Gene loci information

Transcript annotation

  • This transcript has been annotated as Retinal dehydrogenase 1.

Parent gene

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.t27 TTS g4120.t27 30727131 30727131
chr_3 g4120 g4120.t27 isoform g4120.t27 30727171 30729993
chr_3 g4120 g4120.t27 exon g4120.t27.exon1 30727171 30727847
chr_3 g4120 g4120.t27 exon g4120.t27.exon2 30728127 30728445
chr_3 g4120 g4120.t27 cds g4120.t27.CDS1 30728128 30728445
chr_3 g4120 g4120.t27 exon g4120.t27.exon3 30728508 30728731
chr_3 g4120 g4120.t27 cds g4120.t27.CDS2 30728508 30728672
chr_3 g4120 g4120.t27 exon g4120.t27.exon4 30728797 30729002
chr_3 g4120 g4120.t27 exon g4120.t27.exon5 30729866 30729993
chr_3 g4120 g4120.t27 TSS g4120.t27 NA NA

Sequences

>g4120.t27 Gene=g4120 Length=1554
AGTTTCAATTTTGTGCTTCACTAAGCAGCTTCAAATACTTGAAAACGTATAGTGAAATAA
TTTTTTTGTGTGTAACTAAAGCAATCAAAATAATGGCCAATCTAAATCAAGAAATTAAGT
ATACAAAGCTTTTTATCAACAACGAATTTGTTGAATCAGTTACCAAAAAAACTTTTGTGA
CATCAAATCCAGCAAATGGTAAGAAACTTGCAGATGTTGCTGAGGGCGATAAAGATGATG
TAAATTTGGCCGTTGAAGCTGCGAAGAAAGCATTTAAAAGAAGCTCAGAATGGAGAAATA
TGGATCAATCAGCTCGTGCAAGATTGATGCACAAACTCGCTGACTTGATTGATCGCGATT
CGGACATTATTGCAAACGTTGAGTCTTTGGATAATGGAAAACCTTTTAAAATGGCGAAAC
TCGATGTTTATTTTGTTCAATGTTGTTCGTTATTATGCTGGTTATGCAGACAAAATTCAC
GGTAGAACAGTTCCAAGTGATGGCAATCTCTTCAGTTATGTTCGAAAAGAACCAATTGGT
GTATGCGGTCAAATTATTCCGTGGAACTATCCAGCATTGATGGTTGTCTTCAAGTTGGCA
CCTATTTTAGCAACCGGCTGCGTTTCAATTTTGAAACCAGCAGAACAAACTCCACTTTCT
GCACTTTATATTGCATCATTAGTCAAAGAAGCAGGAATACCTGCTGGCGTAGTTAACGTA
ATTACTGGCTATGGGCCAACAGCTGGTGCCGCTATTGCATCACATCCTGATATTCGCAAG
GTTGCATTTACAGGTTCAACTGAAGTTGGAAAATTAATTATGGAAGCTGCTGCAAAATCT
AATTTGAAGAAAGTTTCATTAGAGTTGGGTGAGTAGCTTTAATTTCATTTTTTAAAAAAA
GTTGATGAAGTTGTTCCACTTGCTCAAGATGCTATTTTTACAAACTCTGGTCAGATTTGT
TGTGGAGGATCAAGAACATTTGTACAAGAAAGAATTTATGATGAATTTGTCAAACGTACT
GTTGAAAATGCAAAAAAAAGAAAAGTTGGTTGTCCATTCAAAGAGGATACTGTGCAAGGG
CCACAAGTTGATCAAGATACATTTGATAAGATCTTGAAATACATTGATTATGGCAAAGAA
GATGGTGCAAAATTGGAAGCCGGTGGAAAGAGATGGGGCAATGAAGGTTTCTATATTGAA
CCAACTGTTTTCTCAAATGTTACTGACGATATGCGCATTGCACAAGATGAAATTTTCGGA
CCTGTTCAATCGATTCTCAAGTTCAAGACAATTGATGAAGTTATTGAGCGTGCTAATAAT
ACAACTTATGGATTAGCTGCTGGTGTCTTTACAAATGACATCAATAAAGCTTTGACATTT
GCAAATGCAGTCGAAGCTGGATCAGTTTGGGTTAATTGTTATAATGCAACAAATGTTTGC
TCTCCTTTCGGAGGCTACAAACAGAGTGGTATTGGAAGAGAATTGGGAGAAGAAGGAATC
AATTTATACTTGGAAACTAAAGCAGTTTCTATTAAATTACCAGCCAAAAATTAA

>g4120.t27 Gene=g4120 Length=160
MENLLKWRNSMFILFNVVRYYAGYADKIHGRTVPSDGNLFSYVRKEPIGVCGQIIPWNYP
ALMVVFKLAPILATGCVSILKPAEQTPLSALYIASLVKEAGIPAGVVNVITGYGPTAGAA
IASHPDIRKVAFTGSTEVGKLIMEAAAKSNLKKVSLELGE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g4120.t27 Gene3D G3DSA:3.40.605.10 Aldehyde Dehydrogenase; Chain A 7 160 0
2 g4120.t27 PANTHER PTHR11699:SF269 ALDEHYDE DEHYDROGENASE, MITOCHONDRIAL-LIKE PROTEIN 15 159 0
3 g4120.t27 PANTHER PTHR11699 ALDEHYDE DEHYDROGENASE-RELATED 15 159 0
1 g4120.t27 Pfam PF00171 Aldehyde dehydrogenase family 15 159 0
4 g4120.t27 SUPERFAMILY SSF53720 ALDH-like 13 159 0

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