General information for g4120.t35
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t35 | TTS | g4120.t35 | 30727131 | 30727131 |
| chr_3 | g4120 | g4120.t35 | isoform | g4120.t35 | 30727171 | 30733217 |
| chr_3 | g4120 | g4120.t35 | exon | g4120.t35.exon1 | 30727171 | 30727847 |
| chr_3 | g4120 | g4120.t35 | cds | g4120.t35.CDS1 | 30727843 | 30727847 |
| chr_3 | g4120 | g4120.t35 | exon | g4120.t35.exon2 | 30728136 | 30728429 |
| chr_3 | g4120 | g4120.t35 | cds | g4120.t35.CDS2 | 30728136 | 30728429 |
| chr_3 | g4120 | g4120.t35 | exon | g4120.t35.exon3 | 30732893 | 30733117 |
| chr_3 | g4120 | g4120.t35 | cds | g4120.t35.CDS3 | 30732893 | 30732908 |
| chr_3 | g4120 | g4120.t35 | exon | g4120.t35.exon4 | 30733183 | 30733217 |
| chr_3 | g4120 | g4120.t35 | TSS | g4120.t35 | NA | NA |
Sequences
>g4120.t35 Gene=g4120 Length=1231
ATGGATCAATCAGCTCGTGCAAGATTGATGCACAAACTCGCTGACTTGATTGATCGCGAT
TCGGACATTATTGCAAACGTTGAGTCTTTGGATAATGGAAACCTTTTAAAATGGCGAAAC
TCGATGTTTTTTTTTGTTCAATGTTGCTTCGTTATTATGCTGGTTATGCAGACAAATTTC
ACGGTAGGACAGTTCCAAGTGATGGTAATCTCTTCAGTTATGTTCGAAAAGAACCAATTG
GTGTATGCGGTCAAATTATTCATTGATGGTTGTCTTCAAGTTGGCACCTATTTTAGCAAC
CGGCTGCGTTTCAATTTTGAAACCAGCAGAACAAACTCCACTTTCTGCACTTTATATTGC
ATCATTAGTCAAAGAAGCAGGAATACCTGCTGGCGTAGTTAACGTAATTACTGGCTATGG
GCCAACAGCTGGTGCCGCTATTGCATCACATCCTGATATTCGCAAGGTTGCATTTACAGG
TTCAACTGAAGTTGGAAAATTAATTATGGAAGCTGCTGCAAAATCTAATTTGAAGAAAGT
TTCATTAGAGTTGGTTTAATTTCATTTTTTAAAAAAAGTTGATGAAGTTGTTCCACTTGC
TCAAGATGCTATTTTTACAAACTCTGGTCAGATTTGTTGTGGAGGATCAAGAACATTTGT
ACAAGAAAGAATTTATGATGAATTTGTCAAACGTACTGTTGAAAATGCAAAAAAAAGAAA
AGTTGGTTGTCCATTCAAAGAGGATACTGTGCAAGGGCCACAAGTTGATCAAGATACATT
TGATAAGATCTTGAAATACATTGATTATGGCAAAGAAGATGGTGCAAAATTGGAAGCCGG
TGGAAAGAGATGGGGCAATGAAGGTTTCTATATTGAACCAACTGTTTTCTCAAATGTTAC
TGACGATATGCGCATTGCACAAGATGAAATTTTCGGACCTGTTCAATCGATTCTCAAGTT
CAAGACAATTGATGAAGTTATTGAGCGTGCTAATAATACAACTTATGGATTAGCTGCTGG
TGTCTTTACAAATGACATCAATAAAGCTTTGACATTTGCAAATGCAGTCGAAGCTGGATC
AGTTTGGGTTAATTGTTATAATGCAACAAATGTTTGCTCTCCTTTCGGAGGCTACAAACA
GAGTGGTATTGGAAGAGAATTGGGAGAAGAAGGAATCAATTTATACTTGGAAACTAAAGC
AGTTTCTATTAAATTACCAGCCAAAAATTAA
>g4120.t35 Gene=g4120 Length=104
MRSNYSLMVVFKLAPILATGCVSILKPAEQTPLSALYIASLVKEAGIPAGVVNVITGYGP
TAGAAIASHPDIRKVAFTGSTEVGKLIMEAAAKSNLKKVSLELV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g4120.t35 | Gene3D | G3DSA:3.40.605.10 | Aldehyde Dehydrogenase; Chain A | 3 | 104 | 2.4E-44 |
| 2 | g4120.t35 | PANTHER | PTHR11699:SF269 | ALDEHYDE DEHYDROGENASE, MITOCHONDRIAL-LIKE PROTEIN | 5 | 103 | 1.4E-45 |
| 3 | g4120.t35 | PANTHER | PTHR11699 | ALDEHYDE DEHYDROGENASE-RELATED | 5 | 103 | 1.4E-45 |
| 1 | g4120.t35 | Pfam | PF00171 | Aldehyde dehydrogenase family | 7 | 103 | 5.6E-38 |
| 9 | g4120.t35 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 30 | - |
| 10 | g4120.t35 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 12 | - |
| 11 | g4120.t35 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 13 | 25 | - |
| 12 | g4120.t35 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 26 | 30 | - |
| 8 | g4120.t35 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 31 | 104 | - |
| 4 | g4120.t35 | SUPERFAMILY | SSF53720 | ALDH-like | 7 | 103 | 1.44E-36 |
| 6 | g4120.t35 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
| 13 | g4120.t35 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 20 | - |
| 5 | g4120.t35 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 18 | - |
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: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.
