Gene loci information

Transcript annotation

  • This transcript has been annotated as Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial .

Parent gene

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_3 g635 g635.t12 TSS g635.t12 4679520 4679520
chr_3 g635 g635.t12 isoform g635.t12 4679597 4682657
chr_3 g635 g635.t12 exon g635.t12.exon1 4679597 4679662
chr_3 g635 g635.t12 exon g635.t12.exon2 4679983 4680093
chr_3 g635 g635.t12 cds g635.t12.CDS1 4680018 4680093
chr_3 g635 g635.t12 exon g635.t12.exon3 4680338 4680606
chr_3 g635 g635.t12 cds g635.t12.CDS2 4680338 4680606
chr_3 g635 g635.t12 exon g635.t12.exon4 4681640 4682071
chr_3 g635 g635.t12 cds g635.t12.CDS3 4681640 4682071
chr_3 g635 g635.t12 exon g635.t12.exon5 4682134 4682657
chr_3 g635 g635.t12 cds g635.t12.CDS4 4682134 4682478
chr_3 g635 g635.t12 TTS g635.t12 4683211 4683211

Sequences

>g635.t12 Gene=g635 Length=1402
ATGATTCGATCACTTTCCTCATTTCCACGAAGTGTTGTTCTTCGCATAAGCAATAGAAGT
AATCAGATCCAGCAAACGTTGAGGAATAATATTCATCAACAATGTGCCGTTCAAAAGTTG
GTGCTTACATGCGACACAAATTCTCAAAATTCGTAAGTTATTTCTTTTCTTTCTTATGTG
ATGCAGTTGCAGCTGATGAGGTTGTTATGGAAATTGAAACCGATAAGACAACAGTTGGTG
TTCCAGCTCCATCGCATGGTATCATTGAGGAAATTTTTGTTTCAGACGGTGATACAGTAA
AGGCTGGACAACAGTTGTTCAAAATGAAGTTTACAGATGCCGCACCAGAAAAAGAAGCAT
CAACTTCCACGCCAGAACCTCCAAAAGCAGCTGCTGCACCTTCACCACCACCACCACAAC
CTAAACAAGAAGCACCAAAAGCTGCTCCTCAACCACAAGCAGCACCACCACCTGCTGCAT
CAACACCTCCACCACCGCCTCCAAAACCAGCAGCACCAGCAAAAACCGTTCCAATTGCTG
CCATTCGACATGCACAAGCTATCGATGCTGCCACAGTTAAAGTACCTCCAGCTGATTATA
CAAAAGAAATCACTGGCACACGCACGGAACAGCGTGTAAAAATGAATCGAATGCGTCTAA
AGATTGCATCACGTTTGAAGGAAGCACAAAATGTCAATGCAATGTTAACAACATTCAATG
AAATTGATATGAGTGCAATCATGGAATTCCGCAAGTTGCATCAAGAAACCTTCCAAAAGC
GTTATGGAATTAAATTAGGATTTATGTCAGCTTTCTGTAAAGCTGCTGCTTATGCTCTTC
AAGATCAACCAGTTGTTAATGCTGTTATTGAAGATAATGAAATTGTTTATCGTGATTATG
TTGATATTTCGGTTGCTGTTGCATCACCAAAAGGTTTAGTTGTGCCAGTTTTGCGTAATG
TAGAATCAATGAATTATGCTGAAATTGAATTGGGTATCAATGCTTTGGGCGAGAAAGCTC
GTAATGGAACATTAGCTGTTGAAGATATGGACGGTGGTACTTTTACAATCAGTAATGGAG
GCGTATTTGGTTCACTAATGGGTACTCCAATTATTAATCCACCACAAAGTGCTATTCTCG
GTATGCACGCAACATTTGAGCGACCAGTGGCTATCAAAGGACAAGTGAGTGAAGAAAAAA
AAATTTTGAAATTCTTTTTTTAACTAAAAATTTCTTTCTTTTTCTTTACTTTTGCTTGAT
TTTGAAGGTCGTTATTCGTCCCATGATGTACATCGCACTTACGTATGATCATCGTTTGAT
TGATGGACGTGAGGCTGTGACTTTCTTGCGTAAAATCAAAGCAGGTGTCGAAGATCCAAG
AATCATCTTGGCTGGCGTTTAA

