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 g15755 g15755.t1 TSS g15755.t1 6669926 6669926
chr_4 g15755 g15755.t1 isoform g15755.t1 6670005 6672077
chr_4 g15755 g15755.t1 exon g15755.t1.exon1 6670005 6670073
chr_4 g15755 g15755.t1 cds g15755.t1.CDS1 6670005 6670073
chr_4 g15755 g15755.t1 exon g15755.t1.exon2 6670261 6670474
chr_4 g15755 g15755.t1 cds g15755.t1.CDS2 6670261 6670474
chr_4 g15755 g15755.t1 exon g15755.t1.exon3 6670535 6671440
chr_4 g15755 g15755.t1 cds g15755.t1.CDS3 6670535 6671440
chr_4 g15755 g15755.t1 exon g15755.t1.exon4 6671497 6671547
chr_4 g15755 g15755.t1 cds g15755.t1.CDS4 6671497 6671547
chr_4 g15755 g15755.t1 exon g15755.t1.exon5 6671612 6671625
chr_4 g15755 g15755.t1 cds g15755.t1.CDS5 6671612 6671625
chr_4 g15755 g15755.t1 exon g15755.t1.exon6 6671724 6671783
chr_4 g15755 g15755.t1 cds g15755.t1.CDS6 6671724 6671783
chr_4 g15755 g15755.t1 exon g15755.t1.exon7 6671844 6672077
chr_4 g15755 g15755.t1 cds g15755.t1.CDS7 6671844 6672077
chr_4 g15755 g15755.t1 TTS g15755.t1 6672229 6672229

Sequences

>g15755.t1 Gene=g15755 Length=1548
ATGCTGATAAAGTGTTCAAATTTCTTGTTAAATTCTAAAAATTTTCGAATTTCATTGAAT
CATTTAAAGATCTTCACATGTTCACTCTCAACATCGTCAGTAGTTCAAAGTAAAGCATAT
AAAGGAAAAATTTATAGTTCAACACAAGATGCTGTTGATGATATACCAAATGGATCGAAA
CTTTTAGTTGGTGGTTTTGGTTTATGTGGAATTCCTGAAAATCTCATTCAAGCTCTTTTA
GATACCGGAAAAAAAGATTTAACAATTGTTTCTAATAATGCTGGTGTTGACAATTTCGGT
CTCGGTCTTTTACTAAAAGATCGTCGAATTAAGCGCATGATTGCTTCCTATGTTGGTGAA
AATGCTGAATTTGAGCGGCAATATCTTTCAGGTGAGCTTGAACTTGAATTGACCCCTCAA
GGAACACTTGCCGAGAGAATCAGAGCAGGTGGTGCAGGCATCCCTGCATTTTTTACTCCA
ACTGGCTACGGCACACTTGTTCATGAAGGTGGTTCACCTATTAAATATGGTGAAAATGGT
AAAATTGCAATTCATAGTCAACCACGTGAACTTCGTGAATTTAATGGAATTCCTTACATA
ATGGAAGAAGCTATAACTGGCGATTATGCTTTAGTTCGAGCTTACAAAGCTGATGAAATG
GGAAATTTAATTTTTCGAAAATCAGCGAGAAATTTCAATCCGACAATGTGCAAAGCAGCT
AAAGTCACAATTGCTGAAGTTGAAGAAATTGTCCCAGTTGGTTCACTCCAACCTGATGAA
ATTCATATACCGAGCATTTTTGTGCACCGCATTGTAAGAACAAAACTTGAGAAAAGAATT
GAAAGATTGCAAATTAGTCGACCTGATGGAAAACCATCAAAAACTGCAAAATCAAGAGAA
AGAATTGCAAGAAGAGTTGTATGTGAATTTAAAGATGGAATGAATGTCAATCTAGGCATT
GGTATTCCAGTATTATCAAGCAATTATATCCCAAATGATATTACAGTTCATTTACAATCA
GAAAATGGTGTACTTGGACTTGGACCTTTTCCAGAAGAACATATGGTTGATGCTGACATG
ATAAATGCTGGTAAAGAAACTGTCACGTTAATTACTGGAGCATCAATTTTTTCTTCTGAT
GAATCTTTTGCAATGATTAGAGGTGGTCACATGGACATTACAGTGTTAGGTGCTATGGAA
GTTTCTCAATATGGTGATTTAGCTAATTGGATGATTCCTGGAAAACTTGTAAAGGGCATG
GGCGGAGCAATGGATTTAGTAGCAGCACCTGGAACAAAAACAATCATCACAATGGAACAC
AACAGCAAAGATGGAGCGCCAAAAATTCTCAGTGAATGTTCATTGCCATTGACTGGTAAA
AATTGTGTTGACATGATTGTCACTGAGAAAGCAGTTTTCAATGTTGATAAAGAAAAAGGA
TTAACTTTGATTGAAATTGCTGAAGATATCACATTAGAGCAGCTAATTGCAGCAACTGGA
TGTGAATTTAAAGTTGCTGATGACCTGAAACCAATGCAGCAAGTGTGA

