General information for g879.t4
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.t4 | TTS | g879.t4 | 6630215 | 6630215 |
| chr_3 | g879 | g879.t4 | isoform | g879.t4 | 6630332 | 6631300 |
| chr_3 | g879 | g879.t4 | exon | g879.t4.exon1 | 6630332 | 6630769 |
| chr_3 | g879 | g879.t4 | cds | g879.t4.CDS1 | 6630332 | 6630769 |
| chr_3 | g879 | g879.t4 | exon | g879.t4.exon2 | 6630840 | 6631065 |
| chr_3 | g879 | g879.t4 | cds | g879.t4.CDS2 | 6630840 | 6630872 |
| chr_3 | g879 | g879.t4 | exon | g879.t4.exon3 | 6631293 | 6631300 |
| chr_3 | g879 | g879.t4 | TSS | g879.t4 | 6632126 | 6632126 |
Sequences
>g879.t4 Gene=g879 Length=672
CCTATTGGAGCCAATGGTCTGGCACATCCACGTGATTTCTTAACACCAACAGCTTGGTTT
GAAGATCGTGACATTTCTAATTTCGAAGTAATTTCTAAATTTCAAGGTGCATTATTTTCT
GCATCACAAAATCATTCGTGTTTTGATGTCGTCGCTTGGCACGGAAACTATGTGCCCTAT
AAATATAATCTCGCAAATTTCATGGTCATCAACTCGGTTAGCTTTGATCATTGTGATCCG
AGCATTTTTACAGTTTTAACATGTCCAAGCTTACGTTATGGCACAGCGATTGCTGATTTT
GTCATTTTCCCGCCACGTTGGTCAGTACAAGAACATACATTCCGTCCTCCTTACTATCAT
CGTAACTGCATGAGTGAATTCATGGGCTTAGTTTTAGGCCGTTATGAAGCAAAAGAAGGC
GGATTTTATCCTGGTGGTGCGACACTACACTCGATGATGACTCCCCATGGTCCTGACTAT
GAATGTTTCAATCAAGCGACAAATGCTAAACTCGAACCACAGCGTATTGCAGAAGGAACA
CAGGCATTTATGTTTGAATCATCACTCAGTATGGCAACAACAAAATGGGGACGTGAAACA
TGCAATAAATTGGATAAACAATATTTCGAATGCTGGCAAAAACTTCAAAATAATTTCCGT
ATCAGTTCTTAA
>g879.t4 Gene=g879 Length=156
MVINSVSFDHCDPSIFTVLTCPSLRYGTAIADFVIFPPRWSVQEHTFRPPYYHRNCMSEF
MGLVLGRYEAKEGGFYPGGATLHSMMTPHGPDYECFNQATNAKLEPQRIAEGTQAFMFES
SLSMATTKWGRETCNKLDKQYFECWQKLQNNFRISS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g879.t4 | Gene3D | G3DSA:2.60.120.10 | Jelly Rolls | 1 | 122 | 0 |
| 2 | g879.t4 | PANTHER | PTHR11056:SF0 | HOMOGENTISATE 1,2-DIOXYGENASE | 1 | 153 | 0 |
| 3 | g879.t4 | PANTHER | PTHR11056 | HOMOGENTISATE 1,2-DIOXYGENASE | 1 | 153 | 0 |
| 1 | g879.t4 | Pfam | PF04209 | homogentisate 1,2-dioxygenase | 1 | 152 | 0 |
| 4 | g879.t4 | SUPERFAMILY | SSF51182 | RmlC-like cupins | 1 | 153 | 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