General information for g5288.t8
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial.
Parent gene
- The parent gene g5288 is located on chr_2: 8396548..8397851 (- 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_2 | g5288 | g5288.t8 | isoform | g5288.t8 | 8396548 | 8397851 |
| chr_2 | g5288 | g5288.t8 | exon | g5288.t8.exon1 | 8396548 | 8397364 |
| chr_2 | g5288 | g5288.t8 | cds | g5288.t8.CDS1 | 8396550 | 8397203 |
| chr_2 | g5288 | g5288.t8 | exon | g5288.t8.exon2 | 8397477 | 8397851 |
| chr_2 | g5288 | g5288.t8 | TSS | g5288.t8 | 8397962 | 8397962 |
| chr_2 | g5288 | g5288.t8 | TTS | g5288.t8 | NA | NA |
Sequences
>g5288.t8 Gene=g5288 Length=1192
ATGTTCCGAACGATTGTTGTACGAAATGAGCGCTTGCTTCAGAGTTCTATTCGTCAATTT
AATAAAAATAATACAATTCGCTGCTTGTCATCGCAATGTTTCCAAAAAATTCAGATGACA
AGGTAATTAACATTGTGAAAGACATTAACTAATGAGTTTTAACTAGTTCTATAAAGTGCA
TAATAAGAAAACACTGAAAATGAAAACAAAAAAGAACTTTTCGGCATTTTCACTGCTTCA
ATCAAAATGATTATATCACAATCGACCTCTCTCTATCTCACTCACTCGATTTTATATATT
CCTTGAATTCATTTTTGCTAATATAACATATTTACACATGATCTTTACATTTCTATTTAT
TTCTTTCTTGTGATCCAACATGGAGAATTGGTTTTAATCGATGCTATGCAGATGTACCCG
ATCACATAAAAGTCTTGTTGCCAGCACTGAGTCCGACCATGGAGATGGGAACAATTGTCA
GTTGGGAAAAGAAAGAAGGCGATAAGTTGAATGAAGGTAAAAAGTAATGAAAGTGCATGA
ATCAACATGTGTTATTAAATTTGCATTTACTATTTTTAGGTGACTTGTTAGCTGAAATTG
AAACTGACAAAGCAACAATGGGCTTTGAAACACCGGAAGAAGGATATTTAGCAAAAATTC
TTTATCCAGCTGGTTCAAAAGATATTCCAGTTGGCAAATTAGTCTGTATTATTGTCGAAA
GTGAAGATGATGTTGCAGCTTTCAAAGACTTTAAAGACGATGGTTCAGCTACTTCTTCTT
CTGCACCGAAAAAAGCAGTACCCGAGCCTGCTGCTGCTTCAGCGCCAACGCCTGTTTCTG
CTCCTTCATCTCCACTTCCAGCCGCAACTCGACCATCAGGCGCAATCACTGCAAGTGAAC
AAAAATATGGTGATCGAGTTCTCGCTAGTCCAATGGCACGTCGTTTAGCTGAAGCACAAA
AATTGCGCTTGGAAGGTCAAGGAAGTGGCCTTTATGGTTCATTAACTTCAAAAGATCTTG
GTGGATTACAAACTGAAGGAAGTGCTCCACAAATTTCATCAGCACAAGCACCTGTCATCC
CACCAAGTCAAGCTTATATCGATATTCCAGTTTCAAATGTTCGTGGAGTTATCGCTAAAC
GTTTATTAGAATCAAAAGTTTCTATTCCGCATTATTATCTCACTGTAGATTG
>g5288.t8 Gene=g5288 Length=218
MNQHVLLNLHLLFLGDLLAEIETDKATMGFETPEEGYLAKILYPAGSKDIPVGKLVCIIV
ESEDDVAAFKDFKDDGSATSSSAPKKAVPEPAAASAPTPVSAPSSPLPAATRPSGAITAS
EQKYGDRVLASPMARRLAEAQKLRLEGQGSGLYGSLTSKDLGGLQTEGSAPQISSAQAPV
IPPSQAYIDIPVSNVRGVIAKRLLESKVSIPHYYLTVD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g5288.t8 | CDD | cd06849 | lipoyl_domain | 19 | 59 | 3.32905E-12 |
| 6 | g5288.t8 | Gene3D | G3DSA:2.40.50.100 | - | 14 | 85 | 1.8E-21 |
| 7 | g5288.t8 | Gene3D | G3DSA:3.30.559.10 | Chloramphenicol Acetyltransferase | 172 | 218 | 1.3E-6 |
| 14 | g5288.t8 | MobiDBLite | mobidb-lite | consensus disorder prediction | 78 | 122 | - |
| 2 | g5288.t8 | PANTHER | PTHR23151:SF9 | DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE COMPONENT OF PYRUVATE DEHYDROGENASE COMPLEX, MITOCHONDRIAL | 15 | 218 | 2.4E-55 |
| 3 | g5288.t8 | PANTHER | PTHR23151 | DIHYDROLIPOAMIDE ACETYL/SUCCINYL-TRANSFERASE-RELATED | 15 | 218 | 2.4E-55 |
| 1 | g5288.t8 | Pfam | PF00364 | Biotin-requiring enzyme | 15 | 59 | 2.8E-8 |
| 9 | g5288.t8 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 19 | - |
| 10 | g5288.t8 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 11 | g5288.t8 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 14 | - |
| 12 | g5288.t8 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 15 | 19 | - |
| 8 | g5288.t8 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 20 | 218 | - |
| 4 | g5288.t8 | SUPERFAMILY | SSF51230 | Single hybrid motif | 15 | 77 | 3.01E-14 |
| 5 | g5288.t8 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 19 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5288/g5288.t8; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5288.t8.fa.iupred3.txt does not exist
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
