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.t19 TTS g4122.t19 30743782 30743782
chr_3 g4122 g4122.t19 isoform g4122.t19 30743874 30746107
chr_3 g4122 g4122.t19 exon g4122.t19.exon1 30743874 30744541
chr_3 g4122 g4122.t19 cds g4122.t19.CDS1 30743874 30744541
chr_3 g4122 g4122.t19 exon g4122.t19.exon2 30744597 30744635
chr_3 g4122 g4122.t19 cds g4122.t19.CDS2 30744597 30744635
chr_3 g4122 g4122.t19 exon g4122.t19.exon3 30744726 30745144
chr_3 g4122 g4122.t19 cds g4122.t19.CDS3 30744726 30745144
chr_3 g4122 g4122.t19 exon g4122.t19.exon4 30745203 30745319
chr_3 g4122 g4122.t19 cds g4122.t19.CDS4 30745203 30745319
chr_3 g4122 g4122.t19 exon g4122.t19.exon5 30745375 30745580
chr_3 g4122 g4122.t19 cds g4122.t19.CDS5 30745375 30745580
chr_3 g4122 g4122.t19 exon g4122.t19.exon6 30745637 30745809
chr_3 g4122 g4122.t19 cds g4122.t19.CDS6 30745637 30745693
chr_3 g4122 g4122.t19 exon g4122.t19.exon7 30745871 30746107
chr_3 g4122 g4122.t19 TSS g4122.t19 NA NA

Sequences

>g4122.t19 Gene=g4122 Length=1859
TTTTGTTGCATGCTTTTTTTCTTGTTCTCTTACCGGCATTCAATCATATGTTGTTTACAA
ATAATTTGGCCTATGAACGAATGGAGTTAGTGATTTTTGCGATGTTCTCTCTCTTTCTAT
TTCTCATTTAAGACTTGTTTTCTCTCTCAGAAACGTATTTATCATAACAGAAAACTTTTA
ACTCTCATCACTTGTGTTGGTTTTACTTTTCATTCTAGATAAAGATTAATTACGCAAATT
TAAAAGGTGACATTTTTAAAAGAACCACAAAAATTTTTAAAAATTTCCATCTGGATTTAA
ATTTTAAAATAACATCGTAAAAGAAAATTTCTCGAACAATTGTGAATTGAAAAATGGAAA
CTCCAAAAAATCCTAATCCAAATCCAGATCAAGAAATTCAGTTCACGAAGCTTTTTATCA
ACAATGAATTCGTTGATTCAATCAGTAAAAAGACTTTTGCTACAATTAACCCAGCAAATG
GCAAAAAAATCGCTGACATCGCTGAAGCTGATAAGGCTGATGTCGATTTAGCAGTTAAAG
CTGCACAAAAAGCATTCGAACGTGGCTCTGAATGGCGAAATTTAGATGCTTCAGCTCGTG
GAAGATTACTTTATCGTTTAGCGGACCTAATTGACCGTGATTCAGCTATTCTCTCCAATT
TGGAAACATTAGACAATGGAAAACCTTATGAAGATGCATGTCTGGATGTTTTGTTTAGTG
GTGAATTTTTACGTTATTATGCGGGATTATGTGACAAAATTCATGGCAGAACTGTTCCAA
GTGATGGCAATCTTTTTAGTTATGTTCGCAAAGAACCAATTGGTGTAGTAGGCCAAATTA
TACCTTGGAATTATCCTCTTATGATGGTAAGCTGGAAATGGGCACCGGCTTTAGCTGCTG
GATGCACAATAGTACTTAAACCAGCAGAACAAACTCCCCTTTCGGCTTTATATGTCGCAA
ATCTCGCGAAAGAAGCGGGTTTTCCTGCTGGCGTAGTTAACGTAATTACTGGCTATGGGC
CAACTGTTGGTGCCGCTATTGCATCACATCCTGATATTCGCAAGGTTGCATTTACAGGCT
CAACTGAAGTTGGAAAATTAATTATGGAAGCTGCTGCAAAATCAAATTTGAAGAAAGTTT
CATTAGAGTTGGGTGGCAAGAGTCCTCTCGTCATCTTTGATGACGTAAACATTGATGAAG
CAGTTGATATTGCTCATAATGCAATATTTGCAAACCATGGTCAAAACTGTTGTGCTGGTT
CTCGTACATTCGTTCATGAGAAAATTTATGATGAATTTGTAGAAAAAGCAGCTGAAATGG
CCAAAAATAGAAAACTTGGTTCTCCTTTCGAAATTGGTGTTCAACAGGGACCACAAGTTG
ATGATCAGATGTTTAAAAAAGTTCTCACTTACATTGATTATGGCAAAGAAGATGGTGCAA
AATTGGAAGCCGGTGGAAAGAGATGGGGCAATGAAGGTTTCTATATTGAACCAACTGTTT
TCTCAAATGTTACTGACGATATGCGCATTGCACAAGATGAAATTTTCGGACCTGTTCAAT
CGATTCTCAAGTTCAAGACAATTGATGAAGTTATTGAGCGTGCTAATAATACAACTTATG
GATTAGCTGCTGGAGTTCTAACAAATGACATTAATACAGCTTTGACATTTGCAAATGCAG
TCGAAGCTGGATCAGTTTGGGTTAATTGTTACGATGCTGTTACACCACAAATGCCTTTTG
GAGGATATAAGCAAAGCGGAATTGGAAGAGAATTGGGTGCAGAAGGAATCGAATCTTATC
TTGAAACAAAAGCAGTTTCAATTAAATTACCATCATTTAAAGTACCATCAAAAATCTAA

