General information for g4122.t1
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.t1 | TTS | g4122.t1 | 30743782 | 30743782 |
| chr_3 | g4122 | g4122.t1 | isoform | g4122.t1 | 30743874 | 30745693 |
| chr_3 | g4122 | g4122.t1 | exon | g4122.t1.exon1 | 30743874 | 30744541 |
| chr_3 | g4122 | g4122.t1 | cds | g4122.t1.CDS1 | 30743874 | 30744541 |
| chr_3 | g4122 | g4122.t1 | exon | g4122.t1.exon2 | 30744597 | 30744635 |
| chr_3 | g4122 | g4122.t1 | cds | g4122.t1.CDS2 | 30744597 | 30744635 |
| chr_3 | g4122 | g4122.t1 | exon | g4122.t1.exon3 | 30744726 | 30745144 |
| chr_3 | g4122 | g4122.t1 | cds | g4122.t1.CDS3 | 30744726 | 30745144 |
| chr_3 | g4122 | g4122.t1 | exon | g4122.t1.exon4 | 30745203 | 30745319 |
| chr_3 | g4122 | g4122.t1 | cds | g4122.t1.CDS4 | 30745203 | 30745319 |
| chr_3 | g4122 | g4122.t1 | exon | g4122.t1.exon5 | 30745375 | 30745580 |
| chr_3 | g4122 | g4122.t1 | cds | g4122.t1.CDS5 | 30745375 | 30745580 |
| chr_3 | g4122 | g4122.t1 | exon | g4122.t1.exon6 | 30745637 | 30745693 |
| chr_3 | g4122 | g4122.t1 | cds | g4122.t1.CDS6 | 30745637 | 30745693 |
| chr_3 | g4122 | g4122.t1 | TSS | g4122.t1 | 30745933 | 30745933 |
Sequences
>g4122.t1 Gene=g4122 Length=1506
ATGGAAACTCCAAAAAATCCTAATCCAAATCCAGATCAAGAAATTCAGTTCACGAAGCTT
TTTATCAACAATGAATTCGTTGATTCAATCAGTAAAAAGACTTTTGCTACAATTAACCCA
GCAAATGGCAAAAAAATCGCTGACATCGCTGAAGCTGATAAGGCTGATGTCGATTTAGCA
GTTAAAGCTGCACAAAAAGCATTCGAACGTGGCTCTGAATGGCGAAATTTAGATGCTTCA
GCTCGTGGAAGATTACTTTATCGTTTAGCGGACCTAATTGACCGTGATTCAGCTATTCTC
TCCAATTTGGAAACATTAGACAATGGAAAACCTTATGAAGATGCATGTCTGGATGTTTTG
TTTAGTGGTGAATTTTTACGTTATTATGCGGGATTATGTGACAAAATTCATGGCAGAACT
GTTCCAAGTGATGGCAATCTTTTTAGTTATGTTCGCAAAGAACCAATTGGTGTAGTAGGC
CAAATTATACCTTGGAATTATCCTCTTATGATGGTAAGCTGGAAATGGGCACCGGCTTTA
GCTGCTGGATGCACAATAGTACTTAAACCAGCAGAACAAACTCCCCTTTCGGCTTTATAT
GTCGCAAATCTCGCGAAAGAAGCGGGTTTTCCTGCTGGCGTAGTTAACGTAATTACTGGC
TATGGGCCAACTGTTGGTGCCGCTATTGCATCACATCCTGATATTCGCAAGGTTGCATTT
ACAGGCTCAACTGAAGTTGGAAAATTAATTATGGAAGCTGCTGCAAAATCAAATTTGAAG
AAAGTTTCATTAGAGTTGGGTGGCAAGAGTCCTCTCGTCATCTTTGATGACGTAAACATT
GATGAAGCAGTTGATATTGCTCATAATGCAATATTTGCAAACCATGGTCAAAACTGTTGT
GCTGGTTCTCGTACATTCGTTCATGAGAAAATTTATGATGAATTTGTAGAAAAAGCAGCT
GAAATGGCCAAAAATAGAAAACTTGGTTCTCCTTTCGAAATTGGTGTTCAACAGGGACCA
