General information for g4120.t33
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Retinal dehydrogenase 2.
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.t33 | TTS | g4120.t33 | 30727131 | 30727131 |
| chr_3 | g4120 | g4120.t33 | isoform | g4120.t33 | 30727171 | 30729993 |
| chr_3 | g4120 | g4120.t33 | exon | g4120.t33.exon1 | 30727171 | 30727814 |
| chr_3 | g4120 | g4120.t33 | cds | g4120.t33.CDS1 | 30727171 | 30727814 |
| chr_3 | g4120 | g4120.t33 | exon | g4120.t33.exon2 | 30727890 | 30727928 |
| chr_3 | g4120 | g4120.t33 | cds | g4120.t33.CDS2 | 30727890 | 30727928 |
| chr_3 | g4120 | g4120.t33 | exon | g4120.t33.exon3 | 30728136 | 30728393 |
| chr_3 | g4120 | g4120.t33 | cds | g4120.t33.CDS3 | 30728136 | 30728184 |
| chr_3 | g4120 | g4120.t33 | exon | g4120.t33.exon4 | 30728526 | 30728731 |
| chr_3 | g4120 | g4120.t33 | exon | g4120.t33.exon5 | 30728797 | 30729002 |
| chr_3 | g4120 | g4120.t33 | exon | g4120.t33.exon6 | 30729866 | 30729993 |
| chr_3 | g4120 | g4120.t33 | TSS | g4120.t33 | NA | NA |
Sequences
>g4120.t33 Gene=g4120 Length=1481
AGTTTCAATTTTGTGCTTCACTAAGCAGCTTCAAATACTTGAAAACGTATAGTGAAATAA
TTTTTTTGTGTGTAACTAAAGCAATCAAAATAATGGCCAATCTAAATCAAGAAATTAAGT
ATACAAAGCTTTTTATCAACAACGAATTTGTTGAATCAGTTACCAAAAAAACTTTTGTGA
CATCAAATCCAGCAAATGGTAAGAAACTTGCAGATGTTGCTGAGGGCGATAAAGATGATG
TAAATTTGGCCGTTGAAGCTGCGAAGAAAGCATTTAAAAGAAGCTCAGAATGGAGAAATA
TGGATCAATCAGCTCGTGCAAGATTGATGCACAAACTCGCTGACTTGATTGATCGCGATT
CGGACATTATTGCAAACGTTGAGTCTTTGGATAATGGAAAACCTTTTAAAATGGCGAAAC
TCGATGTTTATTTTGTTCAATGTTGTTCGTTATTATGCTGGTTATGCAGACAAAATTCAC
GGTAGAACAGTTCCAAGTGATGGCAATCTCTTCAGTTATGTTCGAAAAGAACCAATTGGT
CAACCGGCTGCGTTTCAATTTTGAAACCAGCAGAACAAACTCCACTTTCTGCACTTTATA
TTGCATCATTAGTCAAAGAAGCAGGAATACCTGCTGGCGTAGTTAACGTAATTACTGGCT
ATGGGCCAACAGCTGGTGCCGCTATTGCATCACATCCTGATATTCGCAAGGTTGCATTTA
CAGGTTCAACTGAAGTTGGAAAATTAATTATGGAAGCTGCTGCAAAATCTAATTTGAAGA
AAGTTTCATTAGAGTTGGGTGGTAAGAGTCCTCTTGTAATCTTTGATGATGTTAATCTTG
TTCCACTTGCTCAAGATGCTATTTTTACAAACTCTGGTCAGATTTGTTGTGGAGGATCAA
GAACATTTGTACAAGAAAGAATTTATGATGAATTTGTCAAACGTACTGTTGAAAATGCAA
AAAAAAGAAAAGTTGGTTGTCCATTCAAAGAGGATACTGTGCAAGGGCCACAAGTTGATC
AAGATACATTTGATAAGATCTTGAAATACATTGATTATGGCAAAGAAGATGGTGCAAAAT
TGGAAGCCGGTGGAAAGAGATGGGGCAATGAAGGTTTCTATATTGAACCAACTGTTTTCT
CAAATGTTACTGACGATATGCGCATTGCACAAGATGAAATTTTCGGACCTGTTCAATCGA
TTCTCAAGTTCAAGACAATTGATGAAGTTATTGAGCGTGCTAATAATACAACTTATGGAT
TAGCTGCTGGTGTCTTTACAAATGACATCAATAAAGCTTTGACATTTGCAAATGCAGTCG
AAGCTGGATCAGTTTGGGTTAATTGTTATAATGCAACAAATGTTTGCTCTCCTTTCGGAG
GCTACAAACAGAGTGGTATTGGAAGAGAATTGGGAGAAGAAGGAATCAATTTATACTTGG
AAACTAAAGCAGTTTCTATTAAATTACCAGCCAAAAATTAA
>g4120.t33 Gene=g4120 Length=243
MEAAAKSNLKKVSLELGGKSPLVIFDDVNLVPLAQDAIFTNSGQICCGGSRTFVQERIYD
EFVKRTVENAKKRKVGCPFKEDTVQGPQVDQDTFDKILKYIDYGKEDGAKLEAGGKRWGN
EGFYIEPTVFSNVTDDMRIAQDEIFGPVQSILKFKTIDEVIERANNTTYGLAAGVFTNDI
NKALTFANAVEAGSVWVNCYNATNVCSPFGGYKQSGIGRELGEEGINLYLETKAVSIKLP
AKN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g4120.t33 | Gene3D | G3DSA:3.40.605.10 | Aldehyde Dehydrogenase; Chain A | 1 | 235 | 8.3E-95 |
| 8 | g4120.t33 | Gene3D | G3DSA:3.40.309.10 | Aldehyde Dehydrogenase; Chain A | 21 | 207 | 8.3E-95 |
| 2 | g4120.t33 | PANTHER | PTHR11699:SF269 | ALDEHYDE DEHYDROGENASE, MITOCHONDRIAL-LIKE PROTEIN | 1 | 241 | 3.0E-120 |
| 3 | g4120.t33 | PANTHER | PTHR11699 | ALDEHYDE DEHYDROGENASE-RELATED | 1 | 241 | 3.0E-120 |
| 1 | g4120.t33 | Pfam | PF00171 | Aldehyde dehydrogenase family | 2 | 235 | 8.9E-89 |
| 6 | g4120.t33 | ProSitePatterns | PS00687 | Aldehyde dehydrogenases glutamic acid active site. | 14 | 21 | - |
| 5 | g4120.t33 | ProSitePatterns | PS00070 | Aldehyde dehydrogenases cysteine active site. | 39 | 50 | - |
| 4 | g4120.t33 | SUPERFAMILY | SSF53720 | ALDH-like | 1 | 238 | 2.49E-84 |
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