General information for g879.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Homogentisate 1,2-dioxygenase.
Parent gene
- The parent gene g879 is located on chr_3: 6630332..6632086 (- 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_3 | g879 | g879.t2 | isoform | g879.t2 | 6620998 | 6632086 |
| chr_3 | g879 | g879.t2 | exon | g879.t2.exon1 | 6620998 | 6621289 |
| chr_3 | g879 | g879.t2 | exon | g879.t2.exon2 | 6630219 | 6630769 |
| chr_3 | g879 | g879.t2 | cds | g879.t2.CDS1 | 6630332 | 6630769 |
| chr_3 | g879 | g879.t2 | exon | g879.t2.exon3 | 6630840 | 6631065 |
| chr_3 | g879 | g879.t2 | cds | g879.t2.CDS2 | 6630840 | 6631065 |
| chr_3 | g879 | g879.t2 | exon | g879.t2.exon4 | 6631293 | 6631823 |
| chr_3 | g879 | g879.t2 | cds | g879.t2.CDS3 | 6631293 | 6631823 |
| chr_3 | g879 | g879.t2 | exon | g879.t2.exon5 | 6631900 | 6631997 |
| chr_3 | g879 | g879.t2 | cds | g879.t2.CDS4 | 6631900 | 6631997 |
| chr_3 | g879 | g879.t2 | exon | g879.t2.exon6 | 6632072 | 6632086 |
| chr_3 | g879 | g879.t2 | cds | g879.t2.CDS5 | 6632072 | 6632086 |
| chr_3 | g879 | g879.t2 | TSS | g879.t2 | 6632126 | 6632126 |
| chr_3 | g879 | g879.t2 | TTS | g879.t2 | NA | NA |
Sequences
>g879.t2 Gene=g879 Length=1713
ATGCCAGAATATCAATATCTCTCAGGTTTTGGTTCAGAATTCTCTTCGGAGCATCCAAAT
TATAAAAATGCACTGCCAGTAGGTCAAAATACACCACAAAAGTGCGCTTACGGACTCTAC
GCTGAACAATTATCAGGTAGTGCATTTACAGCACCACGAAGTGAAAACGTGCGTACATGG
TTCTATCGTATTCGTCCAACTGCTGTTCACAATCCGTTTCAACGCTATGATAAGGCAAAA
CACTTGAGTACAAATTGGAATGAAATTCATCCCGACCCGAATCAATTTCGATGGAATCCA
TTTGACATTCCCAGCGGTAAAGTTGACTTTGTTGATGGCTTGAATACGATTTGTGGCGCT
GGTGATGCGAAAAGTCGTCATGGCATTGCAATACACATTTATACGTGCAATGCCTCAATG
GAAAATCGTGCTTTCTATAATAGTGATGGTGATTTCTTAATTGTACCACAGCAAGGAGCA
CTTGACATCACCACAGAGTTTGGTAAAATTTATGTTGAACCAAATGAGATTTGTGTCATT
CAACAAGGCATGAGATTTTCTGTTAATGTTTCGGGACCATCACGTGGATACATTTGTGAA
GTTTATGACGGTCATTTCAAATTACCTGATTTAGGACCTATTGGAGCCAATGGTCTGGCA
CATCCACGTGATTTCTTAACACCAACAGCTTGGTTTGAAGATCGTGACATTTCTAATTTC
GAAGTAATTTCTAAATTTCAAGGTGCATTATTTTCTGCATCACAAAATCATTCGTGTTTT
GATGTCGTCGCTTGGCACGGAAACTATGTGCCCTATAAATATAATCTCGCAAATTTCATG
GTCATCAACTCGGTTAGCTTTGATCATTGTGATCCGAGCATTTTTACAGTTTTAACATGT
CCAAGCTTACGTTATGGCACAGCGATTGCTGATTTTGTCATTTTCCCGCCACGTTGGTCA
GTACAAGAACATACATTCCGTCCTCCTTACTATCATCGTAACTGCATGAGTGAATTCATG
GGCTTAGTTTTAGGCCGTTATGAAGCAAAAGAAGGCGGATTTTATCCTGGTGGTGCGACA
CTACACTCGATGATGACTCCCCATGGTCCTGACTATGAATGTTTCAATCAAGCGACAAAT
GCTAAACTCGAACCACAGCGTATTGCAGAAGGAACACAGGCATTTATGTTTGAATCATCA
CTCAGTATGGCAACAACAAAATGGGGACGTGAAACATGCAATAAATTGGATAAACAATAT
TTCGAATGCTGGCAAAAACTTCAAAATAATTTCCGTATCAGTTCTTAATAATTTATGGTC
GATATTTTGGAAAGATTTTTTCTCTTTTGGTGATGGAAAAATTTTTAATGTCAAATAAAA
TGTCTCTAATGATGATAATAATAAAGATAAACTCTCATCCACACACATATATATTTGAGC
TTAATGTCATCAGCTTTATTGACTTTTTCCTTCTTATTCAACATTTACAATTTGATATCG
CTAGAAGCAAGAAGTGAGTGAAAATCTTGAGATATAAAAACTCACCCTTTTCTCCTACTG
TGCATTGCAAGAAGAGATAAAGATGAATGTTCGCCGCGGGGTGAAATTCGAGAGAGCAAG
AGAAAAAAGGATCATAGAAAAAGAGTGGAGAATTTATAATGATGAGATTTGATTTCACTT
TTTTTTATCAATTCAGAAATGAAAAAGTCAAAT
>g879.t2 Gene=g879 Length=435
MPEYQYLSGFGSEFSSEHPNYKNALPVGQNTPQKCAYGLYAEQLSGSAFTAPRSENVRTW
FYRIRPTAVHNPFQRYDKAKHLSTNWNEIHPDPNQFRWNPFDIPSGKVDFVDGLNTICGA
GDAKSRHGIAIHIYTCNASMENRAFYNSDGDFLIVPQQGALDITTEFGKIYVEPNEICVI
QQGMRFSVNVSGPSRGYICEVYDGHFKLPDLGPIGANGLAHPRDFLTPTAWFEDRDISNF
EVISKFQGALFSASQNHSCFDVVAWHGNYVPYKYNLANFMVINSVSFDHCDPSIFTVLTC
PSLRYGTAIADFVIFPPRWSVQEHTFRPPYYHRNCMSEFMGLVLGRYEAKEGGFYPGGAT
LHSMMTPHGPDYECFNQATNAKLEPQRIAEGTQAFMFESSLSMATTKWGRETCNKLDKQY
FECWQKLQNNFRISS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g879.t2 | CDD | cd07000 | cupin_HGO_N | 97 | 203 | 0 |
| 4 | g879.t2 | Gene3D | G3DSA:2.60.120.10 | Jelly Rolls | 265 | 401 | 0 |
| 2 | g879.t2 | PANTHER | PTHR11056 | HOMOGENTISATE 1,2-DIOXYGENASE | 3 | 432 | 0 |
| 1 | g879.t2 | Pfam | PF04209 | homogentisate 1,2-dioxygenase | 5 | 431 | 0 |
| 3 | g879.t2 | SUPERFAMILY | SSF51182 | RmlC-like cupins | 3 | 432 | 0 |
| 5 | g879.t2 | TIGRFAM | TIGR01015 | hmgA: homogentisate 1,2-dioxygenase | 3 | 431 | 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 transcript has been annotated with K00451 (homogentisate 1,2-dioxygenase)
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.
