General information for g6776.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Retinol dehydrogenase 12.
Parent gene
- The parent gene g6776 is located on chr_2: 18563913..18567386 (+ 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 | g6776 | g6776.t1 | TSS | g6776.t1 | 18563759 | 18563759 |
| chr_2 | g6776 | g6776.t1 | isoform | g6776.t1 | 18563913 | 18564968 |
| chr_2 | g6776 | g6776.t1 | exon | g6776.t1.exon1 | 18563913 | 18564007 |
| chr_2 | g6776 | g6776.t1 | cds | g6776.t1.CDS1 | 18563913 | 18564007 |
| chr_2 | g6776 | g6776.t1 | exon | g6776.t1.exon2 | 18564074 | 18564968 |
| chr_2 | g6776 | g6776.t1 | cds | g6776.t1.CDS2 | 18564074 | 18564968 |
| chr_2 | g6776 | g6776.t1 | TTS | g6776.t1 | 18565061 | 18565061 |
Sequences
>g6776.t1 Gene=g6776 Length=990
ATGGATGATGATAATAAAGAAACTCCATTGTGGCTAAAAGCCGTATATTATATTCTTCCA
ATATTTGGCACATCAGGACTACTTTATTTATTTAGATACTTCATGAAGAGTGACATGTAT
AAGAAAGAAACTAAAATTGGTGGAAAAGTCGTTCTTATAACTGGAATTAACTCTGATATT
GGAATTTCAACTGCAATTAATTTGGCAAAACGTGACGGTAAAATCTATATTGCATGTGAT
GACAGTACTCGTGGTGAGGAAGTATTGAAAGAAATTAAAAAAAAATCAAAACGTGACAAC
ATTCACTTTATGAATCTTAATCTGGGATCATTAGAATCTATCCGACAGTTTTCTAAAAAA
TTTCATGAAATGGAAAAAAAGTTAGACATTTTAATTAACAATCATGAATTGGTGGCAAAA
GAAAAATCTAAAACTGTTGAGGGATATGAACTCCATATGGGTGTAAACTATTTGGGACAT
TTTTATCTTACACATCTTTTGCTTGATTTACTTAAAAGTGCAGCTCCTAGTAGAATTATT
TTTGAAAGCTCTCTTGCTTATAAATGGGGTACAATTAACAAGGAAGATTTTATGAGTGAT
AATTCGTATAATCGATTCAAAGCATATTGTAATAGCAAACTGGCTATTCATCTTCTTGTA
CATGAATTGGCAAAAGAATTATCTGGTAGCTTGTGCACAGTGAATATAGCAATGCCTGGT
TTTGTTATAAGTGATATTGTAAGAAGAATTACTGGATTTTCTAAAGTGCAAAAAGTTTTG
GAATGGATGGGAGCAAAATTTATTAACACAGGCAAGGAAGGTGCACAAACAGTAATATTT
ACAGCAGTTGATACTGATATAAGTACTATTTCCGGAAAATGTTATGTTAATTGCAAGGAA
ATTCAACCATCTAGTAAGTCAACTGAAGATGAAACATCCACATGGTTGTGGAAGAAGGGA
GAAGAGATATTGGGTATAAATTACGTTTAG
>g6776.t1 Gene=g6776 Length=329
MDDDNKETPLWLKAVYYILPIFGTSGLLYLFRYFMKSDMYKKETKIGGKVVLITGINSDI
GISTAINLAKRDGKIYIACDDSTRGEEVLKEIKKKSKRDNIHFMNLNLGSLESIRQFSKK
FHEMEKKLDILINNHELVAKEKSKTVEGYELHMGVNYLGHFYLTHLLLDLLKSAAPSRII
FESSLAYKWGTINKEDFMSDNSYNRFKAYCNSKLAIHLLVHELAKELSGSLCTVNIAMPG
FVISDIVRRITGFSKVQKVLEWMGAKFINTGKEGAQTVIFTAVDTDISTISGKCYVNCKE
IQPSSKSTEDETSTWLWKKGEEILGINYV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g6776.t1 | Coils | Coil | Coil | 114 | 134 | - |
| 9 | g6776.t1 | Gene3D | G3DSA:3.40.50.720 | - | 39 | 329 | 4.1E-62 |
| 2 | g6776.t1 | PANTHER | PTHR24320 | RETINOL DEHYDROGENASE | 24 | 325 | 2.4E-91 |
| 3 | g6776.t1 | PANTHER | PTHR24320:SF142 | GH10714P-RELATED | 24 | 325 | 2.4E-91 |
| 6 | g6776.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 50 | 67 | 8.4E-10 |
| 7 | g6776.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 126 | 137 | 8.4E-10 |
| 5 | g6776.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 209 | 228 | 8.4E-10 |
| 4 | g6776.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 230 | 247 | 8.4E-10 |
| 1 | g6776.t1 | Pfam | PF00106 | short chain dehydrogenase | 49 | 249 | 4.5E-25 |
| 12 | g6776.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 13 | - |
| 13 | g6776.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 14 | 35 | - |
| 11 | g6776.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 36 | 329 | - |
| 16 | g6776.t1 | ProSitePatterns | PS00061 | Short-chain dehydrogenases/reductases family signature. | 196 | 224 | - |
| 8 | g6776.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 48 | 301 | 2.49E-44 |
| 15 | g6776.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 15 | 34 | - |
| 14 | g6776.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 46 | 68 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0055114 | NA | NA |
| GO:0016491 | oxidoreductase activity | MF |
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