCGTACTTC
TTAAGAAAATATGCAAAAGGCCAAAAATACACAAAGAAAACTTTAATTGAAAATAAAGTT
GTGATCATCACTGGTGCTAATACGGGAATCGGGAAAGCAACAGCAATTGATTTAGCAAAA
CGGGGTGGAAAAGTTTATATTGCCTGCCGAGACGAAAAACGCGGTGAAGATGCATTGAAA
GAAATCAAGAGAGAAAGTGGAAGTGACAATGTTCACTTTATACAGCTTGATTTAGGTTCA
ACAGAATCAATAAGAGAATTTTCTCAAAAATTTCATGAAAAAGAAGAAAAGTTACACATT
CTTATCAACAACGCTGGAATATTTGCGCCTCCTCAGAAGAAAACTAAAGATGGATTTGAA
ATCACTATAGGTGTCAATCATCTTGGACATTTTCTTTTAACTCATTTACTACTTGATTTA
CTTAAAAATTCAGCACCAAGTCGCATTATCAACGTATCTTCTGGAGCACATAAAATGGTT
CCTATTGAAAAAGATGATTTCATGCAAACTGCAAGACAGAGTAATATGAATGCATATGCC
AAAAGTAAATTAGCTAATGTGATGTTCAGTCAAGAATTGGTTAAGAAATTAAAACATTTT
TCTGTTTCTGTCAACAGTTTGCATCCTGGTGTAGTTCATACTGAAATTACAAGAAGTTGG
CCTCTGTGGGATTTCATTTTGAATATTATTTTCAGGCCATTTTTAAGAACACCAGTGGAA
GGAGCACAAACTCAAATCCGTCTTGCTGTTGATCCAGCATTAGAAAATGTCACTGGAAAA
TATTTTGAAAACTGCAAACAGGCAAAAGTTTCAAAATTTGCTCTTGATCATGACATAGCA
GAATGGCTTTATAAAAAAAGTTATGAACTAGTTAAATTGTAA
>g6798.t1 Gene=g6798 Length=313
MTFCVCLKYTLLGIVILSYFLRKYAKGQKYTKKTLIENKVVIITGANTGIGKATAIDLAK
RGGKVYIACRDEKRGEDALKEIKRESGSDNVHFIQLDLGSTESIREFSQKFHEKEEKLHI
LINNAGIFAPPQKKTKDGFEITIGVNHLGHFLLTHLLLDLLKNSAPSRIINVSSGAHKMV
PIEKDDFMQTARQSNMNAYAKSKLANVMFSQELVKKLKHFSVSVNSLHPGVVHTEITRSW
PLWDFILNIIFRPFLRTPVEGAQTQIRLAVDPALENVTGKYFENCKQAKVSKFALDHDIA
EWLYKKSYELVKL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g6798.t1 | CDD | cd05327 | retinol-DH_like_SDR_c_like | 39 | 304 | 0.0e+00 |
| 13 | g6798.t1 | Gene3D | G3DSA:3.40.50.720 | - | 29 | 313 | 0.0e+00 |
| 2 | g6798.t1 | PANTHER | PTHR24320 | RETINOL DEHYDROGENASE | 10 | 312 | 0.0e+00 |
| 3 | g6798.t1 | PANTHER | PTHR24320:SF142 | GH10714P-RELATED | 10 | 312 | 0.0e+00 |
| 10 | g6798.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 40 | 57 | 0.0e+00 |
| 5 | g6798.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 116 | 127 | 1.1e-05 |
| 9 | g6798.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 116 | 127 | 0.0e+00 |
| 8 | g6798.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 161 | 177 | 0.0e+00 |
| 6 | g6798.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 167 | 175 | 1.1e-05 |
| 4 | g6798.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 199 | 218 | 1.1e-05 |
| 7 | g6798.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 199 | 218 | 0.0e+00 |
| 11 | g6798.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 220 | 237 | 0.0e+00 |
| 1 | g6798.t1 | Pfam | PF00106 | short chain dehydrogenase | 39 | 240 | 0.0e+00 |
| 12 | g6798.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 37 | 289 | 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.