CAAGTTGATGATCAGATGTTTAAAAAAGTTCTCACTTACATTGATTATGGCAAAGAAGAT
GGTGCAAAATTGGAAGCCGGTGGAAAGAGATGGGGCAATGAAGGTTTCTATATTGAACCA
ACTGTTTTCTCAAATGTTACTGACGATATGCGCATTGCACAAGATGAAATTTTCGGACCT
GTTCAATCGATTCTCAAGTTCAAGACAATTGATGAAGTTATTGAGCGTGCTAATAATACA
ACTTATGGATTAGCTGCTGGAGTTCTAACAAATGACATTAATACAGCTTTGACATTTGCA
AATGCAGTCGAAGCTGGATCAGTTTGGGTTAATTGTTACGATGCTGTTACACCACAAATG
CCTTTTGGAGGATATAAGCAAAGCGGAATTGGAAGAGAATTGGGTGCAGAAGGAATCGAA
TCTTATCTTGAAACAAAAGCAGTTTCAATTAAATTACCATCATTTAAAGTACCATCAAAA
ATCTAA
>g4122.t1 Gene=g4122 Length=501
METPKNPNPNPDQEIQFTKLFINNEFVDSISKKTFATINPANGKKIADIAEADKADVDLA
VKAAQKAFERGSEWRNLDASARGRLLYRLADLIDRDSAILSNLETLDNGKPYEDACLDVL
FSGEFLRYYAGLCDKIHGRTVPSDGNLFSYVRKEPIGVVGQIIPWNYPLMMVSWKWAPAL
AAGCTIVLKPAEQTPLSALYVANLAKEAGFPAGVVNVITGYGPTVGAAIASHPDIRKVAF
TGSTEVGKLIMEAAAKSNLKKVSLELGGKSPLVIFDDVNIDEAVDIAHNAIFANHGQNCC
AGSRTFVHEKIYDEFVEKAAEMAKNRKLGSPFEIGVQQGPQVDDQMFKKVLTYIDYGKED
GAKLEAGGKRWGNEGFYIEPTVFSNVTDDMRIAQDEIFGPVQSILKFKTIDEVIERANNT
TYGLAAGVLTNDINTALTFANAVEAGSVWVNCYDAVTPQMPFGGYKQSGIGRELGAEGIE
SYLETKAVSIKLPSFKVPSKI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g4122.t1 | CDD | cd07141 | ALDH_F1AB_F2_RALDH1 | 10 | 491 | 0.0 |
| 7 | g4122.t1 | Gene3D | G3DSA:3.40.605.10 | Aldehyde Dehydrogenase; Chain A | 32 | 488 | 1.5E-197 |
| 8 | g4122.t1 | Gene3D | G3DSA:3.40.309.10 | Aldehyde Dehydrogenase; Chain A | 271 | 460 | 1.5E-197 |
| 2 | g4122.t1 | PANTHER | PTHR11699:SF269 | ALDEHYDE DEHYDROGENASE, MITOCHONDRIAL-LIKE PROTEIN | 11 | 494 | 2.1E-271 |
| 3 | g4122.t1 | PANTHER | PTHR11699 | ALDEHYDE DEHYDROGENASE-RELATED | 11 | 494 | 2.1E-271 |
| 1 | g4122.t1 | Pfam | PF00171 | Aldehyde dehydrogenase family | 27 | 488 | 1.2E-182 |
| 6 | g4122.t1 | ProSitePatterns | PS00687 | Aldehyde dehydrogenases glutamic acid active site. | 264 | 271 | - |
| 5 | g4122.t1 | ProSitePatterns | PS00070 | Aldehyde dehydrogenases cysteine active site. | 292 | 303 | - |
| 4 | g4122.t1 | SUPERFAMILY | SSF53720 | ALDH-like | 13 | 492 | 2.88E-182 |
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 transcript has been annotated with K00128 (aldehyde dehydrogenase (NAD+))
Pathway
- This transcript belongs to the following pathways
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.
