General information for g2992.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 g2992 is located on chr_3: 21865782..21869132 (+ 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 | g2992 | g2992.t1 | isoform | g2992.t1 | 21864757 | 21866607 |
| chr_3 | g2992 | g2992.t1 | exon | g2992.t1.exon1 | 21864757 | 21864792 |
| chr_3 | g2992 | g2992.t1 | cds | g2992.t1.CDS1 | 21864757 | 21864792 |
| chr_3 | g2992 | g2992.t1 | exon | g2992.t1.exon2 | 21864982 | 21865187 |
| chr_3 | g2992 | g2992.t1 | cds | g2992.t1.CDS2 | 21864982 | 21865187 |
| chr_3 | g2992 | g2992.t1 | exon | g2992.t1.exon3 | 21865247 | 21865782 |
| chr_3 | g2992 | g2992.t1 | cds | g2992.t1.CDS3 | 21865247 | 21865782 |
| chr_3 | g2992 | g2992.t1 | exon | g2992.t1.exon4 | 21865853 | 21865891 |
| chr_3 | g2992 | g2992.t1 | cds | g2992.t1.CDS4 | 21865853 | 21865891 |
| chr_3 | g2992 | g2992.t1 | exon | g2992.t1.exon5 | 21865955 | 21866607 |
| chr_3 | g2992 | g2992.t1 | cds | g2992.t1.CDS5 | 21865955 | 21866607 |
| chr_3 | g2992 | g2992.t1 | TSS | g2992.t1 | NA | NA |
| chr_3 | g2992 | g2992.t1 | TTS | g2992.t1 | NA | NA |
Sequences
>g2992.t1 Gene=g2992 Length=1470
ATGGCTAATCCAAATCAAGAAATTAAATACACACAACTTTTCATCAATAATGAGTTCGTT
GACTCAGTAAATAAGAAAACTTTTGTGACATCGAACCCAGCTAATGGCAAGAAATTAGCT
GATGTTGCTGAGGGCGATAAAGCAGATGTTGATTTAGCAGTTGAAGCTGCTAAGAAAGCA
TTTGCACGTGGTTCTGAATGGAGAAATTTAGATGCTTCAGCTCGTGGAAAACTTTTACAT
AAATTAGCTGATTTAATTGATCGTGATTCAGATATTATTGCAAGCATCGAGTCATTAGAT
AATGGAAAACCTTTCATAATGGCAAAAGCCGATATCAATTTTAGTTCGACAGTTCTTCGT
TATTACGCTGGTTATGCTGATAAAGTTCATGGCAGAACAGTGCCAAGTGATGGAAATCTT
TTCAGTTATATTCGTAAAGAACCAGTTGGTGTTGTAGGTCAAATTATACCTTGGAATTTT
CCAGTTTTAATGTTAAGTTGGAAATGGGCACCTGCTTTGGCTGCTGGATGCACATTAGTA
ATCAAACCAGCTGAACAAACTCCATTGACAGCTTTGTATGTTGCTAGTCTCTCAAAAGAA
GCTGGTTTTCCTGATGGCGTTATAAATGTAATCACAGGTTATGGACCAACTGCTGGCGCT
GCAATTGCATCACACTCTGACATACGTAAAGTAGCATTTACTGGCTCAACTGAAGTTGGA
AAAATTATCATGGAAATTGCAGCAAAATCAAATTTGAAAAAAGTCTCATTAGAATTGGGT
GGCAAGAGTCCACTCGTTATTTTTGATGATGTTAACCTTGATGAAGTCGTGCAACTTGCT
CAAGATGCAATTTTCATAAATTCAGGTCAGATTTGCACAGGTGCTTCAAGAACATTTGTG
CAAGAAGGAATTTATGATGAATTTGTAAAACGTACTGTTGAAAATGCAAAAACTAGAAAA
ATTGGATGTCCTTTCAATACTGACACATTGCAAGGACCGCAAGTTGATCAAGATACTTTT
GATAAAATTCTCAATTACATTGATTATGGCAAAGAAGATGGTGCAAAATTGGAAATTGGT
GGAAAGAGATGGGGAAATGAAGGTTTCTTTATTGAACCTACAGTCTTCTCAAATGTCACT
GATGATATGAGAATTGCTCAAGATGAAATTTTTGGACCAGTTCAATCAATCCTTAAATTT
AAAACAATTGATGAAGTCATTGAAAGGGCAAATAAAACAAATTATGGTTTAGCAGCTGGA
ATTTTTACCAATAATATTGAAAATGCTTTGACATTTGCAAACGAAGTCGAAGCTGGATCA
GTTTGGGTTAATTGTTATAATGTTTTTAGATCTCAAGTGCCATTTGGTGGCTACAAACAA
AGTGGAATTGGTTCTGAATTAGGAGAAGAAGGCATCAATTTATATTTAGAAACTAAAGCT
GTTTCTATTAAACTTCCTAATAAAAATTAA
>g2992.t1 Gene=g2992 Length=489
MANPNQEIKYTQLFINNEFVDSVNKKTFVTSNPANGKKLADVAEGDKADVDLAVEAAKKA
FARGSEWRNLDASARGKLLHKLADLIDRDSDIIASIESLDNGKPFIMAKADINFSSTVLR
YYAGYADKVHGRTVPSDGNLFSYIRKEPVGVVGQIIPWNFPVLMLSWKWAPALAAGCTLV
IKPAEQTPLTALYVASLSKEAGFPDGVINVITGYGPTAGAAIASHSDIRKVAFTGSTEVG
KIIMEIAAKSNLKKVSLELGGKSPLVIFDDVNLDEVVQLAQDAIFINSGQICTGASRTFV
QEGIYDEFVKRTVENAKTRKIGCPFNTDTLQGPQVDQDTFDKILNYIDYGKEDGAKLEIG
GKRWGNEGFFIEPTVFSNVTDDMRIAQDEIFGPVQSILKFKTIDEVIERANKTNYGLAAG
IFTNNIENALTFANEVEAGSVWVNCYNVFRSQVPFGGYKQSGIGSELGEEGINLYLETKA
VSIKLPNKN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g2992.t1 | Gene3D | G3DSA:3.40.605.10 | Aldehyde Dehydrogenase; Chain A | 27 | 481 | 4.9E-190 |
| 8 | g2992.t1 | Gene3D | G3DSA:3.40.309.10 | Aldehyde Dehydrogenase; Chain A | 263 | 452 | 4.9E-190 |
| 2 | g2992.t1 | PANTHER | PTHR11699:SF269 | ALDEHYDE DEHYDROGENASE, MITOCHONDRIAL-LIKE PROTEIN | 4 | 487 | 9.8E-256 |
| 3 | g2992.t1 | PANTHER | PTHR11699 | ALDEHYDE DEHYDROGENASE-RELATED | 4 | 487 | 9.8E-256 |
| 1 | g2992.t1 | Pfam | PF00171 | Aldehyde dehydrogenase family | 20 | 481 | 1.0E-178 |
| 6 | g2992.t1 | ProSitePatterns | PS00687 | Aldehyde dehydrogenases glutamic acid active site. | 257 | 264 | - |
| 5 | g2992.t1 | ProSitePatterns | PS00070 | Aldehyde dehydrogenases cysteine active site. | 285 | 296 | - |
| 4 | g2992.t1 | SUPERFAMILY | SSF53720 | ALDH-like | 6 | 485 | 2.09E-178 |
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.
