General information for g6775.t6
Yuki Yoshida
6/2/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Retinol dehydrogenase 12.
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.t6 | TSS | g6775.t6 | 18562263 | 18562263 |
| chr_2 | g6775 | g6775.t6 | isoform | g6775.t6 | 18562371 | 18563461 |
| chr_2 | g6775 | g6775.t6 | exon | g6775.t6.exon1 | 18562371 | 18562784 |
| chr_2 | g6775 | g6775.t6 | cds | g6775.t6.CDS1 | 18562465 | 18562784 |
| chr_2 | g6775 | g6775.t6 | exon | g6775.t6.exon2 | 18562840 | 18563461 |
| chr_2 | g6775 | g6775.t6 | cds | g6775.t6.CDS2 | 18562840 | 18563461 |
| chr_2 | g6775 | g6775.t6 | TTS | g6775.t6 | 18563567 | 18563567 |
Sequences
>g6775.t6 Gene=g6775 Length=1036
ATGGACTGGTGGCTCATTCTATTAATTATAATTTTAGTGTTATTAGGAATTTTTGCTCTT
TTGTATTTATTAAAGTAAGTATACTTGTGTCATAATGTTAATAAAATTTACAGTTATATC
TGTTCAACATAAAAAAATTATTTCATTCAGATTATACATTAGACGAGCAAGATTCACTAA
AACTACTAGAATTACTGATAAAATTGTAATCATCACTGGTGCAAATACAGGCATCGGAAA
AGAGACTGCCATTGACTTGGCAAAACGAGGTGGGAAAATTTATATTGTATGTCGCGATCA
AAAACGCGGTGAGGATGCATTGAAAGAAATAAAAGAAAGAAGTGGCAGTGACAAAGTTCA
TTTCATGCAACTTGATCTGGCTTCTCTAGAATCTGTTCGTAAATTTTCACTAAGATTTCA
TGAATTGGAGCATCAATTGCACATTCTCATAAATAATGCAGGTGTAATGGCCTGTCCAAA
ATCATATACAGCTGATGGATATGAATTGCAATTTGGAACTAATCATTTAGGGCATTTTCT
GCTCACAAATTTATTGCTTGATTTGTTAAAAGCCGGCGCACCGAGTCGAATAGTAGTTGT
GTCTAGTGCTGCATATCAAATCGGTAGAATAAATAAAGAAGATTTGATGTATGAAAAGAG
TTACAATAAATACAAAGCTTATGGGCAAAGTAAACTTGCAAACATTCTATTTACACGTGA
ATTAGCAAAACGACTTGATGGCACAGGTGTCAATGTCAATAGCTGTCATCCTGGCGTTGT
TCAAACTGAATTAGGAAGATATATGGATGAAAATATTCGAAAGTATTTTATCAAACCTAT
TTTAGGTCCATTTTTTAAAATTCCATATGAAGGAGCCCAAACTCAAATTCGATTAGCTGT
TGATCCTGATTTAGATAAAGTGACAGGAAAATATTTTGCCGATTGCAAAGAACATTCACT
AAGAAGTAATGCACAATGTGAAGAAATTGCAGAATGGCTGTGGAAAAAAAGTGCTGAATT
TGTGGGACCTTGTTAA
>g6775.t6 Gene=g6775 Length=313
MLIKFTVISVQHKKIISFRLYIRRARFTKTTRITDKIVIITGANTGIGKETAIDLAKRGG
KIYIVCRDQKRGEDALKEIKERSGSDKVHFMQLDLASLESVRKFSLRFHELEHQLHILIN
NAGVMACPKSYTADGYELQFGTNHLGHFLLTNLLLDLLKAGAPSRIVVVSSAAYQIGRIN
KEDLMYEKSYNKYKAYGQSKLANILFTRELAKRLDGTGVNVNSCHPGVVQTELGRYMDEN
IRKYFIKPILGPFFKIPYEGAQTQIRLAVDPDLDKVTGKYFADCKEHSLRSNAQCEEIAE
WLWKKSAEFVGPC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g6775.t6 | Gene3D | G3DSA:3.40.50.720 | - | 23 | 312 | 0.0e+00 |
| 2 | g6775.t6 | PANTHER | PTHR24320 | RETINOL DEHYDROGENASE | 16 | 311 | 0.0e+00 |
| 3 | g6775.t6 | PANTHER | PTHR24320:SF142 | GH10714P-RELATED | 16 | 311 | 0.0e+00 |
| 8 | g6775.t6 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 37 | 54 | 0.0e+00 |
| 6 | g6775.t6 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 113 | 124 | 5.3e-05 |
| 11 | g6775.t6 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 113 | 124 | 0.0e+00 |
| 10 | g6775.t6 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 158 | 174 | 0.0e+00 |
| 5 | g6775.t6 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 164 | 172 | 5.3e-05 |
| 4 | g6775.t6 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 196 | 215 | 5.3e-05 |
| 9 | g6775.t6 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 196 | 215 | 0.0e+00 |
| 7 | g6775.t6 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 217 | 234 | 0.0e+00 |
| 1 | g6775.t6 | Pfam | PF00106 | short chain dehydrogenase | 36 | 239 | 0.0e+00 |
| 12 | g6775.t6 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 34 | 288 | 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 transcript has been annotated with K11153 (retinol dehydrogenase 12)
Pathway
- This transcript belongs to the following pathways
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.
