General information for g6774.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 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.t1 | TSS | g6774.t1 | 18559579 | 18559579 |
| chr_2 | g6774 | g6774.t1 | isoform | g6774.t1 | 18559627 | 18562076 |
| chr_2 | g6774 | g6774.t1 | exon | g6774.t1.exon1 | 18559627 | 18559697 |
| chr_2 | g6774 | g6774.t1 | cds | g6774.t1.CDS1 | 18559627 | 18559697 |
| chr_2 | g6774 | g6774.t1 | exon | g6774.t1.exon2 | 18559758 | 18560021 |
| chr_2 | g6774 | g6774.t1 | cds | g6774.t1.CDS2 | 18559758 | 18560021 |
| chr_2 | g6774 | g6774.t1 | exon | g6774.t1.exon3 | 18561393 | 18561754 |
| chr_2 | g6774 | g6774.t1 | cds | g6774.t1.CDS3 | 18561393 | 18561754 |
| chr_2 | g6774 | g6774.t1 | exon | g6774.t1.exon4 | 18561817 | 18562076 |
| chr_2 | g6774 | g6774.t1 | cds | g6774.t1.CDS4 | 18561817 | 18562076 |
| chr_2 | g6774 | g6774.t1 | TTS | g6774.t1 | 18562130 | 18562130 |
Sequences
>g6774.t1 Gene=g6774 Length=957
ATGGAAAACTGTTTTTGTGGAAATAAACTTTTAATTTTAATTGGAGTAGCAAGTTTAATC
TATTTTCTAAAAACATATATTCGTCGAGCAAAATTTACTAAAACTACTAGAATCGATGGA
AAAATTGTAATCATCACTGGTGCAAATACAGGCATCGGAAAAGAGACTGCCATTGACTTG
GCTAAACGTGGTGGAAAAATTTATATTGCATGTCGCGATGAAAAACGCGGTGAGGATGCA
TTGAAAGAAATAAAAGAAAGAAGTGACAGTGACAAAGTTCATTTCATGCAACTTGATCTG
GCTTCTCTAGAATCTGTTCGTAAATTTTCACAAAGATTTCATGAGAGAGAAAATCAGTTA
CATATATTGATAAATAATGCAGGAGTAATGGCTTGTCCAAGAATGGAAACTAAAGATGGA
TTTGAATTACAAATTGGAACAAATCATCTTGGACATTTTTTACTTACACATCTATTACTC
GATCTTTTAAAATCAGTGTCTTCATCTCGAATTATTAATGTTTCGTCAGCAGCTCACAAG
TTTGGTGGTGTAAGCAAAAAAGATTTTATGAGTCAAAAAAATTATAATAGATGGTTCGCA
TATGGACAAAGCAAATTGGCGAATATTTTGTTCACACGTGAATTGGCAAAACGACTAAAA
GATTATCCGAATTTAACTGTCAACTCCTGCCACCCTGGTGCTGTTAATACAGAACTTCAA
AGACATATGAATAAATTTCTTTGGGAGTATACATTATTACCAATTCTTGGAATATTTTTT
AAAACTCCATATGAAGGAGCTCAAACCCAAATTAAGTTGGCCGTTGATCCTGATTTAGAA
GGTGTAACAGGAAAATATTTTGTTGATTGCAAAGAAGCCAAAACATCAAAAGCAGCTCAA
AATGATGATGATGCCGAATGGCTTTATAAAAAAAGTATTGAATTAGTAGGACTGTAA
>g6774.t1 Gene=g6774 Length=318
MENCFCGNKLLILIGVASLIYFLKTYIRRAKFTKTTRIDGKIVIITGANTGIGKETAIDL
AKRGGKIYIACRDEKRGEDALKEIKERSDSDKVHFMQLDLASLESVRKFSQRFHERENQL
HILINNAGVMACPRMETKDGFELQIGTNHLGHFLLTHLLLDLLKSVSSSRIINVSSAAHK
FGGVSKKDFMSQKNYNRWFAYGQSKLANILFTRELAKRLKDYPNLTVNSCHPGAVNTELQ
RHMNKFLWEYTLLPILGIFFKTPYEGAQTQIKLAVDPDLEGVTGKYFVDCKEAKTSKAAQ
NDDDAEWLYKKSIELVGL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g6774.t1 | CDD | cd05327 | retinol-DH_like_SDR_c_like | 40 | 309 | 1.79875E-115 |
| 13 | g6774.t1 | Gene3D | G3DSA:3.40.50.720 | - | 27 | 318 | 5.7E-91 |
| 2 | g6774.t1 | PANTHER | PTHR24320 | RETINOL DEHYDROGENASE | 8 | 317 | 1.2E-130 |
| 3 | g6774.t1 | PANTHER | PTHR24320:SF142 | GH10714P-RELATED | 8 | 317 | 1.2E-130 |
| 10 | g6774.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 42 | 59 | 1.1E-19 |
| 4 | g6774.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 118 | 129 | 2.9E-7 |
| 7 | g6774.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 118 | 129 | 1.1E-19 |
| 11 | g6774.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 163 | 179 | 1.1E-19 |
| 6 | g6774.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 169 | 177 | 2.9E-7 |
| 5 | g6774.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 201 | 220 | 2.9E-7 |
| 8 | g6774.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 201 | 220 | 1.1E-19 |
| 9 | g6774.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 223 | 240 | 1.1E-19 |
| 1 | g6774.t1 | Pfam | PF00106 | short chain dehydrogenase | 41 | 245 | 1.2E-37 |
| 15 | g6774.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 5 | - |
| 16 | g6774.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 6 | 27 | - |
| 14 | g6774.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 28 | 318 | - |
| 12 | g6774.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 39 | 293 | 1.25E-61 |
| 18 | g6774.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 10 | 27 | - |
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.
