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 g4122 g4122.t7 TTS g4122.t7 30743782 30743782
chr_3 g4122 g4122.t7 isoform g4122.t7 30743874 30745012
chr_3 g4122 g4122.t7 exon g4122.t7.exon1 30743874 30744541
chr_3 g4122 g4122.t7 cds g4122.t7.CDS1 30743874 30744541
chr_3 g4122 g4122.t7 exon g4122.t7.exon2 30744597 30744635
chr_3 g4122 g4122.t7 cds g4122.t7.CDS2 30744597 30744635
chr_3 g4122 g4122.t7 exon g4122.t7.exon3 30744726 30745012
chr_3 g4122 g4122.t7 cds g4122.t7.CDS3 30744726 30744774
chr_3 g4122 g4122.t7 TSS g4122.t7 30745933 30745933

Sequences

>g4122.t7 Gene=g4122 Length=994
GGTAAGCTGGAAATGGGCACCGGCTTTAGCTGCTGGATGCACAATAGTACTTAAACCAGC
AGAACAAACTCCCCTTTCGGCTTTATATGTCGCAAATCTCGCGAAAGAAGCGGGTTTTCC
TGCTGGCGTAGTTAACGTAATTACTGGCTATGGGCCAACTGTTGGTGCCGCTATTGCATC
ACATCCTGATATTCGCAAGGTTGCATTTACAGGCTCAACTGAAGTTGGAAAATTAATTAT
GGAAGCTGCTGCAAAATCAAATTTGAAGAAAGTTTCATTAGAGTTGGGTGGCAAGAGTCC
TCTCGTCATCTTTGATGACGTAAACATTGATGAAGCAGTTGATATTGCTCATAATGCAAT
ATTTGCAAACCATGGTCAAAACTGTTGTGCTGGTTCTCGTACATTCGTTCATGAGAAAAT
TTATGATGAATTTGTAGAAAAAGCAGCTGAAATGGCCAAAAATAGAAAACTTGGTTCTCC
TTTCGAAATTGGTGTTCAACAGGGACCACAAGTTGATGATCAGATGTTTAAAAAAGTTCT
CACTTACATTGATTATGGCAAAGAAGATGGTGCAAAATTGGAAGCCGGTGGAAAGAGATG
GGGCAATGAAGGTTTCTATATTGAACCAACTGTTTTCTCAAATGTTACTGACGATATGCG
CATTGCACAAGATGAAATTTTCGGACCTGTTCAATCGATTCTCAAGTTCAAGACAATTGA
TGAAGTTATTGAGCGTGCTAATAATACAACTTATGGATTAGCTGCTGGAGTTCTAACAAA
TGACATTAATACAGCTTTGACATTTGCAAATGCAGTCGAAGCTGGATCAGTTTGGGTTAA
TTGTTACGATGCTGTTACACCACAAATGCCTTTTGGAGGATATAAGCAAAGCGGAATTGG
AAGAGAATTGGGTGCAGAAGGAATCGAATCTTATCTTGAAACAAAAGCAGTTTCAATTAA
ATTACCATCATTTAAAGTACCATCAAAAATCTAA

>g4122.t7 Gene=g4122 Length=251
MEAAAKSNLKKVSLELGGKSPLVIFDDVNIDEAVDIAHNAIFANHGQNCCAGSRTFVHEK
IYDEFVEKAAEMAKNRKLGSPFEIGVQQGPQVDDQMFKKVLTYIDYGKEDGAKLEAGGKR
WGNEGFYIEPTVFSNVTDDMRIAQDEIFGPVQSILKFKTIDEVIERANNTTYGLAAGVLT
NDINTALTFANAVEAGSVWVNCYDAVTPQMPFGGYKQSGIGRELGAEGIESYLETKAVSI
KLPSFKVPSKI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g4122.t7 Gene3D G3DSA:3.40.605.10 Aldehyde Dehydrogenase; Chain A 1 238 1.3E-100
8 g4122.t7 Gene3D G3DSA:3.40.309.10 Aldehyde Dehydrogenase; Chain A 21 210 1.3E-100
2 g4122.t7 PANTHER PTHR11699:SF269 ALDEHYDE DEHYDROGENASE, MITOCHONDRIAL-LIKE PROTEIN 1 244 3.1E-134
3 g4122.t7 PANTHER PTHR11699 ALDEHYDE DEHYDROGENASE-RELATED 1 244 3.1E-134
1 g4122.t7 Pfam PF00171 Aldehyde dehydrogenase family 2 238 8.7E-92
6 g4122.t7 ProSitePatterns PS00687 Aldehyde dehydrogenases glutamic acid active site. 14 21 -
5 g4122.t7 ProSitePatterns PS00070 Aldehyde dehydrogenases cysteine active site. 42 53 -
4 g4122.t7 SUPERFAMILY SSF53720 ALDH-like 1 242 2.49E-90

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.

Raw TPM values