General information for g5288.t7
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t7 | TTS | g5288.t7 | 8395472 | 8395472 |
| chr_2 | g5288 | g5288.t7 | isoform | g5288.t7 | 8396386 | 8397851 |
| chr_2 | g5288 | g5288.t7 | exon | g5288.t7.exon1 | 8396386 | 8397160 |
| chr_2 | g5288 | g5288.t7 | cds | g5288.t7.CDS1 | 8396388 | 8397160 |
| chr_2 | g5288 | g5288.t7 | exon | g5288.t7.exon2 | 8397224 | 8397402 |
| chr_2 | g5288 | g5288.t7 | cds | g5288.t7.CDS2 | 8397224 | 8397402 |
| chr_2 | g5288 | g5288.t7 | exon | g5288.t7.exon3 | 8397730 | 8397851 |
| chr_2 | g5288 | g5288.t7 | cds | g5288.t7.CDS3 | 8397730 | 8397851 |
| chr_2 | g5288 | g5288.t7 | TSS | g5288.t7 | 8397962 | 8397962 |
Sequences
>g5288.t7 Gene=g5288 Length=1076
ATGTTCCGAACGATTGTTGTACGAAATGAGCGCTTGCTTCAGAGTTCTATTCGTCAATTT
AATAAAAATAATACAATTCGCTGCTTGTCATCGCAATGTTTCCAAAAAATTCAGATGACA
AGAAACTGCGTTCAAAAGACAAGAATTTTGCAACAACCAGCAACATGGAGAATTGGTTTT
AATCGATGCTATGCAGATGTACCCGATCACATAAAAGTCTTGTTGCCAGCACTGAGTCCG
ACCATGGAGATGGGAACAATTGTCAGTTGGGAAAAGAAAGAAGGCGATAAGTTGAATGAA
GGTGACTTGTTAGCTGAAATTGAAACTGACAAAGCAACAATGGGCTTTGAAACACCGGAA
GAAGGATATTTAGCAAAAATTCTTTATCCAGCTGGTTCAAAAGATATTCCAGTTGGCAAA
TTAGTCTGTATTATTGTCGAAAGTGAAGATGATGTTGCAGCTTTCAAAGACTTTAAAGAC
GATGGTTCAGCTACTTCTTCTTCTGCACCGAAAAAAGCAGTACCCGAGCCTGCTGCTGCT
TCAGCGCCAACGCCTGTTTCTGCTCCTTCATCTCCACTTCCAGCCGCAACTCGACCATCA
GGCGCAATCACTGCAAGTGAACAAAAATATGGTGATCGAGTTCTCGCTAGTCCAATGGCA
CGTCGTTTAGCTGAAGCACAAAAATTGCGCTTGGAAGGTCAAGGAAGTGGCCTTTATGGT
TCATTAACTTCAAAAGATCTTGGTGGATTACAAACTGAAGGAAGTGCTCCACAAATTTCA
TCAGCACAAGCACCTGTCATCCCACCAAGTCAAGCTTATATCGATATTCCAGTTTCAAAT
GTTCGTGGAGTTATCGCTAAACGTTTATTAGAATCAAAAGTTTCTATTCCGCATTATTAT
CTCACTGTAGATTGTAATGTTGATAAAATCCTGGAACTACGTGCTCGTTTCAATAAGTCA
TTAGAAAAGTCTGGAAAGAAATTGTCAATCAATGATTTTATTATTAAAGCTGTAGCAACT
GCTTGCAGAAAAGTTCCTGAATGCAATTCAGCATGGCTAGGAAATACTATTCGACA
>g5288.t7 Gene=g5288 Length=358
MFRTIVVRNERLLQSSIRQFNKNNTIRCLSSQCFQKIQMTRNCVQKTRILQQPATWRIGF
NRCYADVPDHIKVLLPALSPTMEMGTIVSWEKKEGDKLNEGDLLAEIETDKATMGFETPE
EGYLAKILYPAGSKDIPVGKLVCIIVESEDDVAAFKDFKDDGSATSSSAPKKAVPEPAAA
SAPTPVSAPSSPLPAATRPSGAITASEQKYGDRVLASPMARRLAEAQKLRLEGQGSGLYG
SLTSKDLGGLQTEGSAPQISSAQAPVIPPSQAYIDIPVSNVRGVIAKRLLESKVSIPHYY
LTVDCNVDKILELRARFNKSLEKSGKKLSINDFIIKAVATACRKVPECNSAWLGNTIR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g5288.t7 | CDD | cd06849 | lipoyl_domain | 71 | 145 | 1.43479E-30 |
| 7 | g5288.t7 | Gene3D | G3DSA:2.40.50.100 | - | 65 | 171 | 2.2E-37 |
| 8 | g5288.t7 | Gene3D | G3DSA:3.30.559.10 | Chloramphenicol Acetyltransferase | 258 | 358 | 6.8E-29 |
| 11 | g5288.t7 | MobiDBLite | mobidb-lite | consensus disorder prediction | 164 | 208 | - |
| 3 | g5288.t7 | PANTHER | PTHR23151:SF9 | DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE COMPONENT OF PYRUVATE DEHYDROGENASE COMPLEX, MITOCHONDRIAL | 35 | 358 | 7.4E-102 |
| 4 | g5288.t7 | PANTHER | PTHR23151 | DIHYDROLIPOAMIDE ACETYL/SUCCINYL-TRANSFERASE-RELATED | 35 | 358 | 7.4E-102 |
| 1 | g5288.t7 | Pfam | PF00364 | Biotin-requiring enzyme | 73 | 145 | 9.4E-17 |
| 2 | g5288.t7 | Pfam | PF00198 | 2-oxoacid dehydrogenases acyltransferase (catalytic domain) | 272 | 355 | 8.8E-21 |
| 10 | g5288.t7 | ProSitePatterns | PS00189 | 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. | 95 | 124 | - |
| 12 | g5288.t7 | ProSiteProfiles | PS50968 | Biotinyl/lipoyl domain profile. | 70 | 146 | 26.451 |
| 5 | g5288.t7 | SUPERFAMILY | SSF51230 | Single hybrid motif | 69 | 163 | 7.85E-26 |
| 6 | g5288.t7 | SUPERFAMILY | SSF52777 | CoA-dependent acyltransferases | 265 | 356 | 2.62E-23 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5288/g5288.t7; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5288.t7.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0016746 | acyltransferase activity | 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.
