General information for g4120.t26
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.t26 | TTS | g4120.t26 | 30727131 | 30727131 |
| chr_3 | g4120 | g4120.t26 | isoform | g4120.t26 | 30727171 | 30729993 |
| chr_3 | g4120 | g4120.t26 | exon | g4120.t26.exon1 | 30727171 | 30727823 |
| chr_3 | g4120 | g4120.t26 | cds | g4120.t26.CDS1 | 30727171 | 30727823 |
| chr_3 | g4120 | g4120.t26 | exon | g4120.t26.exon2 | 30727890 | 30727928 |
| chr_3 | g4120 | g4120.t26 | cds | g4120.t26.CDS2 | 30727890 | 30727928 |
| chr_3 | g4120 | g4120.t26 | exon | g4120.t26.exon3 | 30728136 | 30728445 |
| chr_3 | g4120 | g4120.t26 | cds | g4120.t26.CDS3 | 30728136 | 30728445 |
| chr_3 | g4120 | g4120.t26 | exon | g4120.t26.exon4 | 30729866 | 30729993 |
| chr_3 | g4120 | g4120.t26 | cds | g4120.t26.CDS4 | 30729866 | 30729901 |
| chr_3 | g4120 | g4120.t26 | TSS | g4120.t26 | NA | NA |
Sequences
>g4120.t26 Gene=g4120 Length=1130
AGTTTCAATTTTGTGCTTCACTAAGCAGCTTCAAATACTTGAAAACGTATAGTGAAATAA
TTTTTTTGTGTGTAACTAAAGCAATCAAAATAATGGCCAATCTAAATCAAGAAATTAAGT
ATACAAAGCCGTGGAACTATCCAGCATTGATGGTTGTCTTCAAGTTGGCACCTATTTTAG
CAACCGGCTGCGTTTCAATTTTGAAACCAGCAGAACAAACTCCACTTTCTGCACTTTATA
TTGCATCATTAGTCAAAGAAGCAGGAATACCTGCTGGCGTAGTTAACGTAATTACTGGCT
ATGGGCCAACAGCTGGTGCCGCTATTGCATCACATCCTGATATTCGCAAGGTTGCATTTA
CAGGTTCAACTGAAGTTGGAAAATTAATTATGGAAGCTGCTGCAAAATCTAATTTGAAGA
AAGTTTCATTAGAGTTGGGTGGTAAGAGTCCTCTTGTAATCTTTGATGATGTTAATCTTG
ATGAAGTTGTTCCACTTGCTCAAGATGCTATTTTTACAAACTCTGGTCAGATTTGTTGTG
GAGGATCAAGAACATTTGTACAAGAAAGAATTTATGATGAATTTGTCAAACGTACTGTTG
AAAATGCAAAAAAAAGAAAAGTTGGTTGTCCATTCAAAGAGGATACTGTGCAAGGGCCAC
AAGTTGATCAAGATACATTTGATAAGATCTTGAAATACATTGATTATGGCAAAGAAGATG
GTGCAAAATTGGAAGCCGGTGGAAAGAGATGGGGCAATGAAGGTTTCTATATTGAACCAA
CTGTTTTCTCAAATGTTACTGACGATATGCGCATTGCACAAGATGAAATTTTCGGACCTG
TTCAATCGATTCTCAAGTTCAAGACAATTGATGAAGTTATTGAGCGTGCTAATAATACAA
CTTATGGATTAGCTGCTGGTGTCTTTACAAATGACATCAATAAAGCTTTGACATTTGCAA
ATGCAGTCGAAGCTGGATCAGTTTGGGTTAATTGTTATAATGCAACAAATGTTTGCTCTC
CTTTCGGAGGCTACAAACAGAGTGGTATTGGAAGAGAATTGGGAGAAGAAGGAATCAATT
TATACTTGGAAACTAAAGCAGTTTCTATTAAATTACCAGCCAAAAATTAA
>g4120.t26 Gene=g4120 Length=345
MANLNQEIKYTKPWNYPALMVVFKLAPILATGCVSILKPAEQTPLSALYIASLVKEAGIP
AGVVNVITGYGPTAGAAIASHPDIRKVAFTGSTEVGKLIMEAAAKSNLKKVSLELGGKSP
LVIFDDVNLDEVVPLAQDAIFTNSGQICCGGSRTFVQERIYDEFVKRTVENAKKRKVGCP
FKEDTVQGPQVDQDTFDKILKYIDYGKEDGAKLEAGGKRWGNEGFYIEPTVFSNVTDDMR
IAQDEIFGPVQSILKFKTIDEVIERANNTTYGLAAGVFTNDINKALTFANAVEAGSVWVN
CYNATNVCSPFGGYKQSGIGRELGEEGINLYLETKAVSIKLPAKN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g4120.t26 | Gene3D | G3DSA:3.40.605.10 | Aldehyde Dehydrogenase; Chain A | 13 | 337 | 1.1E-144 |
| 8 | g4120.t26 | Gene3D | G3DSA:3.40.309.10 | Aldehyde Dehydrogenase; Chain A | 119 | 308 | 1.1E-144 |
| 2 | g4120.t26 | PANTHER | PTHR11699:SF269 | ALDEHYDE DEHYDROGENASE, MITOCHONDRIAL-LIKE PROTEIN | 13 | 343 | 7.5E-176 |
| 3 | g4120.t26 | PANTHER | PTHR11699 | ALDEHYDE DEHYDROGENASE-RELATED | 13 | 343 | 7.5E-176 |
| 1 | g4120.t26 | Pfam | PF00171 | Aldehyde dehydrogenase family | 12 | 337 | 5.0E-137 |
| 6 | g4120.t26 | ProSitePatterns | PS00687 | Aldehyde dehydrogenases glutamic acid active site. | 113 | 120 | - |
| 5 | g4120.t26 | ProSitePatterns | PS00070 | Aldehyde dehydrogenases cysteine active site. | 141 | 152 | - |
| 4 | g4120.t26 | SUPERFAMILY | SSF53720 | ALDH-like | 12 | 340 | 1.09E-129 |
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.
