General information for g4120.t24
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.t24 | TTS | g4120.t24 | 30727131 | 30727131 |
| chr_3 | g4120 | g4120.t24 | isoform | g4120.t24 | 30727171 | 30729002 |
| chr_3 | g4120 | g4120.t24 | exon | g4120.t24.exon1 | 30727171 | 30727823 |
| chr_3 | g4120 | g4120.t24 | exon | g4120.t24.exon2 | 30728118 | 30728445 |
| chr_3 | g4120 | g4120.t24 | cds | g4120.t24.CDS1 | 30728128 | 30728445 |
| chr_3 | g4120 | g4120.t24 | exon | g4120.t24.exon3 | 30728508 | 30728731 |
| chr_3 | g4120 | g4120.t24 | cds | g4120.t24.CDS2 | 30728508 | 30728672 |
| chr_3 | g4120 | g4120.t24 | exon | g4120.t24.exon4 | 30728797 | 30729002 |
| chr_3 | g4120 | g4120.t24 | TSS | g4120.t24 | NA | NA |
Sequences
>g4120.t24 Gene=g4120 Length=1411
CTTTTTATCAACAACGAATTTGTTGAATCAGTTACCAAAAAAACTTTTGTGACATCAAAT
CCAGCAAATGGTAAGAAACTTGCAGATGTTGCTGAGGGCGATAAAGATGATGTAAATTTG
GCCGTTGAAGCTGCGAAGAAAGCATTTAAAAGAAGCTCAGAATGGAGAAATATGGATCAA
TCAGCTCGTGCAAGATTGATGCACAAACTCGCTGACTTGATTGATCGCGATTCGGACATT
ATTGCAAACGTTGAGTCTTTGGATAATGGAAAACCTTTTAAAATGGCGAAACTCGATGTT
TATTTTGTTCAATGTTGTTCGTTATTATGCTGGTTATGCAGACAAAATTCACGGTAGAAC
AGTTCCAAGTGATGGCAATCTCTTCAGTTATGTTCGAAAAGAACCAATTGGTGTATGCGG
TCAAATTATTCCGTGGAACTATCCAGCATTGATGGTTGTCTTCAAGTTGGCACCTATTTT
AGCAACCGGCTGCGTTTCAATTTTGAAACCAGCAGAACAAACTCCACTTTCTGCACTTTA
TATTGCATCATTAGTCAAAGAAGCAGGAATACCTGCTGGCGTAGTTAACGTAATTACTGG
CTATGGGCCAACAGCTGGTGCCGCTATTGCATCACATCCTGATATTCGCAAGGTTGCATT
TACAGGTTCAACTGAAGTTGGAAAATTAATTATGGAAGCTGCTGCAAAATCTAATTTGAA
GAAAGTTTCATTAGAGTTGGGTGAGTAGCGTATTAGACTTGATGAAGTTGTTCCACTTGC
TCAAGATGCTATTTTTACAAACTCTGGTCAGATTTGTTGTGGAGGATCAAGAACATTTGT
ACAAGAAAGAATTTATGATGAATTTGTCAAACGTACTGTTGAAAATGCAAAAAAAAGAAA
AGTTGGTTGTCCATTCAAAGAGGATACTGTGCAAGGGCCACAAGTTGATCAAGATACATT
TGATAAGATCTTGAAATACATTGATTATGGCAAAGAAGATGGTGCAAAATTGGAAGCCGG
TGGAAAGAGATGGGGCAATGAAGGTTTCTATATTGAACCAACTGTTTTCTCAAATGTTAC
TGACGATATGCGCATTGCACAAGATGAAATTTTCGGACCTGTTCAATCGATTCTCAAGTT
CAAGACAATTGATGAAGTTATTGAGCGTGCTAATAATACAACTTATGGATTAGCTGCTGG
TGTCTTTACAAATGACATCAATAAAGCTTTGACATTTGCAAATGCAGTCGAAGCTGGATC
AGTTTGGGTTAATTGTTATAATGCAACAAATGTTTGCTCTCCTTTCGGAGGCTACAAACA
GAGTGGTATTGGAAGAGAATTGGGAGAAGAAGGAATCAATTTATACTTGGAAACTAAAGC
AGTTTCTATTAAATTACCAGCCAAAAATTAA
>g4120.t24 Gene=g4120 Length=160
MENLLKWRNSMFILFNVVRYYAGYADKIHGRTVPSDGNLFSYVRKEPIGVCGQIIPWNYP
ALMVVFKLAPILATGCVSILKPAEQTPLSALYIASLVKEAGIPAGVVNVITGYGPTAGAA
IASHPDIRKVAFTGSTEVGKLIMEAAAKSNLKKVSLELGE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g4120.t24 | Gene3D | G3DSA:3.40.605.10 | Aldehyde Dehydrogenase; Chain A | 7 | 160 | 0 |
| 2 | g4120.t24 | PANTHER | PTHR11699:SF269 | ALDEHYDE DEHYDROGENASE, MITOCHONDRIAL-LIKE PROTEIN | 15 | 159 | 0 |
| 3 | g4120.t24 | PANTHER | PTHR11699 | ALDEHYDE DEHYDROGENASE-RELATED | 15 | 159 | 0 |
| 1 | g4120.t24 | Pfam | PF00171 | Aldehyde dehydrogenase family | 15 | 159 | 0 |
| 4 | g4120.t24 | SUPERFAMILY | SSF53720 | ALDH-like | 13 | 159 | 0 |
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.
