General information for g6774.t9
Yuki Yoshida
6/2/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Retinol dehydrogenase 12.
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.t9 | TSS | g6774.t9 | 18559579 | 18559579 |
| chr_2 | g6774 | g6774.t9 | isoform | g6774.t9 | 18559627 | 18562076 |
| chr_2 | g6774 | g6774.t9 | exon | g6774.t9.exon1 | 18559627 | 18559697 |
| chr_2 | g6774 | g6774.t9 | cds | g6774.t9.CDS1 | 18559627 | 18559697 |
| chr_2 | g6774 | g6774.t9 | exon | g6774.t9.exon2 | 18559797 | 18560021 |
| chr_2 | g6774 | g6774.t9 | cds | g6774.t9.CDS2 | 18559797 | 18560021 |
| chr_2 | g6774 | g6774.t9 | exon | g6774.t9.exon3 | 18561393 | 18561754 |
| chr_2 | g6774 | g6774.t9 | cds | g6774.t9.CDS3 | 18561393 | 18561754 |
| chr_2 | g6774 | g6774.t9 | exon | g6774.t9.exon4 | 18561817 | 18562076 |
| chr_2 | g6774 | g6774.t9 | cds | g6774.t9.CDS4 | 18561817 | 18562076 |
| chr_2 | g6774 | g6774.t9 | TTS | g6774.t9 | 18562130 | 18562130 |
Sequences
>g6774.t9 Gene=g6774 Length=918
ATGGAAAACTGTTTTTGTGGAAATAAACTTTTAATTTTAATTGGAGTAGCAAGTTTAATC
TATTTTCTAAAAATCGATGGAAAAATTGTAATCATCACTGGTGCAAATACAGGCATCGGA
AAAGAGACTGCCATTGACTTGGCTAAACGTGGTGGAAAAATTTATATTGCATGTCGCGAT
GAAAAACGCGGTGAGGATGCATTGAAAGAAATAAAAGAAAGAAGTGACAGTGACAAAGTT
CATTTCATGCAACTTGATCTGGCTTCTCTAGAATCTGTTCGTAAATTTTCACAAAGATTT
CATGAGAGAGAAAATCAGTTACATATATTGATAAATAATGCAGGAGTAATGGCTTGTCCA
AGAATGGAAACTAAAGATGGATTTGAATTACAAATTGGAACAAATCATCTTGGACATTTT
TTACTTACACATCTATTACTCGATCTTTTAAAATCAGTGTCTTCATCTCGAATTATTAAT
GTTTCGTCAGCAGCTCACAAGTTTGGTGGTGTAAGCAAAAAAGATTTTATGAGTCAAAAA
AATTATAATAGATGGTTCGCATATGGACAAAGCAAATTGGCGAATATTTTGTTCACACGT
GAATTGGCAAAACGACTAAAAGATTATCCGAATTTAACTGTCAACTCCTGCCACCCTGGT
GCTGTTAATACAGAACTTCAAAGACATATGAATAAATTTCTTTGGGAGTATACATTATTA
CCAATTCTTGGAATATTTTTTAAAACTCCATATGAAGGAGCTCAAACCCAAATTAAGTTG
GCCGTTGATCCTGATTTAGAAGGTGTAACAGGAAAATATTTTGTTGATTGCAAAGAAGCC
AAAACATCAAAAGCAGCTCAAAATGATGATGATGCCGAATGGCTTTATAAAAAAAGTATT
GAATTAGTAGGACTGTAA
>g6774.t9 Gene=g6774 Length=305
MENCFCGNKLLILIGVASLIYFLKIDGKIVIITGANTGIGKETAIDLAKRGGKIYIACRD
EKRGEDALKEIKERSDSDKVHFMQLDLASLESVRKFSQRFHERENQLHILINNAGVMACP
RMETKDGFELQIGTNHLGHFLLTHLLLDLLKSVSSSRIINVSSAAHKFGGVSKKDFMSQK
NYNRWFAYGQSKLANILFTRELAKRLKDYPNLTVNSCHPGAVNTELQRHMNKFLWEYTLL
PILGIFFKTPYEGAQTQIKLAVDPDLEGVTGKYFVDCKEAKTSKAAQNDDDAEWLYKKSI
ELVGL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g6774.t9 | CDD | cd05327 | retinol-DH_like_SDR_c_like | 27 | 296 | 0e+00 |
| 13 | g6774.t9 | Gene3D | G3DSA:3.40.50.720 | - | 22 | 305 | 0e+00 |
| 2 | g6774.t9 | PANTHER | PTHR24320 | RETINOL DEHYDROGENASE | 23 | 304 | 0e+00 |
| 3 | g6774.t9 | PANTHER | PTHR24320:SF142 | GH10714P-RELATED | 23 | 304 | 0e+00 |
| 11 | g6774.t9 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 29 | 46 | 0e+00 |
| 6 | g6774.t9 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 105 | 116 | 3e-07 |
| 10 | g6774.t9 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 105 | 116 | 0e+00 |
| 7 | g6774.t9 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 150 | 166 | 0e+00 |
| 4 | g6774.t9 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 156 | 164 | 3e-07 |
| 5 | g6774.t9 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 188 | 207 | 3e-07 |
| 9 | g6774.t9 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 188 | 207 | 0e+00 |
| 8 | g6774.t9 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 210 | 227 | 0e+00 |
| 1 | g6774.t9 | Pfam | PF00106 | short chain dehydrogenase | 28 | 232 | 0e+00 |
| 12 | g6774.t9 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 26 | 280 | 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.
