General information for g13288.t3
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 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.t3 | TTS | g13288.t3 | 28916162 | 28916162 |
| chr_1 | g13288 | g13288.t3 | isoform | g13288.t3 | 28916279 | 28917412 |
| chr_1 | g13288 | g13288.t3 | exon | g13288.t3.exon1 | 28916279 | 28916880 |
| chr_1 | g13288 | g13288.t3 | cds | g13288.t3.CDS1 | 28916279 | 28916880 |
| chr_1 | g13288 | g13288.t3 | exon | g13288.t3.exon2 | 28916956 | 28917412 |
| chr_1 | g13288 | g13288.t3 | cds | g13288.t3.CDS2 | 28916956 | 28917412 |
| chr_1 | g13288 | g13288.t3 | TSS | g13288.t3 | NA | NA |
Sequences
>g13288.t3 Gene=g13288 Length=1059
ATGTATCCTAAAATGTGTGAGCGATATATTTGCCATCTTTTGAGTATTCTGACAACTTAT
GACCGACAATCAGCTGATGTTAGTTTACAAATTCTTTATATAATTTATACAGAAATATAT
TTAATTTTAATTATGTTGTCACGCACATTCAGTAAATTTATTAAAAGAAGTGTGAGCTCA
GTAAGAATTGTTGAGGTCGGTCCACGTGATGGACTTCAAAATGAACCTAAAATAGTACCT
GCTACTACAAAAATAGAACTTATTAATCGTCTATCAAAAACTGGTTTGAAAAACATTGAA
GCCACAAGTTTTGTATCTGCCAAGTGGGTGCCACAAATGGGTGATAATGCTGAAGTGTTG
CAAGGAATTGATAAAGTTGATGGAATTTCTTATCCAGTATTGACACCAAATTTAAAAGGT
TTTGAGTCAGCAATTGCTGCTGGAGCAAAAGAAGTTGCATCAGAATCATTTACAAAAAAG
AACGTAAATTGTTCTATAGCAGAAAGTATTGAAAGGTTCAAATCAGTCATTGATGCAGCA
AAAGAGAAAAATATCAAAGTTCGTGGATATGTTTCAACTGTCGTTGGTTGTCCCTATGAA
GGGAAAATTAAACCTTCAGCAGTTGCTATGGTAAGCGAGAAACTTTTCACTATGGGCTGC
TATGAAATTTCACTTGGTGACACTATCGGTGTTGGCACACCAGGAACTTTTAAGGAAATG
CTGAAGGAAGTTTTAAAAGTTGCTCCAGCTGATAAATTTGCAGTACATTGTCATGACACT
TATGGACAAGCTCTTCCAAATATTCTCACATCTCTCGAATTTGATATTGCTGTTGTTGAT
GCTTCTGTGTCAGGATTAGGTGGTTGCCCTTATGCAAGAGGTGCTAGTGGAAATGCTGCA
ACTGAGGATGTTGTGTATATGCTTCATGGTTGTGGAGTTAAAACTGGAATTGATTTAGAA
CTATTAATTGATGCAGGAAAATTCATTTGTGAAGAACTTGGAAGACAATCAGAGTCAAAA
GTAAATCGTGCAACAAGAAAAATTAAACCAAAATTATAA
>g13288.t3 Gene=g13288 Length=352
MYPKMCERYICHLLSILTTYDRQSADVSLQILYIIYTEIYLILIMLSRTFSKFIKRSVSS
VRIVEVGPRDGLQNEPKIVPATTKIELINRLSKTGLKNIEATSFVSAKWVPQMGDNAEVL
QGIDKVDGISYPVLTPNLKGFESAIAAGAKEVASESFTKKNVNCSIAESIERFKSVIDAA
KEKNIKVRGYVSTVVGCPYEGKIKPSAVAMVSEKLFTMGCYEISLGDTIGVGTPGTFKEM
LKEVLKVAPADKFAVHCHDTYGQALPNILTSLEFDIAVVDASVSGLGGCPYARGASGNAA
TEDVVYMLHGCGVKTGIDLELLIDAGKFICEELGRQSESKVNRATRKIKPKL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g13288.t3 | CDD | cd07938 | DRE_TIM_HMGL | 63 | 331 | 1.24026E-176 |
| 4 | g13288.t3 | Gene3D | G3DSA:3.20.20.70 | Aldolase class I | 56 | 348 | 1.4E-126 |
| 2 | g13288.t3 | PANTHER | PTHR42738 | HYDROXYMETHYLGLUTARYL-COA LYASE | 51 | 346 | 2.4E-139 |
| 1 | g13288.t3 | Pfam | PF00682 | HMGL-like | 61 | 328 | 1.4E-52 |
| 6 | g13288.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 26 | - |
| 7 | g13288.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 27 | 46 | - |
| 5 | g13288.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 47 | 352 | - |
| 10 | g13288.t3 | ProSiteProfiles | PS50991 | Pyruvate carboxyltransferase domain. | 61 | 323 | 31.205 |
| 3 | g13288.t3 | SUPERFAMILY | SSF51569 | Aldolase | 59 | 336 | 2.38E-65 |
| 9 | g13288.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 27 | 46 | - |
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