General information for g5288.t6
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.t6 | isoform | g5288.t6 | 8395370 | 8397851 |
| chr_2 | g5288 | g5288.t6 | exon | g5288.t6.exon1 | 8395370 | 8395960 |
| chr_2 | g5288 | g5288.t6 | TTS | g5288.t6 | 8395472 | 8395472 |
| chr_2 | g5288 | g5288.t6 | cds | g5288.t6.CDS1 | 8395831 | 8395960 |
| chr_2 | g5288 | g5288.t6 | exon | g5288.t6.exon2 | 8396020 | 8396322 |
| chr_2 | g5288 | g5288.t6 | cds | g5288.t6.CDS2 | 8396020 | 8396322 |
| chr_2 | g5288 | g5288.t6 | exon | g5288.t6.exon3 | 8396386 | 8397160 |
| chr_2 | g5288 | g5288.t6 | cds | g5288.t6.CDS3 | 8396386 | 8397160 |
| chr_2 | g5288 | g5288.t6 | exon | g5288.t6.exon4 | 8397224 | 8397851 |
| chr_2 | g5288 | g5288.t6 | cds | g5288.t6.CDS4 | 8397224 | 8397281 |
| chr_2 | g5288 | g5288.t6 | TSS | g5288.t6 | 8397962 | 8397962 |
Sequences
>g5288.t6 Gene=g5288 Length=2297
ATGTTCCGAACGATTGTTGTACGAAATGAGCGCTTGCTTCAGAGTTCTATTCGTCAATTT
AATAAAAATAATACAATTCGCTGCTTGTCATCGCAATGTTTCCAAAAAATTCAGATGACA
AGGTAATTAACATTGTGAAAGACATTAACTAATGAGTTTTAACTAGTTCTATAAAGTGCA
TAATAAGAAAACACTGAAAATGAAAACAAAAAAGAACTTTTCGGCATTTTCACTGCTTCA
ATCAAAATGATTATATCACAATCGACCTCTCTCTATCTCACTCACTCGATTTTATATATT
CCTTGAATTCATTTTTGCTAATATAACATATTTACACATGATCTTTACATTTCTATTTAT
TTCTTTCTTGTGATCGTACGATTTTGCCACATTGTAAATATTTCGTAGTCTTAATTCTCA
CTTTCTCTAAACTCTCTCTATATTTCTAGAAACTGCGTTCAAAAGACAAGAATTTTGCAA
CAACCAGCAACATGGAGAATTGGTTTTAATCGATGCTATGCAGATGTACCCGATCACATA
AAAGTCTTGTTGCCAGCACTGAGTCCGACCATGGAGATGGGAACAATTGTCAGTTGGGAA
AAGAAAGAAGGCGATAAGTTGAATGAAGGTGACTTGTTAGCTGAAATTGAAACTGACAAA
GCAACAATGGGCTTTGAAACACCGGAAGAAGGATATTTAGCAAAAATTCTTTATCCAGCT
GGTTCAAAAGATATTCCAGTTGGCAAATTAGTCTGTATTATTGTCGAAAGTGAAGATGAT
GTTGCAGCTTTCAAAGACTTTAAAGACGATGGTTCAGCTACTTCTTCTTCTGCACCGAAA
AAAGCAGTACCCGAGCCTGCTGCTGCTTCAGCGCCAACGCCTGTTTCTGCTCCTTCATCT
CCACTTCCAGCCGCAACTCGACCATCAGGCGCAATCACTGCAAGTGAACAAAAATATGGT
GATCGAGTTCTCGCTAGTCCAATGGCACGTCGTTTAGCTGAAGCACAAAAATTGCGCTTG
GAAGGTCAAGGAAGTGGCCTTTATGGTTCATTAACTTCAAAAGATCTTGGTGGATTACAA
ACTGAAGGAAGTGCTCCACAAATTTCATCAGCACAAGCACCTGTCATCCCACCAAGTCAA
GCTTATATCGATATTCCAGTTTCAAATGTTCGTGGAGTTATCGCTAAACGTTTATTAGAA
TCAAAAGTTTCTATTCCGCATTATTATCTCACTGTAGATTGTAATGTTGATAAAATCCTG
GAACTACGTGCTCGTTTCAATAAGTCATTAGAAAAGTCTGGAAAGAAATTGTCAATCAAT
GATTTTATTATTAAAGCTGTAGCAACTGCTTGCAGAAAAGTTCCTGAATGCAATTCAGCA
TGGCTAGGAAATACTATTCGACAATTCGATTCAGTTGACGTTTCAGTCGCTGTATCAACT
GATAACGGATTGATCACGCCAATTGTATTTAGTGCTGATCGTAAAGGAGTCGAAGCTATC
TCAACAGATGTAAAGACACTTGCAGGAAAAGCTAGAGAAGGAAAATTGCAACCACAAGAA
TTCCAGGGTGGCACTTTCACTGTTTCAAATCTCGGAATGTTTGATGTTACTCATTTCTGT
GCTATCATTAATCCACCACAATCGTGCATCTTGGCAGTTGGTGGTAGTCAAAAACGTCTT
GTTATTGACGAAAATTCTGAAAAGGGCTTCAAAGAAGCAACCTTTATCTCGGTGACTTTA
AGTGCCGATCATAGAACAGTTGATGGAGCTGTTGGAGCCCGTTGGTTGCAATATTTCAGA
AAATATATGGAAGATCCTGCCACAATGTTACTGTAAATTTAAATTAGGTTCTACTTCGAT
CCAAGTCATCTGAGCTGCTTATGCTTTGCAAAGTTTTATAATTTTATCATTTTCACACAT
