General information for g13288.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Hydroxymethylglutaryl-CoA lyase, mitochondrial.
Parent gene
- The parent gene g13288 is located on chr_1: 28916279..28917412 (- 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_1 | g13288 | g13288.t2 | TTS | g13288.t2 | 28916162 | 28916162 |
| chr_1 | g13288 | g13288.t2 | isoform | g13288.t2 | 28916177 | 28916868 |
| chr_1 | g13288 | g13288.t2 | exon | g13288.t2.exon1 | 28916177 | 28916868 |
| chr_1 | g13288 | g13288.t2 | cds | g13288.t2.CDS1 | 28916279 | 28916710 |
| chr_1 | g13288 | g13288.t2 | TSS | g13288.t2 | 28917331 | 28917331 |
Sequences
>g13288.t2 Gene=g13288 Length=692
TTACAAAAAAGAACGTAAATTGTTCTATAGCAGAAAGTATTGAAAGGTTCAAATCAGTCA
TTGATGCAGCAAAAGAGAAAAATATCAAAGTTCGTGGATATGTTTCAACTGTCGTTGGTT
GTCCCTATGAAGGGAAAATTAAACCTTCAGCAGTTGCTATGGTAAGCGAGAAACTTTTCA
CTATGGGCTGCTATGAAATTTCACTTGGTGACACTATCGGTGTTGGCACACCAGGAACTT
TTAAGGAAATGCTGAAGGAAGTTTTAAAAGTTGCTCCAGCTGATAAATTTGCAGTACATT
GTCATGACACTTATGGACAAGCTCTTCCAAATATTCTCACATCTCTCGAATTTGATATTG
CTGTTGTTGATGCTTCTGTGTCAGGATTAGGTGGTTGCCCTTATGCAAGAGGTGCTAGTG
GAAATGCTGCAACTGAGGATGTTGTGTATATGCTTCATGGTTGTGGAGTTAAAACTGGAA
TTGATTTAGAACTATTAATTGATGCAGGAAAATTCATTTGTGAAGAACTTGGAAGACAAT
CAGAGTCAAAAGTAAATCGTGCAACAAGAAAAATTAAACCAAAATTATAATTTGATAGTA
AAACGAGTTAATTATGTGCCTGAAAAATTGAATTTTTGAAACTGATGCATTTATTGTTAA
AATTTATTAAAAATAATTACTGAATAAAAATC
>g13288.t2 Gene=g13288 Length=143
MVSEKLFTMGCYEISLGDTIGVGTPGTFKEMLKEVLKVAPADKFAVHCHDTYGQALPNIL
TSLEFDIAVVDASVSGLGGCPYARGASGNAATEDVVYMLHGCGVKTGIDLELLIDAGKFI
CEELGRQSESKVNRATRKIKPKL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g13288.t2 | Gene3D | G3DSA:3.20.20.70 | Aldolase class I | 1 | 139 | 0.000 |
| 2 | g13288.t2 | PANTHER | PTHR42738 | HYDROXYMETHYLGLUTARYL-COA LYASE | 2 | 138 | 0.000 |
| 3 | g13288.t2 | PANTHER | PTHR42738:SF1 | HYDROXYMETHYLGLUTARYL-COA LYASE, MITOCHONDRIAL | 2 | 138 | 0.000 |
| 1 | g13288.t2 | Pfam | PF00682 | HMGL-like | 2 | 119 | 0.000 |
| 6 | g13288.t2 | ProSiteProfiles | PS50991 | Pyruvate carboxyltransferase domain. | 1 | 114 | 28.631 |
| 4 | g13288.t2 | SUPERFAMILY | SSF51569 | Aldolase | 4 | 127 | 0.000 |
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:0016833 | oxo-acid-lyase activity | MF |
| GO:0003824 | catalytic activity | MF |
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.
