General information for g6775.t1
Yuki Yoshida
6/2/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t1 | TSS | g6775.t1 | 18562263 | 18562263 |
| chr_2 | g6775 | g6775.t1 | isoform | g6775.t1 | 18562371 | 18563461 |
| chr_2 | g6775 | g6775.t1 | exon | g6775.t1.exon1 | 18562371 | 18562444 |
| chr_2 | g6775 | g6775.t1 | cds | g6775.t1.CDS1 | 18562371 | 18562444 |
| chr_2 | g6775 | g6775.t1 | exon | g6775.t1.exon2 | 18562521 | 18562768 |
| chr_2 | g6775 | g6775.t1 | cds | g6775.t1.CDS2 | 18562521 | 18562768 |
| chr_2 | g6775 | g6775.t1 | exon | g6775.t1.exon3 | 18562887 | 18563461 |
| chr_2 | g6775 | g6775.t1 | cds | g6775.t1.CDS3 | 18562887 | 18563461 |
| chr_2 | g6775 | g6775.t1 | TTS | g6775.t1 | 18563567 | 18563567 |
Sequences
>g6775.t1 Gene=g6775 Length=897
ATGGACTGGTGGCTCATTCTATTAATTATAATTTTAGTGTTATTAGGAATTTTTGCTCTT
TTGTATTTATTAAAATTATACATTAGACGAGCAAGATTCACTAAAACTACTAGAATTACT
GATAAAATTGTAATCATCACTGGTGCAAATACAGGCATCGGAAAAGAGACTGCCATTGAC
TTGGCAAAACGAGGTGGGAAAATTTATATTGTATGTCGCGATCAAAAACGCGGTGAGGAT
GCATTGAAAGAAATAAAAGAAAGAAGTGGCAGTGACAAAGTTCATTTCATGCAACTTGAT
CTGGCTTCTCTAGAATCTGTTCGTGTAATGGCCTGTCCAAAATCATATACAGCTGATGGA
TATGAATTGCAATTTGGAACTAATCATTTAGGGCATTTTCTGCTCACAAATTTATTGCTT
GATTTGTTAAAAGCCGGCGCACCGAGTCGAATAGTAGTTGTGTCTAGTGCTGCATATCAA
ATCGGTAGAATAAATAAAGAAGATTTGATGTATGAAAAGAGTTACAATAAATACAAAGCT
TATGGGCAAAGTAAACTTGCAAACATTCTATTTACACGTGAATTAGCAAAACGACTTGAT
GGCACAGGTGTCAATGTCAATAGCTGTCATCCTGGCGTTGTTCAAACTGAATTAGGAAGA
TATATGGATGAAAATATTCGAAAGTATTTTATCAAACCTATTTTAGGTCCATTTTTTAAA
ATTCCATATGAAGGAGCCCAAACTCAAATTCGATTAGCTGTTGATCCTGATTTAGATAAA
GTGACAGGAAAATATTTTGCCGATTGCAAAGAACATTCACTAAGAAGTAATGCACAATGT
GAAGAAATTGCAGAATGGCTGTGGAAAAAAAGTGCTGAATTTGTGGGACCTTGTTAA
>g6775.t1 Gene=g6775 Length=298
MDWWLILLIIILVLLGIFALLYLLKLYIRRARFTKTTRITDKIVIITGANTGIGKETAID
LAKRGGKIYIVCRDQKRGEDALKEIKERSGSDKVHFMQLDLASLESVRVMACPKSYTADG
YELQFGTNHLGHFLLTNLLLDLLKAGAPSRIVVVSSAAYQIGRINKEDLMYEKSYNKYKA
YGQSKLANILFTRELAKRLDGTGVNVNSCHPGVVQTELGRYMDENIRKYFIKPILGPFFK
IPYEGAQTQIRLAVDPDLDKVTGKYFADCKEHSLRSNAQCEEIAEWLWKKSAEFVGPC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g6775.t1 | Gene3D | G3DSA:3.40.50.720 | - | 29 | 297 | 8.5E-74 |
| 4 | g6775.t1 | PANTHER | PTHR24320 | RETINOL DEHYDROGENASE | 9 | 108 | 2.7E-116 |
| 6 | g6775.t1 | PANTHER | PTHR24320:SF142 | GH10714P-RELATED | 9 | 108 | 2.7E-116 |
| 3 | g6775.t1 | PANTHER | PTHR24320 | RETINOL DEHYDROGENASE | 109 | 296 | 2.7E-116 |
| 5 | g6775.t1 | PANTHER | PTHR24320:SF142 | GH10714P-RELATED | 109 | 296 | 2.7E-116 |
| 9 | g6775.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 43 | 60 | 5.7E-13 |
| 8 | g6775.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 143 | 159 | 5.7E-13 |
| 10 | g6775.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 181 | 200 | 5.7E-13 |
| 7 | g6775.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 202 | 219 | 5.7E-13 |
| 1 | g6775.t1 | Pfam | PF00106 | short chain dehydrogenase | 42 | 108 | 2.3E-12 |
| 2 | g6775.t1 | Pfam | PF00106 | short chain dehydrogenase | 121 | 224 | 8.7E-12 |
| 15 | g6775.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 5 | - |
| 16 | g6775.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 6 | 28 | - |
| 14 | g6775.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 29 | 298 | - |
| 12 | g6775.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 40 | 273 | 6.67E-51 |
| 11 | g6775.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 4 | 26 | - |
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.
