Gene loci information

Transcript annotation

  • This transcript has been annotated as Succinyl-CoA:3-ketoacid coenzyme A transferase 1, 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_4 g15758 g15758.t1 TSS g15758.t1 6678194 6678194
chr_4 g15758 g15758.t1 isoform g15758.t1 6678333 6681124
chr_4 g15758 g15758.t1 exon g15758.t1.exon1 6678333 6678395
chr_4 g15758 g15758.t1 cds g15758.t1.CDS1 6678333 6678395
chr_4 g15758 g15758.t1 exon g15758.t1.exon2 6678944 6679073
chr_4 g15758 g15758.t1 cds g15758.t1.CDS2 6678944 6679073
chr_4 g15758 g15758.t1 exon g15758.t1.exon3 6679138 6679221
chr_4 g15758 g15758.t1 cds g15758.t1.CDS3 6679138 6679221
chr_4 g15758 g15758.t1 exon g15758.t1.exon4 6679599 6680567
chr_4 g15758 g15758.t1 cds g15758.t1.CDS4 6679599 6680567
chr_4 g15758 g15758.t1 exon g15758.t1.exon5 6680629 6680642
chr_4 g15758 g15758.t1 cds g15758.t1.CDS5 6680629 6680642
chr_4 g15758 g15758.t1 exon g15758.t1.exon6 6680771 6680830
chr_4 g15758 g15758.t1 cds g15758.t1.CDS6 6680771 6680830
chr_4 g15758 g15758.t1 exon g15758.t1.exon7 6680891 6681124
chr_4 g15758 g15758.t1 cds g15758.t1.CDS7 6680891 6681124
chr_4 g15758 g15758.t1 TTS g15758.t1 6681249 6681249

Sequences

>g15758.t1 Gene=g15758 Length=1554
ATGTTATTAAAGTGCCATAAGTTTGTGATTAAAGGAAACGTAAATTCTATTAATTATTTA
AGAATTTTATCAAATTATTTTTCATCTTCATCAACAAACCAAAGCAAAGCATATAAAGGA
AAAATTTACAGTACGCCAGAAGATGCTGTTGTTGATATACCTGATGGATCAAAACTTCTT
ATAGGCGGTTTTGGTTTATGTGGTTTGCCAGAAAATCTGATAAAAGCTGTGCTTAATACT
GGAAAAAAAGAATTGACAGTTTGCTCAAATAATCCAAGTGTTGATGATTATGGTATCGGT
CTTCTTATTCGTCAAAAACGTGTCAAACGCATGATTGCAACTTATGCTGGTGAAAATAAA
GAATTCGCACGTCAATGGTTCAATGGTGAGCTTGAATTAGAATTGACACCTCAAGGAACA
TTTGCTGAACGAATGCGGGCAGGCGGTGCAGGCATCCCTGCATTTTTTACTCCAACTGGC
TATGGTACACTTATTCATGAAGGTGGAATGCCAATAAAATGGGGAAAAGATGGAAAAGTT
GAAATACCCAGCAAACCAAGAGAAATGAGAATTTTTAATGGCAAACCTTACATAATGGAA
GAAGCTATAACTGGCGATTATGCTTTAGTTCGAGCTTACAAAGCTGATGAAATGGGAAAT
TTAATTTTTAGAACTTCAGCGAGAAATTTCAATCCGACAATGTGCAAAGCAGCTAAAGTC
ACAATTGCTGAAGTTGAAGAAATTGTTCCAGTCGGTTCACTTCAACCTGATGAAATTCAC
ATACCAAGCATTTTTGTGCATCGCATTGTAAAGACAAAACTTGAGAAAAGAATTGAGAAA
TTGACATTACGTCAATCTGAAGGTCAAGCTAAGAAAGAATTGTCAGCAGGTGATAAAATT
AGAGAAAAAATTGCACGAAGAGTTGTATGTGAATTTAAAGATGGAATGAATGTCAATCTT
GGTATTGGTATTCCAGTATTATCAAGCAATTTCATACCAAAAGATGTTTCAATAAATCTT
CAGTCTGAGAATGGAATACTTGGCCTTGGACCTTATCCTGAAGAATATCAAGTTGATGCT
GATTTAATTAATGCTGGCAAAGAACCAGTGACATTAACATTAGGTGCATCAATATTTTCA
TCTGATGAATCTTTCGCTATGATTAGAGGTGGACATATGGATTTGACTGTATTGGGTGCG
ATGGAAGTTTCACAATTTGGTGATTTAGCTAATTGGATGATTCCTGGTAAAATGGTTAAG
GGCATGGGCGGAGCAATGGATTTGGTAGCAGCACCTGGAACAAAAACAATCATCACAATG
GAACACAACAGCAAAGATGGAGCACCGAAAATTCTCAGTGAATGTTCATTGCCATTGACT
GGTAAAAATTGTGTTGACATGATTGTCACTGAAAAAACAGTTTTCAATGTTGATAAAGAA
AAAGGATTAACTTTGATTGAAATTGCTGAAGATATCACATTAGAGCAGCTAATTGCAGCA
ACTGGATGTGAATTTAAAGTTGCTGATGACCTGAAACCAATGCAGCAAGTGTGA

