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_2 g8184 g8184.t1 TSS g8184.t1 28959387 28959387
chr_2 g8184 g8184.t1 isoform g8184.t1 28959488 28961709
chr_2 g8184 g8184.t1 exon g8184.t1.exon1 28959488 28959559
chr_2 g8184 g8184.t1 cds g8184.t1.CDS1 28959488 28959559
chr_2 g8184 g8184.t1 exon g8184.t1.exon2 28959644 28959773
chr_2 g8184 g8184.t1 cds g8184.t1.CDS2 28959644 28959773
chr_2 g8184 g8184.t1 exon g8184.t1.exon3 28959840 28959923
chr_2 g8184 g8184.t1 cds g8184.t1.CDS3 28959840 28959923
chr_2 g8184 g8184.t1 exon g8184.t1.exon4 28959981 28960117
chr_2 g8184 g8184.t1 cds g8184.t1.CDS4 28959981 28960117
chr_2 g8184 g8184.t1 exon g8184.t1.exon5 28960172 28960802
chr_2 g8184 g8184.t1 cds g8184.t1.CDS5 28960172 28960802
chr_2 g8184 g8184.t1 exon g8184.t1.exon6 28960863 28960988
chr_2 g8184 g8184.t1 cds g8184.t1.CDS6 28960863 28960988
chr_2 g8184 g8184.t1 exon g8184.t1.exon7 28961050 28961127
chr_2 g8184 g8184.t1 cds g8184.t1.CDS7 28961050 28961127
chr_2 g8184 g8184.t1 exon g8184.t1.exon8 28961198 28961211
chr_2 g8184 g8184.t1 cds g8184.t1.CDS8 28961198 28961211
chr_2 g8184 g8184.t1 exon g8184.t1.exon9 28961276 28961285
chr_2 g8184 g8184.t1 cds g8184.t1.CDS9 28961276 28961285
chr_2 g8184 g8184.t1 exon g8184.t1.exon10 28961350 28961399
chr_2 g8184 g8184.t1 cds g8184.t1.CDS10 28961350 28961399
chr_2 g8184 g8184.t1 exon g8184.t1.exon11 28961476 28961709
chr_2 g8184 g8184.t1 cds g8184.t1.CDS11 28961476 28961709
chr_2 g8184 g8184.t1 TTS g8184.t1 28961881 28961881

Sequences

>g8184.t1 Gene=g8184 Length=1566
ATGATTTCAAAGTGTTTAAGTTCTTTATTAAAACAAAAAGCAATAGGAATAAACTCAAAT
TACCATCAAAAGATATTAGGCTGCTATTTTTCAATCAGCGCCAGACATAACTCGAAAGCC
TACAAAGGAAAAATTTATTTGAATGCTAAAGATGCAGTCGCTGACATACCCGATGGTGCA
AAAATCTTGGTGGGAGGCTTCGGTTTATGTGGAATTCCTGAGAACCTTATTCAAGGTTTA
TTAGATATTGGCATCAAAGATTTAACAGTTGTCTCGAATAATGCAGGCGTTGATGATTTT
GGACTTGGTCTTCTTCTCAAAGACCGTCGAATTAAACGCATGATAGCATCATATGTCGGC
GAAAATGCAGAATTCGAAAGACAATATTTATCTGGTGACTTAGAACTTGAATTGACTCCA
CAAGGGACATTAGCGGAAAGAATCAGAGCTGGTGGAGCAGGTATTCCTGCATTTTTCACA
CCTACTGGTACTTTTACATTGATTCATGAAGGGGGAAGTCCTATTAAATATGTTAAGGGT
AAAAATAAGGAAGTTGAGATTGCAAGTGCAAAAAGAGAAATGAGAGAATTTAATGGAAAA
CCTTATATCATGGAGGAAGCAATTACTGGCGACTTTGCATTAATTCGTGCTTATAAGGCA
GATGAACTTGGAAATTTGATATTTAGAAAATCAGCTAGAAATTTTAATCCACCTATGGCA
AAAGCAGCTAAAATTACAATTGCAGAAGTTGAAGAAATTGTTCCAATTGGTGCACTTCAA
CCTGATGAAATTCATCTACCTGGTATTTTTGTGCATCGCATTATTCGCGGAAAATTTGAA
AAGAGAATTGAAAGAATAAAAATTACAAAACCAGAAACTAATGAGAAAAAACTGTCAAAA
GAAGCACTACTTCGAGAAAGAATCGTTCGTCGTGTTGCTTGCGAATATAAAGACGGAATG
TATATCAATTTAGGAATTGGAATTCCTGTTTTATCAAGCAATTATATACCTAAAGATATT
ACAGTTCATCTTCAATCAGAAAATGGGATTTTAGGCTTGGGGCCTTTTCCAGAAGAATAT
GCAGTTGATGCTGATTTAATAAATGCTGGAAAAGAAACAGTCACTACTATTCAAGGTGGT
TCATATTTTTCAAGTGACGACTCATTTGGAATGATTAGAGGTGGTCATATGGATATGACT
GTCTTAGGTGCGATGGAAGTTTCTCAATTTGGAGATTTGGCTAATTACATGATTCCCGGA
AAACTTGTTAAGGGAATGGGAGGTGCGATGGATTTAGTTAGTGCACCCAACACAAAAACT
ATTATTACTATGGAACATAACAGTAAAAATGGTGCACCGAAAATTCTAACAGAATGCTCT
TTGCCATTAACAGGCAAGAATTGTGTAGACATGATTATAACTGAAAAAGCTGTATTTGAG
GTTGATAAAGAGAAAGGGTTGACTTTAATTGAAATTGCTCCAGATGTAACAATGGAACAA
TTAGTCGCATCGACAGGTTGTTCTTTTAAAATTGCAGACGAAATAATCCCAATGAAGCAA
ATCTAA

