General information for g9924.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial.
Parent gene
- The parent gene g9924 is located on chr_1: 6057976..6058556 (- 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 | g9924 | g9924.t1 | TTS | g9924.t1 | 6056248 | 6056248 |
| chr_1 | g9924 | g9924.t1 | isoform | g9924.t1 | 6056444 | 6057976 |
| chr_1 | g9924 | g9924.t1 | exon | g9924.t1.exon1 | 6056444 | 6057632 |
| chr_1 | g9924 | g9924.t1 | cds | g9924.t1.CDS1 | 6056444 | 6057632 |
| chr_1 | g9924 | g9924.t1 | exon | g9924.t1.exon2 | 6057706 | 6057821 |
| chr_1 | g9924 | g9924.t1 | cds | g9924.t1.CDS2 | 6057706 | 6057821 |
| chr_1 | g9924 | g9924.t1 | exon | g9924.t1.exon3 | 6057893 | 6057976 |
| chr_1 | g9924 | g9924.t1 | cds | g9924.t1.CDS3 | 6057893 | 6057976 |
| chr_1 | g9924 | g9924.t1 | TSS | g9924.t1 | 6058066 | 6058066 |
Sequences
>g9924.t1 Gene=g9924 Length=1389
ATGTCACAATTATTAAGACAGACTGTTACTAATATTTTACGTAGAAGTACGCACATTTTA
AGATCAAGAACTAACCAAAATTTGGCTGATTCTTTTGCATTTAAACGCAATTTTCACACG
TCTTTGACATTAGAAAAGCTGGTGACATTTAATTTAAGTGACATTGGCGAAGGAATTCAT
GAAGTTACAGTTAAAGAATGGTTTGTTGAGGCAGGAACTGTTGTTAATCAATTTGATAAT
ATTTGCGAGGTTCAGTCTGATAAGGCGTCTGTGACAATCACTTCGAGATATGATGGTAAA
GTTACAAAACTTTATTATTCAGTTGATGATATAGCTTTAGTTGGAAAGCCTCTTGTGGAT
TTTGAAGTGGAAGATGAGGAAAAAGTTGAATCCGATAGTGAATCTGAGGCATCAGCTTAT
TCCTCTGATAGTGATACTGAAGTTATCAAAGGTCGTAAAATATTGACAACACCAAGTGTT
AGAAAAATTGCAAAAGAAAACAATGTTGACCTTTCAAAAGTTCACGGCACTGGAAGAGGA
AATAGAATTTTGAAGGGAGATGTTCTCGAATATTTAAATTTAATTCCAAAAGGCACTCAA
AAGCCTCATCCAACTCTTAAAGAAACGCCAATTGATGAATTTTTAATTCCACCGCCACTA
ACCCATCGTACTGTTGTTTCGCCTCTTGAACATAAAATTGTGCCATTAAAAGGCGTACCA
AAAGTTATGTTCAAATCGATGACTGAGGCACTCAAAATTCCTCATTTTATGTACTCAGAA
GACATCGACATGACTAATATGATGAAAGTTCGTGATGATGTTAAAGAAGAAGCTTTAACA
CGTGGAATAAAATTGACATATATGCCATTCCTCATTAAAGCAGCTAGCGTATGTCTTCAC
AAATATCCAATTTTGAATAGCTCTGTTGATGTAGAACACGAATCTATCATTTACAAGCCA
TATCATAATATTTCAATTGCCATTCATACGCCACAAGGATTGGTTGTGCCAAATATTAAA
AATGTCGAGGCAAAGTCTATTCTCGAGATTGCTCAAGATTTAAATAAACTTCATCAAAAA
GGCTTAAAAGGTGCTCTTAAACCTGAAGATTTTTCGCATGGCACATTCACAATCAGTAAC
ATTGGCAATGTTGGCGGAACAGTTTTAACGCCTGTTATAATGCCACCACAAGTTTGTATT
GGAGCACTTGGTAGAATTAGACCATTACCTCGTTTTAATAAAGATGGTGAAATAATAAAA
GCGCATATTATGAATGTAAGTTTCTCTGGTGATCATCGTATAATTGATGGTGTCACAATG
AGTTCATTCGTTAATTTGTGGAAGCAATATTTGGAAAATCCAAATTTGTTCATGCTTGAT
GGACATTAA
>g9924.t1 Gene=g9924 Length=462
