General information for g13289.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 3-hydroxy-3-methylglutaryl-CoA lyase, cytoplasmic.
Parent gene
- The parent gene g13289 is located on chr_1: 28917451..28918445 (- 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 | g13289 | g13289.t3 | TTS | g13289.t3 | 28917404 | 28917404 |
| chr_1 | g13289 | g13289.t3 | isoform | g13289.t3 | 28917451 | 28918445 |
| chr_1 | g13289 | g13289.t3 | exon | g13289.t3.exon1 | 28917451 | 28917988 |
| chr_1 | g13289 | g13289.t3 | cds | g13289.t3.CDS1 | 28917451 | 28917975 |
| chr_1 | g13289 | g13289.t3 | exon | g13289.t3.exon2 | 28918146 | 28918445 |
| chr_1 | g13289 | g13289.t3 | TSS | g13289.t3 | 28918489 | 28918489 |
Sequences
>g13289.t3 Gene=g13289 Length=838
ATGTTTTCACGGACAGTAACTCAATTCATTAAAAGAAATGTGAGCTCAGTAAGAATTGTA
GAAGTTGGCCCACGTGATGGACTTCAAAATGAAGCTAAAATTCTTCCAACAACCACCAAA
ATTGAGTTTATTAATCGTCTATCAAAAACAGGTTTAAAAAATATTGAAGCCACAAGTTTT
GTGTCAGCAAAATGGATTCCACAGATGGGTGATAATGTTGATGTGATGAAAGGAATTGAA
AAAGTTGATGGAATCACTTATTCAGCCATTGTTCCAAACATGAAAGGATTTGAAGATGCT
AGTTAAATCAATCATGAAGGCAGCAAAAGAGAAAAATATCAAAGTTCGTGGCTATGTTTC
AACTGTTATTTCTTGTCCATATGAAGGAAAAATTAAACCTTCGGAAGTTGCAAAAATTAG
TGAAATGTTACTCAAAGCAGGCTGCTATGAAATATCACTTGGTGACACTATCGGTGTTGG
AACACCTAATTCAATCAGTGAAATGCTTAAAGAGGTTTTAAAAGTTGCTCCAGTTGAAAC
TTTTGCTATTCACTATCATGACACTTATGGACAAGCTCTCTCAAATATTTTGGCATCACT
TGATCTAGGAATTTCTGTTGTTGATGCTTCTGTGTCAGGATTAGGTGGTTGCCCTTATGC
AAGAGGTGCTAGTGGAAATGCCGCAACTGAGGACGTTGTGTATATGCTTCATGGTTGTGG
AGTTAAAACTGGAATCGATTTAGAGCTATTAATTGATGCAGGAAAATTTATTTGTGAAGA
ACTCGGAAGACAATCAGAGTCAAAAGTTAATCGTGCAACAAGAAAAATTAAGCCATAA
>g13289.t3 Gene=g13289 Length=174
MKAAKEKNIKVRGYVSTVISCPYEGKIKPSEVAKISEMLLKAGCYEISLGDTIGVGTPNS
ISEMLKEVLKVAPVETFAIHYHDTYGQALSNILASLDLGISVVDASVSGLGGCPYARGAS
GNAATEDVVYMLHGCGVKTGIDLELLIDAGKFICEELGRQSESKVNRATRKIKP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g13289.t3 | Gene3D | G3DSA:3.20.20.70 | Aldolase class I | 1 | 172 | 0.000 |
| 2 | g13289.t3 | PANTHER | PTHR42738 | HYDROXYMETHYLGLUTARYL-COA LYASE | 1 | 171 | 0.000 |
| 3 | g13289.t3 | PANTHER | PTHR42738:SF1 | HYDROXYMETHYLGLUTARYL-COA LYASE, MITOCHONDRIAL | 1 | 171 | 0.000 |
| 1 | g13289.t3 | Pfam | PF00682 | HMGL-like | 2 | 152 | 0.000 |
| 6 | g13289.t3 | ProSiteProfiles | PS50991 | Pyruvate carboxyltransferase domain. | 1 | 147 | 32.828 |
| 4 | g13289.t3 | SUPERFAMILY | SSF51569 | Aldolase | 2 | 160 | 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. There were no conditions that were differentially expressed