>g635.t12 Gene=g635 Length=373
MCRSKVGAYMRHKFSKFVSYFFSFLCDAVAADEVVMEIETDKTTVGVPAPSHGIIEEIFV
SDGDTVKAGQQLFKMKFTDAAPEKEASTSTPEPPKAAAAPSPPPPQPKQEAPKAAPQPQA
APPPAASTPPPPPPKPAAPAKTVPIAAIRHAQAIDAATVKVPPADYTKEITGTRTEQRVK
MNRMRLKIASRLKEAQNVNAMLTTFNEIDMSAIMEFRKLHQETFQKRYGIKLGFMSAFCK
AAAYALQDQPVVNAVIEDNEIVYRDYVDISVAVASPKGLVVPVLRNVESMNYAEIELGIN
ALGEKARNGTLAVEDMDGGTFTISNGGVFGSLMGTPIINPPQSAILGMHATFERPVAIKG
QVSEEKKILKFFF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g635.t12 CDD cd06849 lipoyl_domain 27 75 2.03908E-14
9 g635.t12 Gene3D G3DSA:2.40.50.100 - 26 78 1.9E-14
10 g635.t12 Gene3D G3DSA:3.30.559.10 Chloramphenicol Acetyltransferase 173 372 5.7E-71
18 g635.t12 MobiDBLite mobidb-lite consensus disorder prediction 79 140 -
17 g635.t12 MobiDBLite mobidb-lite consensus disorder prediction 95 140 -
3 g635.t12 PANTHER PTHR43416 DIHYDROLIPOYLLYSINE-RESIDUE SUCCINYLTRANSFERASE COMPONENT OF 2-OXOGLUTARATE DEHYDROGENASE COMPLEX, MITOCHONDRIAL-RELATED 26 362 6.6E-116
4 g635.t12 PANTHER PTHR43416:SF5 DIHYDROLIPOYLLYSINE-RESIDUE SUCCINYLTRANSFERASE COMPONENT OF 2-OXOGLUTARATE DEHYDROGENASE COMPLEX, MITOCHONDRIAL 26 362 6.6E-116
1 g635.t12 Pfam PF00364 Biotin-requiring enzyme 27 75 4.0E-13
2 g635.t12 Pfam PF00198 2-oxoacid dehydrogenases acyltransferase (catalytic domain) 175 366 1.2E-59
12 g635.t12 Phobius SIGNAL_PEPTIDE Signal peptide region 1 31 -
13 g635.t12 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 16 -
14 g635.t12 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 17 26 -
15 g635.t12 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 27 31 -
11 g635.t12 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 32 373 -
20 g635.t12 ProSiteProfiles PS50968 Biotinyl/lipoyl domain profile. 1 76 17.3
5 g635.t12 SUPERFAMILY SSF51230 Single hybrid motif 27 94 2.22E-14
6 g635.t12 SUPERFAMILY SSF52777 CoA-dependent acyltransferases 175 363 1.65E-65
8 g635.t12 SignalP_EUK SignalP-noTM SignalP-noTM 1 31 -
7 g635.t12 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 30 -
19 g635.t12 TIGRFAM TIGR01347 sucB: dihydrolipoyllysine-residue succinyltransferase, E2 component of oxoglutarate dehydrogenase (succinyl-transferring) complex 26 363 3.1E-120

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:0006099 tricarboxylic acid cycle BP
GO:0045252 oxoglutarate dehydrogenase complex CC
GO:0016746 acyltransferase activity MF
GO:0004149 dihydrolipoyllysine-residue succinyltransferase 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.

Raw TPM values