General information for g4120.t18
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Retinal dehydrogenase 1.
Parent gene
- The parent gene g4120 is located on chr_3: 30730080..30735128 (- 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_3 | g4120 | g4120.t18 | TTS | g4120.t18 | 30727131 | 30727131 |
| chr_3 | g4120 | g4120.t18 | isoform | g4120.t18 | 30727171 | 30728083 |
| chr_3 | g4120 | g4120.t18 | exon | g4120.t18.exon1 | 30727171 | 30727823 |
| chr_3 | g4120 | g4120.t18 | cds | g4120.t18.CDS1 | 30727171 | 30727823 |
| chr_3 | g4120 | g4120.t18 | exon | g4120.t18.exon2 | 30727890 | 30727928 |
| chr_3 | g4120 | g4120.t18 | cds | g4120.t18.CDS2 | 30727890 | 30727928 |
| chr_3 | g4120 | g4120.t18 | exon | g4120.t18.exon3 | 30728016 | 30728083 |
| chr_3 | g4120 | g4120.t18 | cds | g4120.t18.CDS3 | 30728016 | 30728019 |
| chr_3 | g4120 | g4120.t18 | TSS | g4120.t18 | NA | NA |
Sequences
>g4120.t18 Gene=g4120 Length=760
TCTGATGAAGTTAAAATTTAAAATTAAAAGAGTTTAAAATTCATTTTTTCAATTCATTTT
CAATATGAGTGGTAAGAGTCCTCTTGTAATCTTTGATGATGTTAATCTTGATGAAGTTGT
TCCACTTGCTCAAGATGCTATTTTTACAAACTCTGGTCAGATTTGTTGTGGAGGATCAAG
AACATTTGTACAAGAAAGAATTTATGATGAATTTGTCAAACGTACTGTTGAAAATGCAAA
AAAAAGAAAAGTTGGTTGTCCATTCAAAGAGGATACTGTGCAAGGGCCACAAGTTGATCA
AGATACATTTGATAAGATCTTGAAATACATTGATTATGGCAAAGAAGATGGTGCAAAATT
GGAAGCCGGTGGAAAGAGATGGGGCAATGAAGGTTTCTATATTGAACCAACTGTTTTCTC
AAATGTTACTGACGATATGCGCATTGCACAAGATGAAATTTTCGGACCTGTTCAATCGAT
TCTCAAGTTCAAGACAATTGATGAAGTTATTGAGCGTGCTAATAATACAACTTATGGATT
AGCTGCTGGTGTCTTTACAAATGACATCAATAAAGCTTTGACATTTGCAAATGCAGTCGA
AGCTGGATCAGTTTGGGTTAATTGTTATAATGCAACAAATGTTTGCTCTCCTTTCGGAGG
CTACAAACAGAGTGGTATTGGAAGAGAATTGGGAGAAGAAGGAATCAATTTATACTTGGA
AACTAAAGCAGTTTCTATTAAATTACCAGCCAAAAATTAA
>g4120.t18 Gene=g4120 Length=231
MSGKSPLVIFDDVNLDEVVPLAQDAIFTNSGQICCGGSRTFVQERIYDEFVKRTVENAKK
RKVGCPFKEDTVQGPQVDQDTFDKILKYIDYGKEDGAKLEAGGKRWGNEGFYIEPTVFSN
VTDDMRIAQDEIFGPVQSILKFKTIDEVIERANNTTYGLAAGVFTNDINKALTFANAVEA
GSVWVNCYNATNVCSPFGGYKQSGIGRELGEEGINLYLETKAVSIKLPAKN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g4120.t18 | Gene3D | G3DSA:3.40.605.10 | Aldehyde Dehydrogenase; Chain A | 2 | 223 | 4.6E-90 |
| 7 | g4120.t18 | Gene3D | G3DSA:3.40.309.10 | Aldehyde Dehydrogenase; Chain A | 5 | 194 | 4.6E-90 |
| 2 | g4120.t18 | PANTHER | PTHR11699:SF269 | ALDEHYDE DEHYDROGENASE, MITOCHONDRIAL-LIKE PROTEIN | 1 | 229 | 3.8E-114 |
| 3 | g4120.t18 | PANTHER | PTHR11699 | ALDEHYDE DEHYDROGENASE-RELATED | 1 | 229 | 3.8E-114 |
| 1 | g4120.t18 | Pfam | PF00171 | Aldehyde dehydrogenase family | 1 | 223 | 1.4E-85 |
| 5 | g4120.t18 | ProSitePatterns | PS00070 | Aldehyde dehydrogenases cysteine active site. | 27 | 38 | - |
| 4 | g4120.t18 | SUPERFAMILY | SSF53720 | ALDH-like | 1 | 226 | 4.19E-81 |
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:0016620 | oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor | MF |
| 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.
