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.t14 TSS g15755.t14 6669926 6669926
chr_4 g15755 g15755.t14 isoform g15755.t14 6670005 6671135
chr_4 g15755 g15755.t14 exon g15755.t14.exon1 6670005 6670073
chr_4 g15755 g15755.t14 cds g15755.t14.CDS1 6670005 6670073
chr_4 g15755 g15755.t14 exon g15755.t14.exon2 6670261 6670474
chr_4 g15755 g15755.t14 cds g15755.t14.CDS2 6670261 6670474
chr_4 g15755 g15755.t14 exon g15755.t14.exon3 6670535 6671135
chr_4 g15755 g15755.t14 cds g15755.t14.CDS3 6670535 6671133
chr_4 g15755 g15755.t14 TTS g15755.t14 NA NA

Sequences

>g15755.t14 Gene=g15755 Length=884
ATGCTGATAAAGTGTTCAAATTTCTTGTTAAATTCTAAAAATTTTCGAATTTCATTGAAT
CATTTAAAGATCTTCACATGTTCACTCTCAACATCGTCAGTAGTTCAAAGTAAAGCATAT
AAAGGAAAAATTTATAGTTCAACACAAGATGCTGTTGATGATATACCAAATGGATCGAAA
CTTTTAGTTGGTGGTTTTGGTTTATGTGGAATTCCTGAAAATCTCATTCAAGCTCTTTTA
GATACCGGAAAAAAAGATTTAACAATTGTTTCTAATAATGCTGGTGTTGACAATTTCGGT
CTCGGTCTTTTACTAAAAGATCGTCGAATTAAGCGCATGATTGCTTCCTATGTTGGTGAA
AATGCTGAATTTGAGCGGCAATATCTTTCAGGTGAGCTTGAACTTGAATTGACCCCTCAA
GGAACACTTGCCGAGAGAATCAGAGCAGGTGGTGCAGGCATCCCTGCATTTTTTACTCCA
ACTGGCTACGGCACACTTGTTCATGAAGGTGGTTCACCTATTAAATATGGTGAAAATGGT
AAAATTGCAATTCATAGTCAACCACGTGAACTTCGTGAATTTAATGGAATTCCTTACATA
ATGGAAGAAGCTATAACTGGCGATTATGCTTTAGTTCGAGCTTACAAAGCTGATGAAATG
GGAAATTTAATTTTTCGAAAATCAGCGAGAAATTTCAATCCGACAATGTGCAAAGCAGCT
AAAGTCACAATTGCTGAAGTTGAAGAAATTGTCCCAGTTGGTTCACTCCAACCTGATGAA
ATTCATATACCGAGCATTTTTGTGCACCGCATTGTAAGAACAAAACTTGAGAAAAGAATT
GAAAGATTGCAAATTAGTCGACCTGATGGAAAACCATCAAAAAC

>g15755.t14 Gene=g15755 Length=294
MLIKCSNFLLNSKNFRISLNHLKIFTCSLSTSSVVQSKAYKGKIYSSTQDAVDDIPNGSK
LLVGGFGLCGIPENLIQALLDTGKKDLTIVSNNAGVDNFGLGLLLKDRRIKRMIASYVGE
NAEFERQYLSGELELELTPQGTLAERIRAGGAGIPAFFTPTGYGTLVHEGGSPIKYGENG
KIAIHSQPRELREFNGIPYIMEEAITGDYALVRAYKADEMGNLIFRKSARNFNPTMCKAA
KVTIAEVEEIVPVGSLQPDEIHIPSIFVHRIVRTKLEKRIERLQISRPDGKPSK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g15755.t14 Gene3D G3DSA:3.40.1080.10 - 42 274 2.4E-111
2 g15755.t14 PANTHER PTHR13707 KETOACID-COENZYME A TRANSFERASE 22 288 3.2E-125
3 g15755.t14 PANTHER PTHR13707:SF30 SUCCINYL-COA:3-KETOACID COENZYME A TRANSFERASE 1, MITOCHONDRIAL 22 288 3.2E-125
1 g15755.t14 Pfam PF01144 Coenzyme A transferase 47 273 1.5E-77
6 g15755.t14 ProSitePatterns PS01273 Coenzyme A transferases signature 1. 57 72 -
5 g15755.t14 SMART SM00882 CoA_trans_3 45 274 8.4E-91
4 g15755.t14 SUPERFAMILY SSF100950 NagB/RpiA/CoA transferase-like 41 280 3.21E-90
8 g15755.t14 TIGRFAM TIGR02429 pcaI_scoA_fam: 3-oxoacid CoA-transferase, A subunit 43 274 3.6E-78

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

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