Gene loci information

Transcript annotation

  • This transcript has been annotated as 4-hydroxyphenylpyruvate dioxygenase.

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 g5758 g5758.t13 TSS g5758.t13 11775252 11775252
chr_2 g5758 g5758.t13 isoform g5758.t13 11775323 11777800
chr_2 g5758 g5758.t13 exon g5758.t13.exon1 11775323 11775325
chr_2 g5758 g5758.t13 cds g5758.t13.CDS1 11775323 11775325
chr_2 g5758 g5758.t13 exon g5758.t13.exon2 11775671 11775697
chr_2 g5758 g5758.t13 cds g5758.t13.CDS2 11775671 11775697
chr_2 g5758 g5758.t13 exon g5758.t13.exon3 11775758 11775925
chr_2 g5758 g5758.t13 cds g5758.t13.CDS3 11775758 11775925
chr_2 g5758 g5758.t13 exon g5758.t13.exon4 11776002 11776217
chr_2 g5758 g5758.t13 cds g5758.t13.CDS4 11776002 11776217
chr_2 g5758 g5758.t13 exon g5758.t13.exon5 11776273 11776936
chr_2 g5758 g5758.t13 cds g5758.t13.CDS5 11776273 11776936
chr_2 g5758 g5758.t13 exon g5758.t13.exon6 11777355 11777800
chr_2 g5758 g5758.t13 cds g5758.t13.CDS6 11777355 11777389
chr_2 g5758 g5758.t13 TTS g5758.t13 11777800 11777800

Sequences

>g5758.t13 Gene=g5758 Length=1524
ATGACTACATACACTGACAAAGGACCAAAACCCGATGGCGGTAAATTTCTCTCCTTCGAT
CACGTTACATTTTGGGTAAGCAATGCCAAACAAGCATCATCTTATTACATAACACGCTTG
GGTTTCGAACCGTTGGCCTATCAAGGTTTAGAAACTGGATCTCGTCAATATGCTAGGCAC
GTCGTCAAACAAAATCAGATTATTTTTGTATTCGTCTCGCCATATGATACTGATAATTTT
GAAGTTGGTGGACATTTAATTAAACATGGTGATGGTGTTAAGGACATTTCTTTTGCTGTC
GAAGATCTTGACATTATTGTAAATCGTGCACGTGATCGTGGTGCAAAAATTGTTAAAGAT
ATTTGGGAAGAAAAAGATGAATTTGGTTCAGTTCGTTTTGCTGTTTTACAAACTTATGGT
GACACAACACATACTTTGATTGATCGCAAAAATTACAAAGGAATTTTCTTGCCTGGTTAT
AAAGAACATTATTCCAAGAATGATCCACTTCTTAAAATTTTGCCAAAGCCAAATTTACAA
TTTATTGATCATATCGTTGGCAATCAACCAGATCGACAAATGGAATCAGTTGCTGAATGG
TATGTTCGCTGTTTAATGTTTCATCGCTTTTGGTCGGTTGATGACAGTCAAATTCACACT
GAATTTTCTGCCTTACGTTCAATTGTTGTTACTAATTATGAAGAGACAATCAAAATGCCC
ATTAATGAGCCAGCATCAGGAAAGAAAAAATCACAAATTCAAGAATATGTGGACTATTAT
GCCAGTGGTGGTGTTCAACATATTGCATTGAATACAAACGATATTATCGATACAATTACA
AAACTTAAGGAACGTGGACAAGATTTCTTAGTTGTTCCAGATACTTATTATGATATGCTT
GAAAAACGATTGGCAGCTGACAATTTCAAAATCAAAGAAGATTTGGCAGTGTTGAAAAAA
TTGAAAATTTTAATTGATTATGATCAAACTGGATATTTGCTTCAAATTTTTACTAAAAAC
ATGCAAGATCGTCCAACACTTTTCTTGGAAGTTATTCAACGTCGCAATCATAATGTAAGG
TTTCGGAGCAGGAAATTTCAAAGCCCTTTTTGAAGCAATCGAATTGGATCAAGCACAACG
TGGCAATTTGTAATCTTTTTCCTTCAATATTCTCAAACGGAATCAATAATAACGACTCTG
TTCTAGCTTTTCTGTTCTTTTATTGTTTCTTTAGTTTTTTGAGAACAGAAAAAAAACTTC
TTTTCTTCTTTTATTCATAAAATCACATTTCGACAGCAGTGAAATTTCTTTTCTTTTCAT
TTGATTAAAAATAACAAAAGAGAAAAAAGTCTAAGTACAGTAGTGGAAAAGGAGGATATC
CTAATAAACTGCAGGAGCGATGATAACAATATTGAATATTAAATGCAAATTTTTCTCTCT
TCATACAATTTCTTAATGAAAAAAGAGAATATTCTGCAATATATACAAAAAGAAATAAAG
GATATTGCTGCTGGATGCAAAAAT

>g5758.t13 Gene=g5758 Length=370
MTTYTDKGPKPDGGKFLSFDHVTFWVSNAKQASSYYITRLGFEPLAYQGLETGSRQYARH
VVKQNQIIFVFVSPYDTDNFEVGGHLIKHGDGVKDISFAVEDLDIIVNRARDRGAKIVKD
IWEEKDEFGSVRFAVLQTYGDTTHTLIDRKNYKGIFLPGYKEHYSKNDPLLKILPKPNLQ
FIDHIVGNQPDRQMESVAEWYVRCLMFHRFWSVDDSQIHTEFSALRSIVVTNYEETIKMP
INEPASGKKKSQIQEYVDYYASGGVQHIALNTNDIIDTITKLKERGQDFLVVPDTYYDML
EKRLAADNFKIKEDLAVLKKLKILIDYDQTGYLLQIFTKNMQDRPTLFLEVIQRRNHNVR
FRSRKFQSPF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g5758.t13 CDD cd08342 HPPD_N_like 19 162 0.0000000
9 g5758.t13 CDD cd07250 HPPD_C_like 179 357 0.0000000
6 g5758.t13 Gene3D G3DSA:3.10.180.10 2 1 175 0.0000000
7 g5758.t13 Gene3D G3DSA:3.10.180.10 2 176 370 0.0000000
3 g5758.t13 PANTHER PTHR11959 4-HYDROXYPHENYLPYRUVATE DIOXYGENASE 1 368 0.0000000
4 g5758.t13 PANTHER PTHR11959:SF12 4-HYDROXYPHENYLPYRUVATE DIOXYGENASE 1 368 0.0000000
8 g5758.t13 PIRSF PIRSF009283 4HPP_dioxygenase 6 359 0.0000000
2 g5758.t13 Pfam PF13669 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily 20 120 0.0000006
1 g5758.t13 Pfam PF00903 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily 182 303 0.0000000
11 g5758.t13 ProSiteProfiles PS51819 Vicinal oxygen chelate (VOC) domain profile. 18 149 25.8070000
12 g5758.t13 ProSiteProfiles PS51819 Vicinal oxygen chelate (VOC) domain profile. 181 339 20.0970000
5 g5758.t13 SUPERFAMILY SSF54593 Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase 14 358 0.0000000
13 g5758.t13 TIGRFAM TIGR01263 4HPPD: 4-hydroxyphenylpyruvate dioxygenase 18 358 0.0000000

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5758/g5758.t13; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5758.t13.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0009072 aromatic amino acid family metabolic process BP
GO:0016701 oxidoreductase activity, acting on single donors with incorporation of molecular oxygen MF
GO:0003868 4-hydroxyphenylpyruvate dioxygenase activity 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