General information for g9425.t11
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.t11 | TSS | g9425.t11 | 2855702 | 2855702 |
| chr_1 | g9425 | g9425.t11 | isoform | g9425.t11 | 2855799 | 2857514 |
| chr_1 | g9425 | g9425.t11 | exon | g9425.t11.exon1 | 2855799 | 2855878 |
| chr_1 | g9425 | g9425.t11 | cds | g9425.t11.CDS1 | 2855837 | 2855878 |
| chr_1 | g9425 | g9425.t11 | exon | g9425.t11.exon2 | 2856124 | 2856471 |
| chr_1 | g9425 | g9425.t11 | cds | g9425.t11.CDS2 | 2856124 | 2856471 |
| chr_1 | g9425 | g9425.t11 | exon | g9425.t11.exon3 | 2856525 | 2856585 |
| chr_1 | g9425 | g9425.t11 | cds | g9425.t11.CDS3 | 2856525 | 2856585 |
| chr_1 | g9425 | g9425.t11 | exon | g9425.t11.exon4 | 2856653 | 2856803 |
| chr_1 | g9425 | g9425.t11 | cds | g9425.t11.CDS4 | 2856653 | 2856803 |
| chr_1 | g9425 | g9425.t11 | exon | g9425.t11.exon5 | 2856862 | 2857316 |
| chr_1 | g9425 | g9425.t11 | cds | g9425.t11.CDS5 | 2856862 | 2857316 |
| chr_1 | g9425 | g9425.t11 | exon | g9425.t11.exon6 | 2857456 | 2857514 |
| chr_1 | g9425 | g9425.t11 | cds | g9425.t11.CDS6 | 2857456 | 2857514 |
| chr_1 | g9425 | g9425.t11 | TTS | g9425.t11 | 2857573 | 2857573 |
Sequences
>g9425.t11 Gene=g9425 Length=1154
ATGATGCAAAATATTTCGAGAAATACATCAAAGTTATTATGGAGAAATGCTGGAATAGTA
AATACCAACGTCCTTATATTCCATATAAACTCCATCGTCTCGATTCTGGTCCATCAACAA
CTGTTTCAGTAACTCGTGATGAAGCACTTGATATGTATAGAAAAATGCAATCAATTCGTC
GCCTTGAGACAAGTGCCGGTAACTTGTATAAGGAAAAGATTGTTCGTGGATTCTGTCATT
TGTATTCTGGTCAAGAGGCTGTTGCTGTTGGAATGAAAGCTTCGATGCGCGAACAAGACA
ATATTATTTCTGCATATCGTGTTCATGGTTGGACACATTTAATGGGAGTGTCAGTAGCTG
GCGTCTTGTCAGAATTGACTGGTAAAAAAGGTGGTTGTGCTCGTGGAAAAGGCGGTTCAA
TGCATATGTATTCAAAAAATTTCTATGGAGGAAACGGAATTGTTGGCGCTCAAGTGCCAC
TTGGAGCAGGTGTTGCTTTTGCATGCAAATACAAAAACAATGGAGGTGTATGCTTGTCAC
TTTACGGAGATGGTGCATCAAATCAAGGACAAGTTTTTGAAGCTTACAATATGGCTTATC
TCTGGAAATTACCATGCATTTTCATTTGTGAAAACAATGGATATGGCATGGGAACAAGTG
CTGAACGTTCATCAAGCAATACAGAATATTACAAACGTGGTGATGTTTTGCCTGGCTTAT
GGATTGATGGTATGGATGTATTAGCTGTTAAAGAAGGAACACGATTTGCAATTGATTATG
TATTAAAAAATGGTCCTATTGTGATTGAAGCTGCTACTTATCGTTATTCAGGCCATAGCA
TGTCTGATCCAGGCACAAGCTACAGATCACGTGATGAAATTCAAGAAGTTCGTCAAAAAC
GTGATCCAATCACTTCATTTAAAGAGAGAATGCTTGAGACTGGTTTAGCAACAGAAGCTG
ATATTAAGAAAATTGATAGTGAAGTTAAGAAAGAAGTTGATGCAGCAACAGCACTTGCAA
AGAGTGATACTGAAATCCCTGTATCAGAACTCACATGCGATATTTACTCCATGAATCAAG
AGGGTGATGTGCATGGATTGACACCAGACAAAAAGTTAAAGCACACAACACTCAAGACTG
CTGTAAATCTTTAA
>g9425.t11 Gene=g9425 Length=371
MEKCWNSKYQRPYIPYKLHRLDSGPSTTVSVTRDEALDMYRKMQSIRRLETSAGNLYKEK
IVRGFCHLYSGQEAVAVGMKASMREQDNIISAYRVHGWTHLMGVSVAGVLSELTGKKGGC
ARGKGGSMHMYSKNFYGGNGIVGAQVPLGAGVAFACKYKNNGGVCLSLYGDGASNQGQVF
EAYNMAYLWKLPCIFICENNGYGMGTSAERSSSNTEYYKRGDVLPGLWIDGMDVLAVKEG
TRFAIDYVLKNGPIVIEAATYRYSGHSMSDPGTSYRSRDEIQEVRQKRDPITSFKERMLE
TGLATEADIKKIDSEVKKEVDAATALAKSDTEIPVSELTCDIYSMNQEGDVHGLTPDKKL
KHTTLKTAVNL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g9425.t11 | CDD | cd02000 | TPP_E1_PDC_ADC_BCADC | 39 | 327 | 2.32077E-142 |
| 6 | g9425.t11 | Coils | Coil | Coil | 368 | 371 | - |
| 5 | g9425.t11 | Gene3D | G3DSA:3.40.50.970 | - | 2 | 364 | 6.5E-139 |
| 2 | g9425.t11 | PANTHER | PTHR11516:SF55 | PYRUVATE DEHYDROGENASE E1 COMPONENT SUBUNIT ALPHA | 16 | 365 | 4.6E-177 |
| 3 | g9425.t11 | PANTHER | PTHR11516 | PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNIT BACTERIAL AND ORGANELLAR | 16 | 365 | 4.6E-177 |
| 1 | g9425.t11 | Pfam | PF00676 | Dehydrogenase E1 component | 41 | 332 | 1.6E-107 |
| 4 | g9425.t11 | SUPERFAMILY | SSF52518 | Thiamin diphosphate-binding fold (THDP-binding) | 25 | 344 | 2.2E-96 |
| 7 | g9425.t11 | TIGRFAM | TIGR03182 | PDH_E1_alph_y: pyruvate dehydrogenase (acetyl-transferring) E1 component, alpha subunit | 34 | 343 | 7.0E-128 |
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:0043231 | intracellular membrane-bounded organelle | CC |
| GO:0004739 | pyruvate dehydrogenase (acetyl-transferring) activity | MF |
| GO:0016624 | oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor | MF |
| GO:0006086 | acetyl-CoA biosynthetic process from pyruvate | BP |
KEGG
Orthology
- This transcript has been annotated with K00161 (pyruvate dehydrogenase E1 component alpha subunit)
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