General information for g4120.t16
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.t16 | isoform | g4120.t16 | 30727124 | 30728729 |
| chr_3 | g4120 | g4120.t16 | exon | g4120.t16.exon1 | 30727124 | 30727823 |
| chr_3 | g4120 | g4120.t16 | TTS | g4120.t16 | 30727131 | 30727131 |
| chr_3 | g4120 | g4120.t16 | cds | g4120.t16.CDS1 | 30727171 | 30727823 |
| chr_3 | g4120 | g4120.t16 | exon | g4120.t16.exon2 | 30727890 | 30727928 |
| chr_3 | g4120 | g4120.t16 | cds | g4120.t16.CDS2 | 30727890 | 30727928 |
| chr_3 | g4120 | g4120.t16 | exon | g4120.t16.exon3 | 30728136 | 30728445 |
| chr_3 | g4120 | g4120.t16 | cds | g4120.t16.CDS3 | 30728136 | 30728445 |
| chr_3 | g4120 | g4120.t16 | exon | g4120.t16.exon4 | 30728508 | 30728729 |
| chr_3 | g4120 | g4120.t16 | cds | g4120.t16.CDS4 | 30728508 | 30728672 |
| chr_3 | g4120 | g4120.t16 | TSS | g4120.t16 | NA | NA |
Sequences
>g4120.t16 Gene=g4120 Length=1271
TCGCTGACTTGATTGATCGCGATTCGGACATTATTGCAAACGTTGAGTCTTTGGATAATG
GAAAACCTTTTAAAATGGCGAAACTCGATGTTTATTTTGTTCAATGTTGTTCGTTATTAT
GCTGGTTATGCAGACAAAATTCACGGTAGAACAGTTCCAAGTGATGGCAATCTCTTCAGT
TATGTTCGAAAAGAACCAATTGGTGTATGCGGTCAAATTATTCCGTGGAACTATCCAGCA
TTGATGGTTGTCTTCAAGTTGGCACCTATTTTAGCAACCGGCTGCGTTTCAATTTTGAAA
CCAGCAGAACAAACTCCACTTTCTGCACTTTATATTGCATCATTAGTCAAAGAAGCAGGA
ATACCTGCTGGCGTAGTTAACGTAATTACTGGCTATGGGCCAACAGCTGGTGCCGCTATT
GCATCACATCCTGATATTCGCAAGGTTGCATTTACAGGTTCAACTGAAGTTGGAAAATTA
ATTATGGAAGCTGCTGCAAAATCTAATTTGAAGAAAGTTTCATTAGAGTTGGGTGGTAAG
AGTCCTCTTGTAATCTTTGATGATGTTAATCTTGATGAAGTTGTTCCACTTGCTCAAGAT
GCTATTTTTACAAACTCTGGTCAGATTTGTTGTGGAGGATCAAGAACATTTGTACAAGAA
AGAATTTATGATGAATTTGTCAAACGTACTGTTGAAAATGCAAAAAAAAGAAAAGTTGGT
TGTCCATTCAAAGAGGATACTGTGCAAGGGCCACAAGTTGATCAAGATACATTTGATAAG
ATCTTGAAATACATTGATTATGGCAAAGAAGATGGTGCAAAATTGGAAGCCGGTGGAAAG
AGATGGGGCAATGAAGGTTTCTATATTGAACCAACTGTTTTCTCAAATGTTACTGACGAT
ATGCGCATTGCACAAGATGAAATTTTCGGACCTGTTCAATCGATTCTCAAGTTCAAGACA
ATTGATGAAGTTATTGAGCGTGCTAATAATACAACTTATGGATTAGCTGCTGGTGTCTTT
ACAAATGACATCAATAAAGCTTTGACATTTGCAAATGCAGTCGAAGCTGGATCAGTTTGG
GTTAATTGTTATAATGCAACAAATGTTTGCTCTCCTTTCGGAGGCTACAAACAGAGTGGT
ATTGGAAGAGAATTGGGAGAAGAAGGAATCAATTTATACTTGGAAACTAAAGCAGTTTCT
ATTAAATTACCAGCCAAAAATTAAATTTCCTCACACATTATTTTGAAATAAAGAAATTTT
GCAAAATAAAT
>g4120.t16 Gene=g4120 Length=388
MENLLKWRNSMFILFNVVRYYAGYADKIHGRTVPSDGNLFSYVRKEPIGVCGQIIPWNYP
ALMVVFKLAPILATGCVSILKPAEQTPLSALYIASLVKEAGIPAGVVNVITGYGPTAGAA
IASHPDIRKVAFTGSTEVGKLIMEAAAKSNLKKVSLELGGKSPLVIFDDVNLDEVVPLAQ
DAIFTNSGQICCGGSRTFVQERIYDEFVKRTVENAKKRKVGCPFKEDTVQGPQVDQDTFD
KILKYIDYGKEDGAKLEAGGKRWGNEGFYIEPTVFSNVTDDMRIAQDEIFGPVQSILKFK
TIDEVIERANNTTYGLAAGVFTNDINKALTFANAVEAGSVWVNCYNATNVCSPFGGYKQS
GIGRELGEEGINLYLETKAVSIKLPAKN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g4120.t16 | Gene3D | G3DSA:3.40.605.10 | Aldehyde Dehydrogenase; Chain A | 15 | 380 | 2.4E-162 |
| 8 | g4120.t16 | Gene3D | G3DSA:3.40.309.10 | Aldehyde Dehydrogenase; Chain A | 162 | 351 | 2.4E-162 |
| 2 | g4120.t16 | PANTHER | PTHR11699:SF269 | ALDEHYDE DEHYDROGENASE, MITOCHONDRIAL-LIKE PROTEIN | 15 | 386 | 1.5E-200 |
| 3 | g4120.t16 | PANTHER | PTHR11699 | ALDEHYDE DEHYDROGENASE-RELATED | 15 | 386 | 1.5E-200 |
| 1 | g4120.t16 | Pfam | PF00171 | Aldehyde dehydrogenase family | 15 | 380 | 2.6E-152 |
| 6 | g4120.t16 | ProSitePatterns | PS00687 | Aldehyde dehydrogenases glutamic acid active site. | 156 | 163 | - |
| 5 | g4120.t16 | ProSitePatterns | PS00070 | Aldehyde dehydrogenases cysteine active site. | 184 | 195 | - |
| 4 | g4120.t16 | SUPERFAMILY | SSF53720 | ALDH-like | 14 | 383 | 4.19E-144 |
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. There were no conditions that were differentially expressed