Gene loci information

Transcript annotation

  • This transcript has been annotated as Homogentisate 1,2-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_3 g879 g879.t6 TTS g879.t6 6630215 6630215
chr_3 g879 g879.t6 isoform g879.t6 6630332 6632086
chr_3 g879 g879.t6 exon g879.t6.exon1 6630332 6630750
chr_3 g879 g879.t6 cds g879.t6.CDS1 6630745 6630750
chr_3 g879 g879.t6 exon g879.t6.exon2 6630840 6631065
chr_3 g879 g879.t6 cds g879.t6.CDS2 6630840 6631065
chr_3 g879 g879.t6 exon g879.t6.exon3 6631293 6631823
chr_3 g879 g879.t6 cds g879.t6.CDS3 6631293 6631519
chr_3 g879 g879.t6 exon g879.t6.exon4 6631900 6632086
chr_3 g879 g879.t6 TSS g879.t6 6632126 6632126

Sequences

>g879.t6 Gene=g879 Length=1363
ATGCCAGAATATCAAGTGAGTATTTTGTTAATTTGAAAATTAAACTATTTTTATTCTCAC
GCACATAATCGTTATCACAATCATCTCAGTATCTCTCAGGTTTTGGTTCAGAATTCTCTT
CGGAGCATCCAAATTATAAAAATGCACTGCCAGTAGGTCAAAATACACCACAAAAGTGCG
CTTACGGACTCTACGCTGAACAATTATCAGGTAGTGCATTTACAGCACCACGAAGTGAAA
ACGTGCGTACATGGTTCTATCGTATTCGTCCAACTGCTGTTCACAATCCGTTTCAACGCT
ATGATAAGGCAAAACACTTGAGTACAAATTGGAATGAAATTCATCCCGACCCGAATCAAT
TTCGATGGAATCCATTTGACATTCCCAGCGGTAAAGTTGACTTTGTTGATGGCTTGAATA
CGATTTGTGGCGCTGGTGATGCGAAAAGTCGTCATGGCATTGCAATACACATTTATACGT
GCAATGCCTCAATGGAAAATCGTGCTTTCTATAATAGTGATGGTGATTTCTTAATTGTAC
CACAGCAAGGAGCACTTGACATCACCACAGAGTTTGGTAAAATTTATGTTGAACCAAATG
AGATTTGTGTCATTCAACAAGGCATGAGATTTTCTGTTAATGTTTCGGGACCATCACGTG
GATACATTTGTGAAGTTTATGACGGTCATTTCAAATTACCTGATTTAGGACCTATTGGAG
CCAATGGTCTGGCACATCCACGTGATTTCTTAACACCAACAGCTTGGTTTGAAGATCGTG
ACATTTCTAATTTCGAAGTAATTTCTAAATTTCAAGGTGCATTATTTTCTGCATCACAAA
ATCATTCGTGTTTTGATGTCGTCGCTTGGCACGGAAACTATGTGCCCTATAAATATAATC
TCGCAAATTTCATGGTCATCAACTCGGTTAGCTTTGATCATTGTTTTTAACATGTCCAAG
CTTACGTTATGGCACAGCGATTGCTGATTTTGTCATTTTCCCGCCACGTTGGTCAGTACA
AGAACATACATTCCGTCCTCCTTACTATCATCGTAACTGCATGAGTGAATTCATGGGCTT
AGTTTTAGGCCGTTATGAAGCAAAAGAAGGCGGATTTTATCCTGGTGGTGCGACACTACA
CTCGATGATGACTCCCCATGGTCCTGACTATGAATGTTTCAATCAAGCGACAAATGCTAA
ACTCGAACCACAGCGTATTGCAGAAGGAACACAGGCATTTATGTTTGAATCATCACTCAG
TATGGCAACAACAAAATGGGGACGTGAAACATGCAATAAATTGGATAAACAATATTTCGA
ATGCTGGCAAAAACTTCAAAATAATTTCCGTATCAGTTCTTAA

>g879.t6 Gene=g879 Length=152
MENRAFYNSDGDFLIVPQQGALDITTEFGKIYVEPNEICVIQQGMRFSVNVSGPSRGYIC
EVYDGHFKLPDLGPIGANGLAHPRDFLTPTAWFEDRDISNFEVISKFQGALFSASQNHSC
FDVVAWHGNYVPYKYNLANFMVINSVSFDHCF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
4 g879.t6 CDD cd07000 cupin_HGO_N 1 64 0
2 g879.t6 PANTHER PTHR11056 HOMOGENTISATE 1,2-DIOXYGENASE 1 150 0
1 g879.t6 Pfam PF04209 homogentisate 1,2-dioxygenase 1 151 0
3 g879.t6 SUPERFAMILY SSF51182 RmlC-like cupins 1 151 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:0004411 homogentisate 1,2-dioxygenase activity MF
GO:0055114 NA NA
GO:0006570 tyrosine metabolic process BP
GO:0006559 L-phenylalanine catabolic process BP

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