>g15758.t1 Gene=g15758 Length=517
MLLKCHKFVIKGNVNSINYLRILSNYFSSSSTNQSKAYKGKIYSTPEDAVVDIPDGSKLL
IGGFGLCGLPENLIKAVLNTGKKELTVCSNNPSVDDYGIGLLIRQKRVKRMIATYAGENK
EFARQWFNGELELELTPQGTFAERMRAGGAGIPAFFTPTGYGTLIHEGGMPIKWGKDGKV
EIPSKPREMRIFNGKPYIMEEAITGDYALVRAYKADEMGNLIFRTSARNFNPTMCKAAKV
TIAEVEEIVPVGSLQPDEIHIPSIFVHRIVKTKLEKRIEKLTLRQSEGQAKKELSAGDKI
REKIARRVVCEFKDGMNVNLGIGIPVLSSNFIPKDVSINLQSENGILGLGPYPEEYQVDA
DLINAGKEPVTLTLGASIFSSDESFAMIRGGHMDLTVLGAMEVSQFGDLANWMIPGKMVK
GMGGAMDLVAAPGTKTIITMEHNSKDGAPKILSECSLPLTGKNCVDMIVTEKTVFNVDKE
KGLTLIEIAEDITLEQLIAATGCEFKVADDLKPMQQV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g15758.t1 Gene3D G3DSA:3.40.1080.10 - 40 272 7.2E-103
6 g15758.t1 Gene3D G3DSA:3.40.1080.10 - 297 512 1.1E-103
3 g15758.t1 PANTHER PTHR13707 KETOACID-COENZYME A TRANSFERASE 34 516 2.8E-233
8 g15758.t1 PIRSF PIRSF000858 SCOT-t 38 517 1.3E-117
2 g15758.t1 Pfam PF01144 Coenzyme A transferase 45 271 6.0E-70
1 g15758.t1 Pfam PF01144 Coenzyme A transferase 302 498 3.7E-41
10 g15758.t1 ProSitePatterns PS01273 Coenzyme A transferases signature 1. 55 70 -
9 g15758.t1 ProSitePatterns PS01274 Coenzyme A transferases signature 2. 340 348 -
12 g15758.t1 SMART SM00882 CoA_trans_3 43 272 1.3E-81
11 g15758.t1 SMART SM00882 CoA_trans_3 302 500 2.7E-70
4 g15758.t1 SUPERFAMILY SSF100950 NagB/RpiA/CoA transferase-like 41 345 1.48E-90
5 g15758.t1 SUPERFAMILY SSF100950 NagB/RpiA/CoA transferase-like 299 516 1.43E-71
13 g15758.t1 TIGRFAM TIGR02429 pcaI_scoA_fam: 3-oxoacid CoA-transferase, A subunit 41 272 4.7E-72
14 g15758.t1 TIGRFAM TIGR02428 pcaJ_scoB_fam: 3-oxoacid CoA-transferase, B subunit 301 507 8.1E-88

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:0008410 CoA-transferase activity MF
GO:0046952 ketone body catabolic process BP

KEGG

Orthology

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.

Raw TPM values