>g15755.t1 Gene=g15755 Length=515
MLIKCSNFLLNSKNFRISLNHLKIFTCSLSTSSVVQSKAYKGKIYSSTQDAVDDIPNGSK
LLVGGFGLCGIPENLIQALLDTGKKDLTIVSNNAGVDNFGLGLLLKDRRIKRMIASYVGE
NAEFERQYLSGELELELTPQGTLAERIRAGGAGIPAFFTPTGYGTLVHEGGSPIKYGENG
KIAIHSQPRELREFNGIPYIMEEAITGDYALVRAYKADEMGNLIFRKSARNFNPTMCKAA
KVTIAEVEEIVPVGSLQPDEIHIPSIFVHRIVRTKLEKRIERLQISRPDGKPSKTAKSRE
RIARRVVCEFKDGMNVNLGIGIPVLSSNYIPNDITVHLQSENGVLGLGPFPEEHMVDADM
INAGKETVTLITGASIFSSDESFAMIRGGHMDITVLGAMEVSQYGDLANWMIPGKLVKGM
GGAMDLVAAPGTKTIITMEHNSKDGAPKILSECSLPLTGKNCVDMIVTEKAVFNVDKEKG
LTLIEIAEDITLEQLIAATGCEFKVADDLKPMQQV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g15755.t1 Gene3D G3DSA:3.40.1080.10 - 42 274 1.2E-110
7 g15755.t1 Gene3D G3DSA:3.40.1080.10 - 294 510 6.0E-106
3 g15755.t1 PANTHER PTHR13707 KETOACID-COENZYME A TRANSFERASE 36 514 1.0E-242
8 g15755.t1 PIRSF PIRSF000858 SCOT-t 40 515 2.4E-122
1 g15755.t1 Pfam PF01144 Coenzyme A transferase 47 273 7.4E-77
2 g15755.t1 Pfam PF01144 Coenzyme A transferase 300 496 4.2E-41
10 g15755.t1 ProSitePatterns PS01273 Coenzyme A transferases signature 1. 57 72 -
9 g15755.t1 ProSitePatterns PS01274 Coenzyme A transferases signature 2. 338 346 -
11 g15755.t1 SMART SM00882 CoA_trans_3 45 274 8.4E-91
12 g15755.t1 SMART SM00882 CoA_trans_3 300 498 2.9E-70
5 g15755.t1 SUPERFAMILY SSF100950 NagB/RpiA/CoA transferase-like 43 343 1.35E-96
4 g15755.t1 SUPERFAMILY SSF100950 NagB/RpiA/CoA transferase-like 298 514 1.43E-73
13 g15755.t1 TIGRFAM TIGR02429 pcaI_scoA_fam: 3-oxoacid CoA-transferase, A subunit 43 274 1.8E-77
14 g15755.t1 TIGRFAM TIGR02428 pcaJ_scoB_fam: 3-oxoacid CoA-transferase, B subunit 298 505 5.0E-89

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