General information for g4225.t2
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.t2 | TSS | g4225.t2 | 354940 | 354940 |
| chr_2 | g4225 | g4225.t2 | isoform | g4225.t2 | 354979 | 356751 |
| chr_2 | g4225 | g4225.t2 | exon | g4225.t2.exon1 | 354979 | 355033 |
| chr_2 | g4225 | g4225.t2 | exon | g4225.t2.exon2 | 355096 | 355439 |
| chr_2 | g4225 | g4225.t2 | cds | g4225.t2.CDS1 | 355258 | 355439 |
| chr_2 | g4225 | g4225.t2 | exon | g4225.t2.exon3 | 355512 | 356751 |
| chr_2 | g4225 | g4225.t2 | cds | g4225.t2.CDS2 | 355512 | 356751 |
| chr_2 | g4225 | g4225.t2 | TTS | g4225.t2 | 356777 | 356777 |
Sequences
>g4225.t2 Gene=g4225 Length=1639
ATGTCAGCAAAGCAAGAATTTAAGGGGAATAAAATTAAAGATTTGATAAGAGAGAGATTA
TAAATTTGGAAATTATGATGTATCAGTGTGGACTAGAACAGTCACGGAAGAAATTATTGA
TCCAATTGAAGGTGAAATAAGTGGAGAGATACCTCGATGGATCAATGGATGTTCATTATT
GCAAAATGGTCCAGGCGCATATGAAATTGGAGATGTCATGTTTAATCATGTTTTTGATGG
CATGGCTCTTTTACATCGCTTTAATATTGTTGATGGAAAAGTCACATATCAAAATCGTTT
TGTAAAGAGTAATGCTTATGAAGCAGTTAAGAAGGAAAATCGAATTGTTTTTGGTGAATT
TGGAACTGCTCCTGATCCTGTTGGAAATATTTTCCAACGTTTTCTTTCACTCTTCAAGAC
TAAAACAGATAGTACTACTGATAACACATTGGTAACAATTTTTCCAATTGGTAACGACTT
TTATGCTTTCACTGAAACTCCTAAAATTCGTAAATTTAACACAACAACTCTTGAAACTTT
AAACTTGGTCAATTTGAAAGAATACACAGGAATTGTCTATCAACCAGCTCATGCTATTGT
CACAGAAGACGGAAGTCTTTACAATATCGGTACGAGTATTTCTTCAGCAGGTGCGCAATA
CATTCTCTATTGCATTCCAAATGTTGAAAATAAATTTGAGAATGTAAAAATTGTGTCAAA
AATCACTCCAAAGCGTAAAACATATCCATCATATATGCATTCATTTGGCATCACTGAAAA
CTATTTCATCGTTATCGAGCAACCATTCACTATTTCAATATATGAGCTAACCAAATCACT
TTTTATAAGAAAAAACTTTTTGGACGCTTTCAAATGGTTCGAAAATGAACCAACATACGT
TCATTTGATTGATCGCAAAACTGGAGTTAAAATTCACACTTTTGAGACAGAAACATTTTT
CTTTTTTCATACAATCAATGCTTATGAAGATAATGATCAAGTCGTGCTTGATATTATTTG
TTATGAAGGTCCTGAACTTGTTAAAGGCTTGTTGCTTCAAAATATGAAACAATTACAAAA
GGCAAAAGCAAAAACAAAAATGTTGACATCACGTCCATTGCGTTTTGTTTTTCCATTGAA
ATATTCCACAGAGAACAAAGTTGATAAAAATTTGGTTTATTTAAAAGGGACTGACGCAAC
AGCTTATATGCAACAGAGTGGAACTGTTATATGCTTTCCTGAGTTACTTTGTAACCATTC
ATTTGAATTTGGTACCGTTTATTATGATAAATATTTTGGCAAGAAATACAAATTTTTCTA
TGGTGTTGGAATGGATCTTTATACAGAATTTCCAGAACAGTTGATTAAAGTCAACACGGA
AACAAAAGAAGTTCAAATTTGGCAAGAGGAAAATGTTTACCCTAGTGAGCCACTATTTAT
TCCATCGCCAAATTCAGCTTCTGAAGATGATGGCATTATTATTAGTGCATTGTTAAAGGG
AAATGAAAACACAAACTTCATTGCATTTTTAATTTTGGATGGAAAAACTTTTAGGGAAAT
CGGAAGATGTGAATTTAAAAATTTACCATCAGCAATTACAAAAGTTTTTCATGGTTGGTT
CTTAGATCAGAGAAAATAA
>g4225.t2 Gene=g4225 Length=473
MFNHVFDGMALLHRFNIVDGKVTYQNRFVKSNAYEAVKKENRIVFGEFGTAPDPVGNIFQ
RFLSLFKTKTDSTTDNTLVTIFPIGNDFYAFTETPKIRKFNTTTLETLNLVNLKEYTGIV
YQPAHAIVTEDGSLYNIGTSISSAGAQYILYCIPNVENKFENVKIVSKITPKRKTYPSYM
HSFGITENYFIVIEQPFTISIYELTKSLFIRKNFLDAFKWFENEPTYVHLIDRKTGVKIH
TFETETFFFFHTINAYEDNDQVVLDIICYEGPELVKGLLLQNMKQLQKAKAKTKMLTSRP
LRFVFPLKYSTENKVDKNLVYLKGTDATAYMQQSGTVICFPELLCNHSFEFGTVYYDKYF
GKKYKFFYGVGMDLYTEFPEQLIKVNTETKEVQIWQEENVYPSEPLFIPSPNSASEDDGI
IISALLKGNENTNFIAFLILDGKTFREIGRCEFKNLPSAITKVFHGWFLDQRK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g4225.t2 | PANTHER | PTHR10543 | BETA-CAROTENE DIOXYGENASE | 1 | 470 | 0 |
| 3 | g4225.t2 | PANTHER | PTHR10543:SF57 | RETINOID ISOMEROHYDROLASE | 1 | 470 | 0 |
| 1 | g4225.t2 | Pfam | PF03055 | Retinal pigment epithelial membrane protein | 2 | 469 | 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.
