General information for g4120.t25
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.t25 | TTS | g4120.t25 | 30727131 | 30727131 |
| chr_3 | g4120 | g4120.t25 | isoform | g4120.t25 | 30727171 | 30729993 |
| chr_3 | g4120 | g4120.t25 | exon | g4120.t25.exon1 | 30727171 | 30727823 |
| chr_3 | g4120 | g4120.t25 | cds | g4120.t25.CDS1 | 30727171 | 30727823 |
| chr_3 | g4120 | g4120.t25 | exon | g4120.t25.exon2 | 30727890 | 30727928 |
| chr_3 | g4120 | g4120.t25 | cds | g4120.t25.CDS2 | 30727890 | 30727928 |
| chr_3 | g4120 | g4120.t25 | exon | g4120.t25.exon3 | 30728136 | 30728445 |
| chr_3 | g4120 | g4120.t25 | cds | g4120.t25.CDS3 | 30728136 | 30728424 |
| chr_3 | g4120 | g4120.t25 | exon | g4120.t25.exon4 | 30728508 | 30728731 |
| chr_3 | g4120 | g4120.t25 | exon | g4120.t25.exon5 | 30728797 | 30729002 |
| chr_3 | g4120 | g4120.t25 | exon | g4120.t25.exon6 | 30729866 | 30729993 |
| chr_3 | g4120 | g4120.t25 | TSS | g4120.t25 | NA | NA |
Sequences
>g4120.t25 Gene=g4120 Length=1560
AGTTTCAATTTTGTGCTTCACTAAGCAGCTTCAAATACTTGAAAACGTATAGTGAAATAA
TTTTTTTGTGTGTAACTAAAGCAATCAAAATAATGGCCAATCTAAATCAAGAAATTAAGT
ATACAAAGCTTTTTATCAACAACGAATTTGTTGAATCAGTTACCAAAAAAACTTTTGTGA
CATCAAATCCAGCAAATGGTAAGAAACTTGCAGATGTTGCTGAGGGCGATAAAGATGATG
TAAATTTGGCCGTTGAAGCTGCGAAGAAAGCATTTAAAAGAAGCTCAGAATGGAGAAATA
TGGATCAATCAGCTCGTGCAAGATTGATGCACAAACTCGCTGACTTGATTGATCGCGATT
CGGACATTATTGCAAACGTTGAGTCTTTGGATAATGGAAAACCTTTTAAAATGGCGAAAC
TCGATGTTTATTTTGTTCAATGTTGTTCGTTATTATGCTGGTTATGCAGACAAAATTCAC
GGTAGAACAGTTCCAAGTGATGGCAATCTCTTCAGTTATGTTCGAAAAGAACCAATTGGT
GTATGCGGTCAAATTATTCCGTGGAACTATCCAGCATTGATGGTTGTCTTCAAGTTGGCA
CCTATTTTAGCAACCGGCTGCGTTTCAATTTTGAAACCAGCAGAACAAACTCCACTTTCT
GCACTTTATATTGCATCATTAGTCAAAGAAGCAGGAATACCTGCTGGCGTAGTTAACGTA
ATTACTGGCTATGGGCCAACAGCTGGTGCCGCTATTGCATCACATCCTGATATTCGCAAG
GTTGCATTTACAGGTTCAACTGAAGTTGGAAAATTAATTATGGAAGCTGCTGCAAAATCT
AATTTGAAGAAAGTTTCATTAGAGTTGGGTGGTAAGAGTCCTCTTGTAATCTTTGATGAT
GTTAATCTTGATGAAGTTGTTCCACTTGCTCAAGATGCTATTTTTACAAACTCTGGTCAG
ATTTGTTGTGGAGGATCAAGAACATTTGTACAAGAAAGAATTTATGATGAATTTGTCAAA
CGTACTGTTGAAAATGCAAAAAAAAGAAAAGTTGGTTGTCCATTCAAAGAGGATACTGTG
CAAGGGCCACAAGTTGATCAAGATACATTTGATAAGATCTTGAAATACATTGATTATGGC
AAAGAAGATGGTGCAAAATTGGAAGCCGGTGGAAAGAGATGGGGCAATGAAGGTTTCTAT
ATTGAACCAACTGTTTTCTCAAATGTTACTGACGATATGCGCATTGCACAAGATGAAATT
TTCGGACCTGTTCAATCGATTCTCAAGTTCAAGACAATTGATGAAGTTATTGAGCGTGCT
AATAATACAACTTATGGATTAGCTGCTGGTGTCTTTACAAATGACATCAATAAAGCTTTG
ACATTTGCAAATGCAGTCGAAGCTGGATCAGTTTGGGTTAATTGTTATAATGCAACAAAT
GTTTGCTCTCCTTTCGGAGGCTACAAACAGAGTGGTATTGGAAGAGAATTGGGAGAAGAA
GGAATCAATTTATACTTGGAAACTAAAGCAGTTTCTATTAAATTACCAGCCAAAAATTAA
>g4120.t25 Gene=g4120 Length=326
MVVFKLAPILATGCVSILKPAEQTPLSALYIASLVKEAGIPAGVVNVITGYGPTAGAAIA
SHPDIRKVAFTGSTEVGKLIMEAAAKSNLKKVSLELGGKSPLVIFDDVNLDEVVPLAQDA
IFTNSGQICCGGSRTFVQERIYDEFVKRTVENAKKRKVGCPFKEDTVQGPQVDQDTFDKI
LKYIDYGKEDGAKLEAGGKRWGNEGFYIEPTVFSNVTDDMRIAQDEIFGPVQSILKFKTI
DEVIERANNTTYGLAAGVFTNDINKALTFANAVEAGSVWVNCYNATNVCSPFGGYKQSGI
GRELGEEGINLYLETKAVSIKLPAKN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g4120.t25 | Gene3D | G3DSA:3.40.605.10 | Aldehyde Dehydrogenase; Chain A | 1 | 318 | 6.7E-139 |
| 8 | g4120.t25 | Gene3D | G3DSA:3.40.309.10 | Aldehyde Dehydrogenase; Chain A | 100 | 289 | 6.7E-139 |
| 2 | g4120.t25 | PANTHER | PTHR11699:SF269 | ALDEHYDE DEHYDROGENASE, MITOCHONDRIAL-LIKE PROTEIN | 1 | 324 | 7.5E-170 |
| 3 | g4120.t25 | PANTHER | PTHR11699 | ALDEHYDE DEHYDROGENASE-RELATED | 1 | 324 | 7.5E-170 |
| 1 | g4120.t25 | Pfam | PF00171 | Aldehyde dehydrogenase family | 1 | 318 | 6.4E-131 |
| 10 | g4120.t25 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 23 | - |
| 11 | g4120.t25 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 5 | - |
| 12 | g4120.t25 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 6 | 18 | - |
| 13 | g4120.t25 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 19 | 23 | - |
| 9 | g4120.t25 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 24 | 326 | - |
| 6 | g4120.t25 | ProSitePatterns | PS00687 | Aldehyde dehydrogenases glutamic acid active site. | 94 | 101 | - |
| 5 | g4120.t25 | ProSitePatterns | PS00070 | Aldehyde dehydrogenases cysteine active site. | 122 | 133 | - |
| 4 | g4120.t25 | SUPERFAMILY | SSF53720 | ALDH-like | 1 | 321 | 3.8E-124 |
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.
