General information for g13289.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Hydroxymethylglutaryl-CoA lyase, mitochondrial.
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.t2 | TTS | g13289.t2 | 28917404 | 28917404 |
| chr_1 | g13289 | g13289.t2 | isoform | g13289.t2 | 28917451 | 28918445 |
| chr_1 | g13289 | g13289.t2 | exon | g13289.t2.exon1 | 28917451 | 28918046 |
| chr_1 | g13289 | g13289.t2 | cds | g13289.t2.CDS1 | 28917451 | 28918046 |
| chr_1 | g13289 | g13289.t2 | exon | g13289.t2.exon2 | 28918121 | 28918445 |
| chr_1 | g13289 | g13289.t2 | cds | g13289.t2.CDS2 | 28918121 | 28918445 |
| chr_1 | g13289 | g13289.t2 | TSS | g13289.t2 | 28918489 | 28918489 |
Sequences
>g13289.t2 Gene=g13289 Length=921
ATGTTTTCACGGACAGTAACTCAATTCATTAAAAGAAATGTGAGCTCAGTAAGAATTGTA
GAAGTTGGCCCACGTGATGGACTTCAAAATGAAGCTAAAATTCTTCCAACAACCACCAAA
ATTGAGTTTATTAATCGTCTATCAAAAACAGGTTTAAAAAATATTGAAGCCACAAGTTTT
GTGTCAGCAAAATGGATTCCACAGATGGGTGATAATGTTGATGTGATGAAAGGAATTGAA
AAAGTTGATGGAATCACTTATTCAGCCATTGTTCCAAACATGAAAGGATTTGAAGATGCT
GTTGAAACAAAAACAACTGAAATTGCATCTGAAACTTTTACTAAGAAAAATTTCAACTGT
ACAATAGCAGAAGGAGTTGAAAGAGTTAAATCAATCATGAAGGCAGCAAAAGAGAAAAAT
ATCAAAGTTCGTGGCTATGTTTCAACTGTTATTTCTTGTCCATATGAAGGAAAAATTAAA
CCTTCGGAAGTTGCAAAAATTAGTGAAATGTTACTCAAAGCAGGCTGCTATGAAATATCA
CTTGGTGACACTATCGGTGTTGGAACACCTAATTCAATCAGTGAAATGCTTAAAGAGGTT
TTAAAAGTTGCTCCAGTTGAAACTTTTGCTATTCACTATCATGACACTTATGGACAAGCT
CTCTCAAATATTTTGGCATCACTTGATCTAGGAATTTCTGTTGTTGATGCTTCTGTGTCA
GGATTAGGTGGTTGCCCTTATGCAAGAGGTGCTAGTGGAAATGCCGCAACTGAGGACGTT
GTGTATATGCTTCATGGTTGTGGAGTTAAAACTGGAATCGATTTAGAGCTATTAATTGAT
GCAGGAAAATTTATTTGTGAAGAACTCGGAAGACAATCAGAGTCAAAAGTTAATCGTGCA
ACAAGAAAAATTAAGCCATAA
>g13289.t2 Gene=g13289 Length=306
MFSRTVTQFIKRNVSSVRIVEVGPRDGLQNEAKILPTTTKIEFINRLSKTGLKNIEATSF
VSAKWIPQMGDNVDVMKGIEKVDGITYSAIVPNMKGFEDAVETKTTEIASETFTKKNFNC
TIAEGVERVKSIMKAAKEKNIKVRGYVSTVISCPYEGKIKPSEVAKISEMLLKAGCYEIS
LGDTIGVGTPNSISEMLKEVLKVAPVETFAIHYHDTYGQALSNILASLDLGISVVDASVS
GLGGCPYARGASGNAATEDVVYMLHGCGVKTGIDLELLIDAGKFICEELGRQSESKVNRA
TRKIKP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g13289.t2 | CDD | cd07938 | DRE_TIM_HMGL | 19 | 287 | 0.000 |
| 4 | g13289.t2 | Gene3D | G3DSA:3.20.20.70 | Aldolase class I | 12 | 304 | 0.000 |
| 2 | g13289.t2 | PANTHER | PTHR42738 | HYDROXYMETHYLGLUTARYL-COA LYASE | 9 | 302 | 0.000 |
| 1 | g13289.t2 | Pfam | PF00682 | HMGL-like | 17 | 284 | 0.000 |
| 5 | g13289.t2 | ProSiteProfiles | PS50991 | Pyruvate carboxyltransferase domain. | 17 | 279 | 34.009 |
| 3 | g13289.t2 | SUPERFAMILY | SSF51569 | Aldolase | 14 | 292 | 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 transcript has been annotated with K01640 (hydroxymethylglutaryl-CoA lyase)
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. There were no conditions that were differentially expressed