MSQLLRQTVTNILRRSTHILRSRTNQNLADSFAFKRNFHTSLTLEKLVTFNLSDIGEGIH
EVTVKEWFVEAGTVVNQFDNICEVQSDKASVTITSRYDGKVTKLYYSVDDIALVGKPLVD
FEVEDEEKVESDSESEASAYSSDSDTEVIKGRKILTTPSVRKIAKENNVDLSKVHGTGRG
NRILKGDVLEYLNLIPKGTQKPHPTLKETPIDEFLIPPPLTHRTVVSPLEHKIVPLKGVP
KVMFKSMTEALKIPHFMYSEDIDMTNMMKVRDDVKEEALTRGIKLTYMPFLIKAASVCLH
KYPILNSSVDVEHESIIYKPYHNISIAIHTPQGLVVPNIKNVEAKSILEIAQDLNKLHQK
GLKGALKPEDFSHGTFTISNIGNVGGTVLTPVIMPPQVCIGALGRIRPLPRFNKDGEIIK
AHIMNVSFSGDHRIIDGVTMSSFVNLWKQYLENPNLFMLDGH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g9924.t1 | CDD | cd06849 | lipoyl_domain | 48 | 121 | 7.39435E-21 |
| 10 | g9924.t1 | Gene3D | G3DSA:2.40.50.100 | - | 44 | 135 | 4.6E-23 |
| 11 | g9924.t1 | Gene3D | G3DSA:4.10.320.10 | Dihydrolipoamide Transferase | 148 | 195 | 1.5E-17 |
| 12 | g9924.t1 | Gene3D | G3DSA:3.30.559.10 | Chloramphenicol Acetyltransferase | 240 | 460 | 7.8E-91 |
| 4 | g9924.t1 | PANTHER | PTHR43178:SF5 | LIPOAMIDE ACYLTRANSFERASE COMPONENT OF BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE COMPLEX, MITOCHONDRIAL | 41 | 460 | 8.7E-168 |
| 5 | g9924.t1 | PANTHER | PTHR43178 | DIHYDROLIPOAMIDE ACETYLTRANSFERASE COMPONENT OF PYRUVATE DEHYDROGENASE COMPLEX | 41 | 460 | 8.7E-168 |
| 1 | g9924.t1 | Pfam | PF00364 | Biotin-requiring enzyme | 49 | 120 | 3.0E-16 |
| 3 | g9924.t1 | Pfam | PF02817 | e3 binding domain | 155 | 189 | 1.3E-15 |
| 2 | g9924.t1 | Pfam | PF00198 | 2-oxoacid dehydrogenases acyltransferase (catalytic domain) | 230 | 459 | 2.1E-82 |
| 9 | g9924.t1 | ProSitePatterns | PS00189 | 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. | 72 | 101 | - |
| 14 | g9924.t1 | ProSiteProfiles | PS50968 | Biotinyl/lipoyl domain profile. | 47 | 122 | 23.055 |
| 13 | g9924.t1 | ProSiteProfiles | PS51826 | Peripheral subunit-binding (PSBD) domain profile. | 155 | 192 | 21.039 |
| 6 | g9924.t1 | SUPERFAMILY | SSF51230 | Single hybrid motif | 47 | 137 | 6.94E-20 |
| 8 | g9924.t1 | SUPERFAMILY | SSF47005 | Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex | 151 | 192 | 1.01E-11 |
| 7 | g9924.t1 | SUPERFAMILY | SSF52777 | CoA-dependent acyltransferases | 219 | 459 | 1.91E-77 |
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:0016746 | acyltransferase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K09699 (2-oxoisovalerate dehydrogenase E2 component (dihydrolipoyl transacylase))
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.
