General information for g9425.t16
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Probable pyruvate dehydrogenase E1 component subunit alpha, mitochondrial.
Parent gene
- The parent gene g9425 is located on chr_1: 2857514..2859684 (+ 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 | g9425 | g9425.t16 | TSS | g9425.t16 | 2855702 | 2855702 |
| chr_1 | g9425 | g9425.t16 | isoform | g9425.t16 | 2856524 | 2857514 |
| chr_1 | g9425 | g9425.t16 | exon | g9425.t16.exon1 | 2856524 | 2856585 |
| chr_1 | g9425 | g9425.t16 | exon | g9425.t16.exon2 | 2856653 | 2856803 |
| chr_1 | g9425 | g9425.t16 | cds | g9425.t16.CDS1 | 2856754 | 2856803 |
| chr_1 | g9425 | g9425.t16 | exon | g9425.t16.exon3 | 2856862 | 2857316 |
| chr_1 | g9425 | g9425.t16 | cds | g9425.t16.CDS2 | 2856862 | 2857316 |
| chr_1 | g9425 | g9425.t16 | exon | g9425.t16.exon4 | 2857456 | 2857514 |
| chr_1 | g9425 | g9425.t16 | cds | g9425.t16.CDS3 | 2857456 | 2857514 |
| chr_1 | g9425 | g9425.t16 | TTS | g9425.t16 | 2857573 | 2857573 |
Sequences
>g9425.t16 Gene=g9425 Length=727
GTATTCAAAAAATTTCTATGGAGGAAACGGAATTGTTGGCGCTCAAGTGCCACTTGGAGC
AGGTGTTGCTTTTGCATGCAAATACAAAAACAATGGAGGTGTATGCTTGTCACTTTACGG
AGATGGTGCATCAAATCAAGGACAAGTTTTTGAAGCTTACAATATGGCTTATCTCTGGAA
ATTACCATGCATTTTCATTTGTGAAAACAATGGATATGGCATGGGAACAAGTGCTGAACG
TTCATCAAGCAATACAGAATATTACAAACGTGGTGATGTTTTGCCTGGCTTATGGATTGA
TGGTATGGATGTATTAGCTGTTAAAGAAGGAACACGATTTGCAATTGATTATGTATTAAA
AAATGGTCCTATTGTGATTGAAGCTGCTACTTATCGTTATTCAGGCCATAGCATGTCTGA
TCCAGGCACAAGCTACAGATCACGTGATGAAATTCAAGAAGTTCGTCAAAAACGTGATCC
AATCACTTCATTTAAAGAGAGAATGCTTGAGACTGGTTTAGCAACAGAAGCTGATATTAA
GAAAATTGATAGTGAAGTTAAGAAAGAAGTTGATGCAGCAACAGCACTTGCAAAGAGTGA
TACTGAAATCCCTGTATCAGAACTCACATGCGATATTTACTCCATGAATCAAGAGGGTGA
TGTGCATGGATTGACACCAGACAAAAAGTTAAAGCACACAACACTCAAGACTGCTGTAAA
TCTTTAA
>g9425.t16 Gene=g9425 Length=187
MAYLWKLPCIFICENNGYGMGTSAERSSSNTEYYKRGDVLPGLWIDGMDVLAVKEGTRFA
IDYVLKNGPIVIEAATYRYSGHSMSDPGTSYRSRDEIQEVRQKRDPITSFKERMLETGLA
TEADIKKIDSEVKKEVDAATALAKSDTEIPVSELTCDIYSMNQEGDVHGLTPDKKLKHTT
LKTAVNL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g9425.t16 | Gene3D | G3DSA:3.40.50.970 | - | 1 | 180 | 0 |
| 2 | g9425.t16 | PANTHER | PTHR11516:SF55 | PYRUVATE DEHYDROGENASE E1 COMPONENT SUBUNIT ALPHA | 1 | 181 | 0 |
| 3 | g9425.t16 | PANTHER | PTHR11516 | PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNIT BACTERIAL AND ORGANELLAR | 1 | 181 | 0 |
| 1 | g9425.t16 | Pfam | PF00676 | Dehydrogenase E1 component | 1 | 149 | 0 |
| 4 | g9425.t16 | SUPERFAMILY | SSF52518 | Thiamin diphosphate-binding fold (THDP-binding) | 1 | 160 | 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:0016624 | oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor | 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.
