Gene loci information

Transcript annotation

  • This transcript has been annotated as Succinate–CoA ligase [ADP/GDP-forming] subunit alpha, 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_1 g10274 g10274.t6 TSS g10274.t6 8605526 8605526
chr_1 g10274 g10274.t6 isoform g10274.t6 8605625 8607395
chr_1 g10274 g10274.t6 exon g10274.t6.exon1 8605625 8605658
chr_1 g10274 g10274.t6 exon g10274.t6.exon2 8606258 8606481
chr_1 g10274 g10274.t6 exon g10274.t6.exon3 8606535 8607121
chr_1 g10274 g10274.t6 cds g10274.t6.CDS1 8606852 8607121
chr_1 g10274 g10274.t6 exon g10274.t6.exon4 8607180 8607395
chr_1 g10274 g10274.t6 cds g10274.t6.CDS2 8607180 8607395
chr_1 g10274 g10274.t6 TTS g10274.t6 8608133 8608133

Sequences

>g10274.t6 Gene=g10274 Length=1061
ATGGCTTCATCGAGAATGTTGTTGAAAGTGAAAGATGGTTTACAGCTGGGAAAATTCGGC
GTACGTTTTGCAAGTTATGAAGCAACGAGAAAGAATTTGAGACTTACGAAAGATACAAAA
GTAATCTGTCAAGGCTTTACCGGAAAACAGGGCACTTTCCATTCACAACAAGCTCTCGAA
TATGGAACAAAACTTATCGGAGGTGTCAGCCCAGGCAAAGGAGGCCGCACTCATTTGGAT
TTGCCAGTTTTTAATACTGTTGCTGAAGCCAGACAAGCGACTGGAGCGGAAGCAACTGTA
ATTTATGTACCACCTCCAGGCGCCGCGAAAGCCATTATGGAAGCTCTTGATGCAGAAATG
CCTTTAATTGTAGCAATCACTGAAGGAATTCCTCAACACGACATGGTGAAAGTTAAGAAT
CGTCTATTGAATCAAGATAAATCACGATTAGTTGGACCTAATTGTCCTGGGATCATTGCT
CCAGAAGCTGTAAGTAACTACAATAGTAAATTATCATGACAATAGGACATTCTTTAGATT
GCGTATATATTTATTTTTAGTGTAAAATTGGCATTATGCCTGGTCATATTCATAAGAAAG
GAGTCATTGGTGTTGTCTCGCGTTCGGGAACTTTGACTTATGAGGCTGTGCATCAAACAA
CAGAAGTCGGTTTAGGACAAACGTTATGCGTCGGAATTGGAGGTGATCCTTTCAATGGAA
CTGATTTCATCGATTGTTTAGATATTTTCCTTAAAGACCCTGAAACTAAGGGTATCATTT
TGATTGGTGAAATTGGTGGTGTTGCTGAGGAAAAGGCTGCTGACTTTTTGACTGAATATA
ATTCAGGTATCAAAGCTAAGCCAGTTGTGTCATTTATTGCTGGTCTCTCTGCACCGCCTG
GACGTAGAATGGGTCATGCGGGTGCTATTATTTCTGGAGGAAAAGGAGGTGCTCAAGACA
AAATTAATGCACTTGAGAAAGCTGGTGTTATTGTTACTAGAAGTCCTGCTCAAATGGGAC
GCGAATTATATAAAGAAATGAAACGACTTGAACTCGTTTAA

>g10274.t6 Gene=g10274 Length=161
MPGHIHKKGVIGVVSRSGTLTYEAVHQTTEVGLGQTLCVGIGGDPFNGTDFIDCLDIFLK
DPETKGIILIGEIGGVAEEKAADFLTEYNSGIKAKPVVSFIAGLSAPPGRRMGHAGAIIS
GGKGGAQDKINALEKAGVIVTRSPAQMGRELYKEMKRLELV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g10274.t6 Gene3D G3DSA:3.40.50.261 - 1 156 5.8E-67
2 g10274.t6 PANTHER PTHR11117:SF2 SUCCINATE–COA LIGASE [ADP/GDP-FORMING] SUBUNIT ALPHA, MITOCHONDRIAL 1 157 3.9E-80
3 g10274.t6 PANTHER PTHR11117 SUCCINYL-COA LIGASE SUBUNIT ALPHA 1 157 3.9E-80
4 g10274.t6 PRINTS PR01798 Succinyl-CoA synthase signature 40 58 1.9E-28
5 g10274.t6 PRINTS PR01798 Succinyl-CoA synthase signature 71 84 1.9E-28
6 g10274.t6 PRINTS PR01798 Succinyl-CoA synthase signature 107 124 1.9E-28
1 g10274.t6 Pfam PF00549 CoA-ligase 14 138 1.2E-23
9 g10274.t6 ProSitePatterns PS01216 ATP-citrate lyase / succinyl-CoA ligases family signature 1. 15 44 -
8 g10274.t6 ProSitePatterns PS00399 ATP-citrate lyase / succinyl-CoA ligases family active site. 103 116 -
7 g10274.t6 SUPERFAMILY SSF52210 Succinyl-CoA synthetase domains 1 153 1.7E-47

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:0003824 catalytic 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