General information for g6774.t6
Yuki Yoshida
6/2/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t6 | TSS | g6774.t6 | 18559579 | 18559579 |
| chr_2 | g6774 | g6774.t6 | isoform | g6774.t6 | 18559627 | 18561403 |
| chr_2 | g6774 | g6774.t6 | exon | g6774.t6.exon1 | 18559627 | 18559697 |
| chr_2 | g6774 | g6774.t6 | cds | g6774.t6.CDS1 | 18559627 | 18559697 |
| chr_2 | g6774 | g6774.t6 | exon | g6774.t6.exon2 | 18559758 | 18560797 |
| chr_2 | g6774 | g6774.t6 | cds | g6774.t6.CDS2 | 18559758 | 18560025 |
| chr_2 | g6774 | g6774.t6 | TTS | g6774.t6 | 18560306 | 18560306 |
| chr_2 | g6774 | g6774.t6 | exon | g6774.t6.exon3 | 18561341 | 18561403 |
Sequences
>g6774.t6 Gene=g6774 Length=1174
ATGGAAAACTGTTTTTGTGGAAATAAACTTTTAATTTTAATTGGAGTAGCAAGTTTAATC
TATTTTCTAAAAACATATATTCGTCGAGCAAAATTTACTAAAACTACTAGAATCGATGGA
AAAATTGTAATCATCACTGGTGCAAATACAGGCATCGGAAAAGAGACTGCCATTGACTTG
GCTAAACGTGGTGGAAAAATTTATATTGCATGTCGCGATGAAAAACGCGGTGAGGATGCA
TTGAAAGAAATAAAAGAAAGAAGTGACAGTGACAAAGTTCATTTCATGCAACTTGATCTG
GCTTCTCTAGAATCTGTTCGTAAATTTTCACAAAGGTGATAAAACCAGTGACCAAGTACC
CGTGTTGCAGATCGGTGTACTTAAGCGCATTTTCGGTGCCTAGATCAGTGTTTGTTACAA
AATAACAGTATTATCAGATTCATTTTAATGAAAATAGGTCTGCAATTTAAAATATATGGA
TCGAGTTAATTTTTAATTATATGAGAAATTGGTCCGTAAAGTCTCGGTATATAGCACCAT
CGCGAGTCAAATTTAATTTTTGTAAAACACTTTTAGTTTCAAATGTTATGATTTAATAAA
TTTAAATTGTGGTGAAAATCAATCGTTTAGCAGAAATTCTTTATTTTGGTTTAATTGTTT
ATATGGAAATATAATCCATTAAAATTCGAGTTATTTAACTGTTACGAGCGATTCTTAATC
GTTTGACTTTCCGATTTCTTTGTAAAATATTTTGTTTGATTGATTCGATAATAACGGTCG
AGTCGAATTCAAACATGTGTTGCGCGACAATTGTTTGCAACATTTTGTTGTATGACAAAA
TGTTGCGCGATAAAAAATTTTGTTTACAAATTTTCAATTTGGAAATTTAAATTCGCAATT
TCCCAAGTTATATGACTAATGACAGAAATTTAAATAAGCGTCGCCGCACTAACTTTTTAG
CACAAATCTAACACAGCAAACCGGAAGTCGCTAGCTATTGTAGTTTTCGAGATCTCAGAG
GGACAGCCAGCCAGCCAGCCAGCCAGCCAGCCAGCCAGCCAGCCAAAGTGAATGTATAAG
CTGCATTGTTGTTCCAAAAATGCGCTAAAAAAAATGCAGCTTAACTCTTATCTTATCTTC
TTACACTTTTTCAATATTACTAGATTTCATGAGA
>g6774.t6 Gene=g6774 Length=112
MENCFCGNKLLILIGVASLIYFLKTYIRRAKFTKTTRIDGKIVIITGANTGIGKETAIDL
AKRGGKIYIACRDEKRGEDALKEIKERSDSDKVHFMQLDLASLESVRKFSQR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g6774.t6 | Gene3D | G3DSA:3.40.50.720 | - | 24 | 112 | 1.7E-24 |
| 2 | g6774.t6 | PANTHER | PTHR24320 | RETINOL DEHYDROGENASE | 8 | 111 | 3.6E-32 |
| 3 | g6774.t6 | PANTHER | PTHR24320:SF142 | GH10714P-RELATED | 8 | 111 | 3.6E-32 |
| 1 | g6774.t6 | Pfam | PF00106 | short chain dehydrogenase | 41 | 111 | 8.1E-14 |
| 8 | g6774.t6 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 5 | - |
| 9 | g6774.t6 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 6 | 27 | - |
| 7 | g6774.t6 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 28 | 112 | - |
| 5 | g6774.t6 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 25 | 110 | 5.19E-20 |
| 4 | g6774.t6 | 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.
