Gene loci information

Transcript annotation

  • This transcript has been annotated as Carotenoid isomerooxygenase.

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_2 g4225 g4225.t3 TSS g4225.t3 354940 354940
chr_2 g4225 g4225.t3 isoform g4225.t3 355096 356205
chr_2 g4225 g4225.t3 exon g4225.t3.exon1 355096 355439
chr_2 g4225 g4225.t3 cds g4225.t3.CDS1 355258 355439
chr_2 g4225 g4225.t3 exon g4225.t3.exon2 355512 356205
chr_2 g4225 g4225.t3 cds g4225.t3.CDS2 355512 356205
chr_2 g4225 g4225.t3 TTS g4225.t3 356777 356777

Sequences

>g4225.t3 Gene=g4225 Length=1038
GATTATAAATTTGGAAATTATGATGTATCAGTGTGGACTAGAACAGTCACGGAAGAAATT
ATTGATCCAATTGAAGGTGAAATAAGTGGAGAGATACCTCGATGGATCAATGGATGTTCA
TTATTGCAAAATGGTCCAGGCGCATATGAAATTGGAGATGTCATGTTTAATCATGTTTTT
GATGGCATGGCTCTTTTACATCGCTTTAATATTGTTGATGGAAAAGTCACATATCAAAAT
CGTTTTGTAAAGAGTAATGCTTATGAAGCAGTTAAGAAGGAAAATCGAATTGTTTTTGGT
GAATTTGGAACTGCTCCTGATCCTGTTGGAAATATTTTCCAACGTTTTCTTTCACTCTTC
AAGACTAAAACAGATAGTACTACTGATAACACATTGGTAACAATTTTTCCAATTGGTAAC
GACTTTTATGCTTTCACTGAAACTCCTAAAATTCGTAAATTTAACACAACAACTCTTGAA
ACTTTAAACTTGGTCAATTTGAAAGAATACACAGGAATTGTCTATCAACCAGCTCATGCT
ATTGTCACAGAAGACGGAAGTCTTTACAATATCGGTACGAGTATTTCTTCAGCAGGTGCG
CAATACATTCTCTATTGCATTCCAAATGTTGAAAATAAATTTGAGAATGTAAAAATTGTG
TCAAAAATCACTCCAAAGCGTAAAACATATCCATCATATATGCATTCATTTGGCATCACT
GAAAACTATTTCATCGTTATCGAGCAACCATTCACTATTTCAATATATGAGCTAACCAAA
TCACTTTTTATAAGAAAAAACTTTTTGGACGCTTTCAAATGGTTCGAAAATGAACCAACA
TACGTTCATTTGATTGATCGCAAAACTGGAGTTAAAATTCACACTTTTGAGACAGAAACA
TTTTTCTTTTTTCATACAATCAATGCTTATGAAGATAATGATCAAGTCGTGCTTGATATT
ATTTGTTATGAAGGTCCTGAACTTGTTAAAGGCTTGTTGCTTCAAAATATGAAACAATTA
CAAAAGGCAAAAGCAAAA

>g4225.t3 Gene=g4225 Length=292
MFNHVFDGMALLHRFNIVDGKVTYQNRFVKSNAYEAVKKENRIVFGEFGTAPDPVGNIFQ
RFLSLFKTKTDSTTDNTLVTIFPIGNDFYAFTETPKIRKFNTTTLETLNLVNLKEYTGIV
YQPAHAIVTEDGSLYNIGTSISSAGAQYILYCIPNVENKFENVKIVSKITPKRKTYPSYM
HSFGITENYFIVIEQPFTISIYELTKSLFIRKNFLDAFKWFENEPTYVHLIDRKTGVKIH
TFETETFFFFHTINAYEDNDQVVLDIICYEGPELVKGLLLQNMKQLQKAKAK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g4225.t3 PANTHER PTHR10543 BETA-CAROTENE DIOXYGENASE 1 290 0
3 g4225.t3 PANTHER PTHR10543:SF57 RETINOID ISOMEROHYDROLASE 1 290 0
1 g4225.t3 Pfam PF03055 Retinal pigment epithelial membrane protein 2 288 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:0016702 oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen MF
GO:0055114 NA NA

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