Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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_4 g15953 g15953.t48 TSS g15953.t48 7525541 7525541
chr_4 g15953 g15953.t48 isoform g15953.t48 7526449 7527866
chr_4 g15953 g15953.t48 exon g15953.t48.exon1 7526449 7526722
chr_4 g15953 g15953.t48 cds g15953.t48.CDS1 7526605 7526722
chr_4 g15953 g15953.t48 exon g15953.t48.exon2 7527394 7527866
chr_4 g15953 g15953.t48 cds g15953.t48.CDS2 7527394 7527866
chr_4 g15953 g15953.t48 TTS g15953.t48 7527880 7527880

Sequences

>g15953.t48 Gene=g15953 Length=747
GCTGTCAATGTGTTCCGAAGTGTTGCATCATATGCCGATAAAATTTTCGGTCGTACAGTT
CCAAGTGATGGTGCTCTCTTCAGTTATACTCGTAAAGAACCAGTTGGTGTTGTTGGTCTT
ATCACACCATGGAATTATCCAATTCTACTTGTTGCTATGAAAGTTGGACCAGCATTAGCT
GCTGGCTGCACAATTATTCATAAGCCAGCTGAACAAACGCCATTGACTGCTTTATATGTT
GCTGCATTATCAAAAGAAGCTGGATTTCCTGCTGGACCACAAGTTGATAAAGATACTTTT
GACAAAGTTTTGACTTACATTGAATATGGAAAACAAGATGGTGCAAAATTGGAACTTGGT
GGCAAACGATGGGGAACTGAAGGTTATTTCATTGAACCAACAATTTTCTCAAATGTCACT
GACAATATGAGAATTGCTCGTGATGAAATTTTCGGACCAGTCATGTCAATTTTGAAATTT
AAGACACTTGAAGAAGTAATTGATCGTGCAAATAATACTGAATATGGTTTGTCATCAACT
GTTTTTACTAAAAATATTGAACAAGCTTTTGCATTTGCAAATCAAGTTGAAGCTGGTAAT
GTGAAAGTTAACAGTGGCGGCATGGGAAATAATTTACCATTTGGTGGTTATAAACAATCA
GGAATCGGCAGAGAAGGCGGTGATTATGGTGTTGAATTGTATTTGGAAACTAAAGCTGTG
TCAATTAAAATGCCTTACAAAATGTAA

>g15953.t48 Gene=g15953 Length=196
MKVGPALAAGCTIIHKPAEQTPLTALYVAALSKEAGFPAGPQVDKDTFDKVLTYIEYGKQ
DGAKLELGGKRWGTEGYFIEPTIFSNVTDNMRIARDEIFGPVMSILKFKTLEEVIDRANN
TEYGLSSTVFTKNIEQAFAFANQVEAGNVKVNSGGMGNNLPFGGYKQSGIGREGGDYGVE
LYLETKAVSIKMPYKM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g15953.t48 Gene3D G3DSA:3.40.605.10 Aldehyde Dehydrogenase; Chain A 1 41 0
9 g15953.t48 Gene3D G3DSA:3.40.309.10 Aldehyde Dehydrogenase; Chain A 42 160 0
7 g15953.t48 Gene3D G3DSA:3.40.605.10 Aldehyde Dehydrogenase; Chain A 161 188 0
2 g15953.t48 PANTHER PTHR11699:SF269 ALDEHYDE DEHYDROGENASE, MITOCHONDRIAL-LIKE PROTEIN 2 40 0
4 g15953.t48 PANTHER PTHR11699 ALDEHYDE DEHYDROGENASE-RELATED 2 40 0
3 g15953.t48 PANTHER PTHR11699:SF269 ALDEHYDE DEHYDROGENASE, MITOCHONDRIAL-LIKE PROTEIN 40 194 0
5 g15953.t48 PANTHER PTHR11699 ALDEHYDE DEHYDROGENASE-RELATED 40 194 0
1 g15953.t48 Pfam PF00171 Aldehyde dehydrogenase family 40 188 0
6 g15953.t48 SUPERFAMILY SSF53720 ALDH-like 2 191 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: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 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