>g4122.t19 Gene=g4122 Length=501
METPKNPNPNPDQEIQFTKLFINNEFVDSISKKTFATINPANGKKIADIAEADKADVDLA
VKAAQKAFERGSEWRNLDASARGRLLYRLADLIDRDSAILSNLETLDNGKPYEDACLDVL
FSGEFLRYYAGLCDKIHGRTVPSDGNLFSYVRKEPIGVVGQIIPWNYPLMMVSWKWAPAL
AAGCTIVLKPAEQTPLSALYVANLAKEAGFPAGVVNVITGYGPTVGAAIASHPDIRKVAF
TGSTEVGKLIMEAAAKSNLKKVSLELGGKSPLVIFDDVNIDEAVDIAHNAIFANHGQNCC
AGSRTFVHEKIYDEFVEKAAEMAKNRKLGSPFEIGVQQGPQVDDQMFKKVLTYIDYGKED
GAKLEAGGKRWGNEGFYIEPTVFSNVTDDMRIAQDEIFGPVQSILKFKTIDEVIERANNT
TYGLAAGVLTNDINTALTFANAVEAGSVWVNCYDAVTPQMPFGGYKQSGIGRELGAEGIE
SYLETKAVSIKLPSFKVPSKI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g4122.t19 CDD cd07141 ALDH_F1AB_F2_RALDH1 10 491 0.0
7 g4122.t19 Gene3D G3DSA:3.40.605.10 Aldehyde Dehydrogenase; Chain A 32 488 1.5E-197
8 g4122.t19 Gene3D G3DSA:3.40.309.10 Aldehyde Dehydrogenase; Chain A 271 460 1.5E-197
2 g4122.t19 PANTHER PTHR11699:SF269 ALDEHYDE DEHYDROGENASE, MITOCHONDRIAL-LIKE PROTEIN 11 494 2.1E-271
3 g4122.t19 PANTHER PTHR11699 ALDEHYDE DEHYDROGENASE-RELATED 11 494 2.1E-271
1 g4122.t19 Pfam PF00171 Aldehyde dehydrogenase family 27 488 1.2E-182
6 g4122.t19 ProSitePatterns PS00687 Aldehyde dehydrogenases glutamic acid active site. 264 271 -
5 g4122.t19 ProSitePatterns PS00070 Aldehyde dehydrogenases cysteine active site. 292 303 -
4 g4122.t19 SUPERFAMILY SSF53720 ALDH-like 13 492 2.88E-182

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

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.

Raw TPM values