General information for g4122.t12
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Retinal dehydrogenase 1.
Parent gene
- The parent gene g4122 is located on chr_3: 30744881..30746107 (- 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 | g4122 | g4122.t12 | TTS | g4122.t12 | 30743782 | 30743782 |
| chr_3 | g4122 | g4122.t12 | isoform | g4122.t12 | 30743874 | 30745693 |
| chr_3 | g4122 | g4122.t12 | exon | g4122.t12.exon1 | 30743874 | 30744541 |
| chr_3 | g4122 | g4122.t12 | cds | g4122.t12.CDS1 | 30743874 | 30744541 |
| chr_3 | g4122 | g4122.t12 | exon | g4122.t12.exon2 | 30744597 | 30744635 |
| chr_3 | g4122 | g4122.t12 | cds | g4122.t12.CDS2 | 30744597 | 30744635 |
| chr_3 | g4122 | g4122.t12 | exon | g4122.t12.exon3 | 30744726 | 30745144 |
| chr_3 | g4122 | g4122.t12 | cds | g4122.t12.CDS3 | 30744726 | 30745017 |
| chr_3 | g4122 | g4122.t12 | exon | g4122.t12.exon4 | 30745203 | 30745693 |
| chr_3 | g4122 | g4122.t12 | TSS | g4122.t12 | 30745933 | 30745933 |
Sequences
>g4122.t12 Gene=g4122 Length=1617
ATGGAAACTCCAAAAAATCCTAATCCAAATCCAGATCAAGAAATTCAGTTCACGAAGGTA
TTAAATTAAATAGATTTTTTTACATTATTTGAATCTTCTTCTTTTTAACTCAGCTTTTTA
TCAACAATGAATTCGTTGATTCAATCAGTAAAAAGACTTTTGCTACAATTAACCCAGCAA
ATGGCAAAAAAATCGCTGACATCGCTGAAGCTGATAAGGCTGATGTCGATTTAGCAGTTA
AAGCTGCACAAAAAGCATTCGAACGTGGCTCTGAATGGCGAAATTTAGATGCTTCAGCTC
GTGGAAGATTACTTTATCGGTAAATGAAAGAAAATTATTTTAATTTTAATATGTGTTGAT
TTTTTATTTTACAGTTTAGCGGACCTAATTGACCGTGATTCAGCTATTCTCTCCAATTTG
GAAACATTAGACAATGGAAAACCTTATGAAGATGCATGTCTGGATGTTTTGTTTAGTGGT
GAATTTTTACGTTATTATGCGGGATTATGTGACAAAATTCATGGCAGAACTGTTCCAAGT
GATGGCAATCTTTTTAGTTATGTTCGCAAAGAACCAATTGGTGTAGTAGGCCAAATTATA
CCTTGGAATTATCCTCTTATGATGGTAAGCTGGAAATGGGCACCGGCTTTAGCTGCTGGA
TGCACAATAGTACTTAAACCAGCAGAACAAACTCCCCTTTCGGCTTTATATGTCGCAAAT
CTCGCGAAAGAAGCGGGTTTTCCTGCTGGCGTAGTTAACGTAATTACTGGCTATGGGCCA
ACTGTTGGTGCCGCTATTGCATCACATCCTGATATTCGCAAGGTTGCATTTACAGGCTCA
ACTGAAGTTGGAAAATTAATTATGGAAGCTGCTGCAAAATCAAATTTGAAGAAAGTTTCA
TTAGAGTTGGGTGGCAAGAGTCCTCTCGTCATCTTTGATGACGTAAACATTGATGAAGCA
GTTGATATTGCTCATAATGCAATATTTGCAAACCATGGTCAAAACTGTTGTGCTGGTTCT
CGTACATTCGTTCATGAGAAAATTTATGATGAATTTGTAGAAAAAGCAGCTGAAATGGCC
AAAAATAGAAAACTTGGTTCTCCTTTCGAAATTGGTGTTCAACAGGGACCACAAGTTGAT
GATCAGATGTTTAAAAAAGTTCTCACTTACATTGATTATGGCAAAGAAGATGGTGCAAAA
TTGGAAGCCGGTGGAAAGAGATGGGGCAATGAAGGTTTCTATATTGAACCAACTGTTTTC
TCAAATGTTACTGACGATATGCGCATTGCACAAGATGAAATTTTCGGACCTGTTCAATCG
ATTCTCAAGTTCAAGACAATTGATGAAGTTATTGAGCGTGCTAATAATACAACTTATGGA
TTAGCTGCTGGAGTTCTAACAAATGACATTAATACAGCTTTGACATTTGCAAATGCAGTC
GAAGCTGGATCAGTTTGGGTTAATTGTTACGATGCTGTTACACCACAAATGCCTTTTGGA
GGATATAAGCAAAGCGGAATTGGAAGAGAATTGGGTGCAGAAGGAATCGAATCTTATCTT
GAAACAAAAGCAGTTTCAATTAAATTACCATCATTTAAAGTACCATCAAAAATCTAA
>g4122.t12 Gene=g4122 Length=332
MMVSWKWAPALAAGCTIVLKPAEQTPLSALYVANLAKEAGFPAGVVNVITGYGPTVGAAI
ASHPDIRKVAFTGSTEVGKLIMEAAAKSNLKKVSLELGGKSPLVIFDDVNIDEAVDIAHN
AIFANHGQNCCAGSRTFVHEKIYDEFVEKAAEMAKNRKLGSPFEIGVQQGPQVDDQMFKK
VLTYIDYGKEDGAKLEAGGKRWGNEGFYIEPTVFSNVTDDMRIAQDEIFGPVQSILKFKT
IDEVIERANNTTYGLAAGVLTNDINTALTFANAVEAGSVWVNCYDAVTPQMPFGGYKQSG
IGRELGAEGIESYLETKAVSIKLPSFKVPSKI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g4122.t12 | Gene3D | G3DSA:3.40.605.10 | Aldehyde Dehydrogenase; Chain A | 1 | 98 | 1.0E-44 |
| 9 | g4122.t12 | Gene3D | G3DSA:3.40.309.10 | Aldehyde Dehydrogenase; Chain A | 99 | 327 | 2.2E-84 |
| 2 | g4122.t12 | PANTHER | PTHR11699:SF269 | ALDEHYDE DEHYDROGENASE, MITOCHONDRIAL-LIKE PROTEIN | 1 | 325 | 1.0E-185 |
| 3 | g4122.t12 | PANTHER | PTHR11699 | ALDEHYDE DEHYDROGENASE-RELATED | 1 | 325 | 1.0E-185 |
| 1 | g4122.t12 | Pfam | PF00171 | Aldehyde dehydrogenase family | 1 | 319 | 1.7E-134 |
| 11 | g4122.t12 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 24 | - |
| 12 | g4122.t12 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 7 | - |
| 13 | g4122.t12 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 8 | 19 | - |
| 14 | g4122.t12 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 20 | 24 | - |
| 10 | g4122.t12 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 25 | 332 | - |
| 6 | g4122.t12 | ProSitePatterns | PS00687 | Aldehyde dehydrogenases glutamic acid active site. | 95 | 102 | - |
| 5 | g4122.t12 | ProSitePatterns | PS00070 | Aldehyde dehydrogenases cysteine active site. | 123 | 134 | - |
| 4 | g4122.t12 | SUPERFAMILY | SSF53720 | ALDH-like | 1 | 323 | 4.32E-130 |
| 7 | g4122.t12 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 12 | - |
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.
