General information for g4225.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Carotenoid isomerooxygenase.
Parent gene
- The parent gene g4225 is located on chr_2: 355096..356751 (+ strand)
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.t1 | TSS | g4225.t1 | 354940 | 354940 |
| chr_2 | g4225 | g4225.t1 | isoform | g4225.t1 | 354979 | 356751 |
| chr_2 | g4225 | g4225.t1 | exon | g4225.t1.exon1 | 354979 | 355035 |
| chr_2 | g4225 | g4225.t1 | cds | g4225.t1.CDS1 | 354979 | 355035 |
| chr_2 | g4225 | g4225.t1 | exon | g4225.t1.exon2 | 355096 | 355439 |
| chr_2 | g4225 | g4225.t1 | cds | g4225.t1.CDS2 | 355096 | 355439 |
| chr_2 | g4225 | g4225.t1 | exon | g4225.t1.exon3 | 355512 | 356751 |
| chr_2 | g4225 | g4225.t1 | cds | g4225.t1.CDS3 | 355512 | 356751 |
| chr_2 | g4225 | g4225.t1 | TTS | g4225.t1 | 356777 | 356777 |
Sequences
>g4225.t1 Gene=g4225 Length=1641
ATGTCAGCAAAGCAAGAATTTAAGGGGAATAAAATTAAAGATTTGATAAGAGAGAGTGAT
TATAAATTTGGAAATTATGATGTATCAGTGTGGACTAGAACAGTCACGGAAGAAATTATT
GATCCAATTGAAGGTGAAATAAGTGGAGAGATACCTCGATGGATCAATGGATGTTCATTA
TTGCAAAATGGTCCAGGCGCATATGAAATTGGAGATGTCATGTTTAATCATGTTTTTGAT
GGCATGGCTCTTTTACATCGCTTTAATATTGTTGATGGAAAAGTCACATATCAAAATCGT
TTTGTAAAGAGTAATGCTTATGAAGCAGTTAAGAAGGAAAATCGAATTGTTTTTGGTGAA
TTTGGAACTGCTCCTGATCCTGTTGGAAATATTTTCCAACGTTTTCTTTCACTCTTCAAG
ACTAAAACAGATAGTACTACTGATAACACATTGGTAACAATTTTTCCAATTGGTAACGAC
TTTTATGCTTTCACTGAAACTCCTAAAATTCGTAAATTTAACACAACAACTCTTGAAACT
TTAAACTTGGTCAATTTGAAAGAATACACAGGAATTGTCTATCAACCAGCTCATGCTATT
GTCACAGAAGACGGAAGTCTTTACAATATCGGTACGAGTATTTCTTCAGCAGGTGCGCAA
TACATTCTCTATTGCATTCCAAATGTTGAAAATAAATTTGAGAATGTAAAAATTGTGTCA
AAAATCACTCCAAAGCGTAAAACATATCCATCATATATGCATTCATTTGGCATCACTGAA
AACTATTTCATCGTTATCGAGCAACCATTCACTATTTCAATATATGAGCTAACCAAATCA
CTTTTTATAAGAAAAAACTTTTTGGACGCTTTCAAATGGTTCGAAAATGAACCAACATAC
GTTCATTTGATTGATCGCAAAACTGGAGTTAAAATTCACACTTTTGAGACAGAAACATTT
TTCTTTTTTCATACAATCAATGCTTATGAAGATAATGATCAAGTCGTGCTTGATATTATT
TGTTATGAAGGTCCTGAACTTGTTAAAGGCTTGTTGCTTCAAAATATGAAACAATTACAA
AAGGCAAAAGCAAAAACAAAAATGTTGACATCACGTCCATTGCGTTTTGTTTTTCCATTG
AAATATTCCACAGAGAACAAAGTTGATAAAAATTTGGTTTATTTAAAAGGGACTGACGCA
ACAGCTTATATGCAACAGAGTGGAACTGTTATATGCTTTCCTGAGTTACTTTGTAACCAT
TCATTTGAATTTGGTACCGTTTATTATGATAAATATTTTGGCAAGAAATACAAATTTTTC
TATGGTGTTGGAATGGATCTTTATACAGAATTTCCAGAACAGTTGATTAAAGTCAACACG
GAAACAAAAGAAGTTCAAATTTGGCAAGAGGAAAATGTTTACCCTAGTGAGCCACTATTT
ATTCCATCGCCAAATTCAGCTTCTGAAGATGATGGCATTATTATTAGTGCATTGTTAAAG
GGAAATGAAAACACAAACTTCATTGCATTTTTAATTTTGGATGGAAAAACTTTTAGGGAA
ATCGGAAGATGTGAATTTAAAAATTTACCATCAGCAATTACAAAAGTTTTTCATGGTTGG
TTCTTAGATCAGAGAAAATAA
>g4225.t1 Gene=g4225 Length=546
MSAKQEFKGNKIKDLIRESDYKFGNYDVSVWTRTVTEEIIDPIEGEISGEIPRWINGCSL
LQNGPGAYEIGDVMFNHVFDGMALLHRFNIVDGKVTYQNRFVKSNAYEAVKKENRIVFGE
FGTAPDPVGNIFQRFLSLFKTKTDSTTDNTLVTIFPIGNDFYAFTETPKIRKFNTTTLET
LNLVNLKEYTGIVYQPAHAIVTEDGSLYNIGTSISSAGAQYILYCIPNVENKFENVKIVS
KITPKRKTYPSYMHSFGITENYFIVIEQPFTISIYELTKSLFIRKNFLDAFKWFENEPTY
VHLIDRKTGVKIHTFETETFFFFHTINAYEDNDQVVLDIICYEGPELVKGLLLQNMKQLQ
KAKAKTKMLTSRPLRFVFPLKYSTENKVDKNLVYLKGTDATAYMQQSGTVICFPELLCNH
SFEFGTVYYDKYFGKKYKFFYGVGMDLYTEFPEQLIKVNTETKEVQIWQEENVYPSEPLF
IPSPNSASEDDGIIISALLKGNENTNFIAFLILDGKTFREIGRCEFKNLPSAITKVFHGW
FLDQRK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g4225.t1 | PANTHER | PTHR10543 | BETA-CAROTENE DIOXYGENASE | 25 | 543 | 0.00e+00 |
| 3 | g4225.t1 | PANTHER | PTHR10543:SF57 | RETINOID ISOMEROHYDROLASE | 25 | 543 | 0.00e+00 |
| 1 | g4225.t1 | Pfam | PF03055 | Retinal pigment epithelial membrane protein | 34 | 542 | 0.00e+00 |
| 4 | g4225.t1 | SUPERFAMILY | SSF50998 | Quinoprotein alcohol dehydrogenase-like | 71 | 523 | 7.85e-05 |
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 transcript has been annotated with K11158 (retinoid isomerohydrolase / lutein isomerase)
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.
