General information for g6799.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 g6799 is located on chr_2: 18779725..18780914 (+ 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 | g6799 | g6799.t1 | TSS | g6799.t1 | 18779689 | 18779689 |
| chr_2 | g6799 | g6799.t1 | isoform | g6799.t1 | 18779725 | 18780914 |
| chr_2 | g6799 | g6799.t1 | exon | g6799.t1.exon1 | 18779725 | 18779798 |
| chr_2 | g6799 | g6799.t1 | cds | g6799.t1.CDS1 | 18779725 | 18779798 |
| chr_2 | g6799 | g6799.t1 | exon | g6799.t1.exon2 | 18779854 | 18779924 |
| chr_2 | g6799 | g6799.t1 | cds | g6799.t1.CDS2 | 18779854 | 18779924 |
| chr_2 | g6799 | g6799.t1 | exon | g6799.t1.exon3 | 18779985 | 18780177 |
| chr_2 | g6799 | g6799.t1 | cds | g6799.t1.CDS3 | 18779985 | 18780177 |
| chr_2 | g6799 | g6799.t1 | exon | g6799.t1.exon4 | 18780238 | 18780593 |
| chr_2 | g6799 | g6799.t1 | cds | g6799.t1.CDS4 | 18780238 | 18780593 |
| chr_2 | g6799 | g6799.t1 | exon | g6799.t1.exon5 | 18780646 | 18780914 |
| chr_2 | g6799 | g6799.t1 | cds | g6799.t1.CDS5 | 18780646 | 18780914 |
| chr_2 | g6799 | g6799.t1 | TTS | g6799.t1 | 18780930 | 18780930 |
Sequences
>g6799.t1 Gene=g6799 Length=963
ATGGAGTGGTGGTTGATATTGATTATTGTTCTTTCTGTCCTTATTGCTTTTGGAACTTTT
TTATATCTTTTTAGATTATACATGAGACAAGGAAGATATAAAAAACAAAATAGAATTGAT
CATAACGTTGTGATAATAACAGGAGCTAATACGGGGATTGGAAAAGAGACTGCAATTGAT
TTAGCTCGACGAGGTGCAAGAGTTTATATTGCATGTCGGGACATTAAAAGAGGACTTGAT
GCACTTGATGACATAAGAAGACATAGTAGAAGTGACTTTGTATATTTCTTACAATTAGAC
TTAGCTTCTTTTGATTCAATAAGAAATTTTGTTCAAAGATTTCGAGAGCATGAACACAAA
TTGCACATTCTTATCAATAATGCCGGACTTTTGGCGAAAAACTCAAATACCAAAGATGGG
TTTGAAATGACTATTGGTGTGAATCATTTGGGTCATTTTCTTCTAACACATTTGCTTCTT
GATTTGTTAATTGTTTCTGCACCAAGTAGAATTGTCAACGTTTCATCTCTTGGACATAAA
TTTGCAAAACTTGAATATGATGACTTTGACAGTAATAAGAAAATGTCTGTAGCTACTGCA
TATGCAAAGAGTAAATTAATGAATATTTTATTCACACGAAAATTAGCACAAAAATTGATT
GCTGAAAAAGTTAGCGTCAACAGTTGTCATCCAGGTTGTGTTCGAACTGAAATTGCAAGA
AATTTTTCAACATATGATTTCTTGACTACAAAAATTCTTGGAGAATTTTTAAAATCTCCA
TATGAAGGTGCTCAAACACAAATTCGAATAGCAGTTGATCCAGAACTGGAAAATGTTACA
GGAAAATATTTTGTTGATTGTAAACCAGCAAGTGTCTCTAAAGAAGCTAAAAATGATGAA
AAAGCTGAATGGTTATATCGAAAAAGTTATGAACTTGTTGGACTTGAAAAAATAGAACTT
TAA
>g6799.t1 Gene=g6799 Length=320
MEWWLILIIVLSVLIAFGTFLYLFRLYMRQGRYKKQNRIDHNVVIITGANTGIGKETAID
LARRGARVYIACRDIKRGLDALDDIRRHSRSDFVYFLQLDLASFDSIRNFVQRFREHEHK
LHILINNAGLLAKNSNTKDGFEMTIGVNHLGHFLLTHLLLDLLIVSAPSRIVNVSSLGHK
FAKLEYDDFDSNKKMSVATAYAKSKLMNILFTRKLAQKLIAEKVSVNSCHPGCVRTEIAR
NFSTYDFLTTKILGEFLKSPYEGAQTQIRIAVDPELENVTGKYFVDCKPASVSKEAKNDE
KAEWLYRKSYELVGLEKIEL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g6799.t1 | Gene3D | G3DSA:3.40.50.720 | - | 30 | 317 | 5.2E-78 |
| 2 | g6799.t1 | PANTHER | PTHR24320 | RETINOL DEHYDROGENASE | 11 | 315 | 3.7E-115 |
| 3 | g6799.t1 | PANTHER | PTHR24320:SF142 | GH10714P-RELATED | 11 | 315 | 3.7E-115 |
| 10 | g6799.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 43 | 60 | 1.4E-17 |
| 5 | g6799.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 119 | 130 | 3.7E-6 |
| 9 | g6799.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 119 | 130 | 1.4E-17 |
| 11 | g6799.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 163 | 179 | 1.4E-17 |
| 6 | g6799.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 169 | 177 | 3.7E-6 |
| 4 | g6799.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 201 | 220 | 3.7E-6 |
| 8 | g6799.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 201 | 220 | 1.4E-17 |
| 7 | g6799.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 222 | 239 | 1.4E-17 |
| 1 | g6799.t1 | Pfam | PF00106 | short chain dehydrogenase | 42 | 242 | 6.4E-35 |
| 16 | g6799.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 5 | - |
| 17 | g6799.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 6 | 28 | - |
| 15 | g6799.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 29 | 320 | - |
| 13 | g6799.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 41 | 290 | 8.24E-55 |
| 12 | g6799.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. There were no conditions that were differentially expressed