AGGAGAAAAATTCATATTTTCAACAAAAAATTCTTTTTTCGTTATAAAAATTTAATCATA
ATTGGTTTATCTATATTGTATGTAGAAAATGTTCTGCGCTGGAGTGCAACTATAAAAAAA
AGATTGATCTAAATTTAAGCACTGAACTGTACTCAATGAATCTGAAATAACAAAACAAGG
AAAAAGCATCCTAACAAGTTGAAAGAACTTGATAAAAAATGTTTAAAAAAACATGAAAAC
GTTAGTTTAAAAATAAAATATAAATTATTCGAATGAAAATTTTTGCTATTACATAAACTT
ATATTTGCAGCTTACTGAAAAAAAAAATGCATTCCACTTTAATATGAAAAGGAAAAAGAA
AAAAAATCGAGGCCAAT
>g5288.t6 Gene=g5288 Length=421
MEMGTIVSWEKKEGDKLNEGDLLAEIETDKATMGFETPEEGYLAKILYPAGSKDIPVGKL
VCIIVESEDDVAAFKDFKDDGSATSSSAPKKAVPEPAAASAPTPVSAPSSPLPAATRPSG
AITASEQKYGDRVLASPMARRLAEAQKLRLEGQGSGLYGSLTSKDLGGLQTEGSAPQISS
AQAPVIPPSQAYIDIPVSNVRGVIAKRLLESKVSIPHYYLTVDCNVDKILELRARFNKSL
EKSGKKLSINDFIIKAVATACRKVPECNSAWLGNTIRQFDSVDVSVAVSTDNGLITPIVF
SADRKGVEAISTDVKTLAGKAREGKLQPQEFQGGTFTVSNLGMFDVTHFCAIINPPQSCI
LAVGGSQKRLVIDENSEKGFKEATFISVTLSADHRTVDGAVGARWLQYFRKYMEDPATML
L
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g5288.t6 | CDD | cd06849 | lipoyl_domain | 1 | 64 | 1.19828E-23 |
| 7 | g5288.t6 | Gene3D | G3DSA:2.40.50.100 | - | 1 | 90 | 1.3E-31 |
| 8 | g5288.t6 | Gene3D | G3DSA:3.30.559.10 | Chloramphenicol Acetyltransferase | 177 | 419 | 1.6E-93 |
| 11 | g5288.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 82 | 127 | - |
| 3 | g5288.t6 | PANTHER | PTHR23151:SF9 | DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE COMPONENT OF PYRUVATE DEHYDROGENASE COMPLEX, MITOCHONDRIAL | 1 | 421 | 4.4E-167 |
| 4 | g5288.t6 | PANTHER | PTHR23151 | DIHYDROLIPOAMIDE ACETYL/SUCCINYL-TRANSFERASE-RELATED | 1 | 421 | 4.4E-167 |
| 1 | g5288.t6 | Pfam | PF00364 | Biotin-requiring enzyme | 3 | 64 | 1.9E-14 |
| 2 | g5288.t6 | Pfam | PF00198 | 2-oxoacid dehydrogenases acyltransferase (catalytic domain) | 191 | 421 | 6.5E-78 |
| 10 | g5288.t6 | ProSitePatterns | PS00189 | 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. | 14 | 43 | - |
| 13 | g5288.t6 | ProSiteProfiles | PS50968 | Biotinyl/lipoyl domain profile. | 1 | 65 | 24.195 |
| 5 | g5288.t6 | SUPERFAMILY | SSF51230 | Single hybrid motif | 2 | 82 | 1.7E-21 |
| 6 | g5288.t6 | SUPERFAMILY | SSF52777 | CoA-dependent acyltransferases | 184 | 421 | 3.65E-80 |
| 12 | g5288.t6 | TIGRFAM | TIGR01349 | PDHac_trf_mito: pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase | 1 | 421 | 6.5E-158 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5288/g5288.t6; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5288.t6.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0004742 | dihydrolipoyllysine-residue acetyltransferase activity | MF |
| GO:0045254 | pyruvate dehydrogenase complex | CC |
| GO:0016746 | acyltransferase activity | MF |
| GO:0006090 | pyruvate metabolic process | BP |
KEGG
Orthology
- This transcript has been annotated with K00627 (pyruvate dehydrogenase E2 component (dihydrolipoamide acetyltransferase))
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.
