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.t5 TSS g10274.t5 8605526 8605526
chr_1 g10274 g10274.t5 isoform g10274.t5 8605625 8607395
chr_1 g10274 g10274.t5 exon g10274.t5.exon1 8605625 8605658
chr_1 g10274 g10274.t5 cds g10274.t5.CDS1 8605625 8605658
chr_1 g10274 g10274.t5 exon g10274.t5.exon2 8606258 8606481
chr_1 g10274 g10274.t5 cds g10274.t5.CDS2 8606258 8606481
chr_1 g10274 g10274.t5 exon g10274.t5.exon3 8606535 8606765
chr_1 g10274 g10274.t5 cds g10274.t5.CDS3 8606535 8606765
chr_1 g10274 g10274.t5 exon g10274.t5.exon4 8606837 8607121
chr_1 g10274 g10274.t5 cds g10274.t5.CDS4 8606837 8607121
chr_1 g10274 g10274.t5 exon g10274.t5.exon5 8607283 8607395
chr_1 g10274 g10274.t5 cds g10274.t5.CDS5 8607283 8607375
chr_1 g10274 g10274.t5 TTS g10274.t5 8608133 8608133

Sequences

>g10274.t5 Gene=g10274 Length=887
ATGGCTTCATCGAGAATGTTGTTGAAAGTGAAAGATGGTTTACAGCTGGGAAAATTCGGC
GTACGTTTTGCAAGTTATGAAGCAACGAGAAAGAATTTGAGACTTACGAAAGATACAAAA
GTAATCTGTCAAGGCTTTACCGGAAAACAGGGCACTTTCCATTCACAACAAGCTCTCGAA
TATGGAACAAAACTTATCGGAGGTGTCAGCCCAGGCAAAGGAGGCCGCACTCATTTGGAT
TTGCCAGTTTTTAATACTGTTGCTGAAGCCAGACAAGCGACTGGAGCGGAAGCAACTGTA
ATTTATGTACCACCTCCAGGCGCCGCGAAAGCCATTATGGAAGCTCTTGATGCAGAAATG
CCTTTAATTGTAGCAATCACTGAAGGAATTCCTCAACACGACATGGTGAAAGTTAAGAAT
CGTCTATTGAATCAAGATAAATCACGATTAGTTGGACCTAATTGTCCTGGGATCATTGCT
CCAGAAGCTTGTAAAATTGGCATTATGCCTGGTCATATTCATAAGAAAGGAGTCATTGGT
GTTGTCTCGCGTTCGGGAACTTTGACTTATGAGGCTGTGCATCAAACAACAGAAGTCGGT
TTAGGACAAACGTTATGCGTCGGAATTGGAGGTGATCCTTTCAATGGAACTGATTTCATC
GATTGTTTAGATATTTTCCTTAAAGACCCTGAAACTAAGGGTATCATTTTGATTGGTGAA
ATTGGTGGTGTTGCTGAGGAAAAGGCTGCTGACTTTTTGACTGAATATAATTCAGTGCTC
AAGACAAAATTAATGCACTTGAGAAAGCTGGTGTTATTGTTACTAGAAGTCCTGCTCAAA
TGGGACGCGAATTATATAAAGAAATGAAACGACTTGAACTCGTTTAA

>g10274.t5 Gene=g10274 Length=288
MASSRMLLKVKDGLQLGKFGVRFASYEATRKNLRLTKDTKVICQGFTGKQGTFHSQQALE
YGTKLIGGVSPGKGGRTHLDLPVFNTVAEARQATGAEATVIYVPPPGAAKAIMEALDAEM
PLIVAITEGIPQHDMVKVKNRLLNQDKSRLVGPNCPGIIAPEACKIGIMPGHIHKKGVIG
VVSRSGTLTYEAVHQTTEVGLGQTLCVGIGGDPFNGTDFIDCLDIFLKDPETKGIILIGE
IGGVAEEKAADFLTEYNSVLKTKLMHLRKLVLLLLEVLLKWDANYIKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g10274.t5 Gene3D G3DSA:3.40.50.720 - 33 154 1.2E-49
11 g10274.t5 Gene3D G3DSA:3.40.50.261 - 155 267 3.0E-47
3 g10274.t5 PANTHER PTHR11117:SF2 SUCCINATE–COA LIGASE [ADP/GDP-FORMING] SUBUNIT ALPHA, MITOCHONDRIAL 21 259 6.2E-128
4 g10274.t5 PANTHER PTHR11117 SUCCINYL-COA LIGASE SUBUNIT ALPHA 21 259 6.2E-128
7 g10274.t5 PRINTS PR01798 Succinyl-CoA synthase signature 112 129 4.1E-24
6 g10274.t5 PRINTS PR01798 Succinyl-CoA synthase signature 208 226 4.1E-24
5 g10274.t5 PRINTS PR01798 Succinyl-CoA synthase signature 239 252 4.1E-24
2 g10274.t5 Pfam PF02629 CoA binding domain 36 129 1.8E-29
1 g10274.t5 Pfam PF00549 CoA-ligase 182 260 1.0E-14
12 g10274.t5 ProSitePatterns PS01216 ATP-citrate lyase / succinyl-CoA ligases family signature 1. 183 212 -
13 g10274.t5 SMART SM00881 CoA_binding_2 35 130 1.3E-29
8 g10274.t5 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 26 153 2.95E-41
9 g10274.t5 SUPERFAMILY SSF52210 Succinyl-CoA synthetase domains 154 265 1.57E-34
14 g10274.t5 TIGRFAM TIGR01019 sucCoAalpha: succinate-CoA ligase, alpha subunit 35 255 1.2E-106

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. There were no conditions that were differentially expressed