General information for g15953.t51
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 g15953 is located on chr_4: 7527217..7535654 (+ 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_4 | g15953 | g15953.t51 | TSS | g15953.t51 | 7525541 | 7525541 |
| chr_4 | g15953 | g15953.t51 | isoform | g15953.t51 | 7526565 | 7527866 |
| chr_4 | g15953 | g15953.t51 | exon | g15953.t51.exon1 | 7526565 | 7526878 |
| chr_4 | g15953 | g15953.t51 | cds | g15953.t51.CDS1 | 7526605 | 7526878 |
| chr_4 | g15953 | g15953.t51 | exon | g15953.t51.exon2 | 7527019 | 7527067 |
| chr_4 | g15953 | g15953.t51 | cds | g15953.t51.CDS2 | 7527019 | 7527067 |
| chr_4 | g15953 | g15953.t51 | exon | g15953.t51.exon3 | 7527238 | 7527866 |
| chr_4 | g15953 | g15953.t51 | cds | g15953.t51.CDS3 | 7527238 | 7527244 |
| chr_4 | g15953 | g15953.t51 | TTS | g15953.t51 | 7527880 | 7527880 |
Sequences
>g15953.t51 Gene=g15953 Length=992
TCTTATCACACCATGGAATTATCCAATTCTACTTGTTGCTATGAAAGTTGGACCAGCATT
AGCTGCTGGCTGCACAATTATTCATAAGCCAGCTGAACAAACGCCATTGACTGCTTTATA
TGTTGCTGCATTATCAAAAGAAGCTGGATTTCCTGCTGGTGTCCTTAATGTTATTCCTGG
TTATGGACCAACTGCTGGTGCTGCAATTACAAGCCATGCAGATGTCAGAAAAGTTGGTTT
CACTGGTTCAACTGAGGTTGGAAAATTAATCATGGAAGCAGCTGCAAAATCTAATTTGAA
AAAAGTTTCATTAGAACTTGGTGGCAAGAGTCCATTCGTGGTTTTTGATGACGTAAATTG
TAACAGTTGAAGGAGTTTTCACAAATGCAGGTCAAATTTGTATCGCTCCAAGTCGAACAT
TTGTGCAAGAATCAATTTATGATGAATTTGTTAAGAAAGTTGTTGCATATGCGAAAAATA
GAAAATTGGGCTCACAATTTACTAGTGGAGTACAACAAGGACCACAAGTTGATAAAGATA
CTTTTGACAAAGTTTTGACTTACATTGAATATGGAAAACAAGATGGTGCAAAATTGGAAC
TTGGTGGCAAACGATGGGGAACTGAAGGTTATTTCATTGAACCAACAATTTTCTCAAATG
TCACTGACAATATGAGAATTGCTCGTGATGAAATTTTCGGACCAGTCATGTCAATTTTGA
AATTTAAGACACTTGAAGAAGTAATTGATCGTGCAAATAATACTGAATATGGTTTGTCAT
CAACTGTTTTTACTAAAAATATTGAACAAGCTTTTGCATTTGCAAATCAAGTTGAAGCTG
GTAATGTGAAAGTTAACAGTGGCGGCATGGGAAATAATTTACCATTTGGTGGTTATAAAC
AATCAGGAATCGGCAGAGAAGGCGGTGATTATGGTGTTGAATTGTATTTGGAAACTAAAG
CTGTGTCAATTAAAATGCCTTACAAAATGTAA
>g15953.t51 Gene=g15953 Length=109
MKVGPALAAGCTIIHKPAEQTPLTALYVAALSKEAGFPAGVLNVIPGYGPTAGAAITSHA
DVRKVGFTGSTEVGKLIMEAAAKSNLKKVSLELGGKSPFVVFDDVNCNS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g15953.t51 | Gene3D | G3DSA:3.40.605.10 | Aldehyde Dehydrogenase; Chain A | 1 | 108 | 9.0E-50 |
| 2 | g15953.t51 | PANTHER | PTHR11699:SF269 | ALDEHYDE DEHYDROGENASE, MITOCHONDRIAL-LIKE PROTEIN | 2 | 107 | 1.5E-53 |
| 3 | g15953.t51 | PANTHER | PTHR11699 | ALDEHYDE DEHYDROGENASE-RELATED | 2 | 107 | 1.5E-53 |
| 1 | g15953.t51 | Pfam | PF00171 | Aldehyde dehydrogenase family | 2 | 108 | 1.1E-44 |
| 5 | g15953.t51 | ProSitePatterns | PS00687 | Aldehyde dehydrogenases glutamic acid active site. | 91 | 98 | - |
| 4 | g15953.t51 | SUPERFAMILY | SSF53720 | ALDH-like | 2 | 107 | 4.06E-43 |
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. There were no conditions that were differentially expressed