>g8184.t1 Gene=g8184 Length=521
MISKCLSSLLKQKAIGINSNYHQKILGCYFSISARHNSKAYKGKIYLNAKDAVADIPDGA
KILVGGFGLCGIPENLIQGLLDIGIKDLTVVSNNAGVDDFGLGLLLKDRRIKRMIASYVG
ENAEFERQYLSGDLELELTPQGTLAERIRAGGAGIPAFFTPTGTFTLIHEGGSPIKYVKG
KNKEVEIASAKREMREFNGKPYIMEEAITGDFALIRAYKADELGNLIFRKSARNFNPPMA
KAAKITIAEVEEIVPIGALQPDEIHLPGIFVHRIIRGKFEKRIERIKITKPETNEKKLSK
EALLRERIVRRVACEYKDGMYINLGIGIPVLSSNYIPKDITVHLQSENGILGLGPFPEEY
AVDADLINAGKETVTTIQGGSYFSSDDSFGMIRGGHMDMTVLGAMEVSQFGDLANYMIPG
KLVKGMGGAMDLVSAPNTKTIITMEHNSKNGAPKILTECSLPLTGKNCVDMIITEKAVFE
VDKEKGLTLIEIAPDVTMEQLVASTGCSFKIADEIIPMKQI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g8184.t1 Gene3D G3DSA:3.40.1080.10 - 39 277 4.6E-106
6 g8184.t1 Gene3D G3DSA:3.40.1080.10 - 300 515 9.4E-104
3 g8184.t1 PANTHER PTHR13707 KETOACID-COENZYME A TRANSFERASE 39 520 4.7E-238
8 g8184.t1 PIRSF PIRSF000858 SCOT-t 41 521 1.0E-118
1 g8184.t1 Pfam PF01144 Coenzyme A transferase 48 275 2.1E-76
2 g8184.t1 Pfam PF01144 Coenzyme A transferase 306 503 2.5E-41
10 g8184.t1 ProSitePatterns PS01273 Coenzyme A transferases signature 1. 58 73 -
9 g8184.t1 ProSitePatterns PS01274 Coenzyme A transferases signature 2. 344 352 -
12 g8184.t1 SMART SM00882 CoA_trans_3 46 277 6.4E-91
11 g8184.t1 SMART SM00882 CoA_trans_3 306 504 8.2E-73
4 g8184.t1 SUPERFAMILY SSF100950 NagB/RpiA/CoA transferase-like 44 349 2.03E-93
5 g8184.t1 SUPERFAMILY SSF100950 NagB/RpiA/CoA transferase-like 305 519 5.02E-69
13 g8184.t1 TIGRFAM TIGR02429 pcaI_scoA_fam: 3-oxoacid CoA-transferase, A subunit 44 185 1.3E-43
14 g8184.t1 TIGRFAM TIGR02428 pcaJ_scoB_fam: 3-oxoacid CoA-transferase, B subunit 305 511 1.7E-87

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