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.t9 TSS g10274.t9 8605526 8605526
chr_1 g10274 g10274.t9 isoform g10274.t9 8605625 8608301
chr_1 g10274 g10274.t9 exon g10274.t9.exon1 8605625 8605662
chr_1 g10274 g10274.t9 exon g10274.t9.exon2 8606269 8606481
chr_1 g10274 g10274.t9 exon g10274.t9.exon3 8606535 8606765
chr_1 g10274 g10274.t9 cds g10274.t9.CDS1 8606613 8606765
chr_1 g10274 g10274.t9 exon g10274.t9.exon4 8606837 8607121
chr_1 g10274 g10274.t9 cds g10274.t9.CDS2 8606837 8607121
chr_1 g10274 g10274.t9 exon g10274.t9.exon5 8607180 8608301
chr_1 g10274 g10274.t9 cds g10274.t9.CDS3 8607180 8607395
chr_1 g10274 g10274.t9 TTS g10274.t9 NA NA

Sequences

>g10274.t9 Gene=g10274 Length=1889
ATGGCTTCATCGAGAATGTTGTTGAAAGTGAAAGGTTACTGGGAAAATTCGGCGTACGTT
TTGCAAGTTATGAAGCAACGAGAAAGAATTTGAGACTTACGAAAGATACAAAAGTAATCT
GTCAAGGCTTTACCGGAAAACAGGGCACTTTCCATTCACAACAAGCTCTCGAATATGGAA
CAAAACTTATCGGAGGTGTCAGCCCAGGCAAAGGAGGCCGCACTCATTTGGATTTGCCAG
TTTTTAATACTGTTGCTGAAGCCAGACAAGCGACTGGAGCGGAAGCAACTGTAATTTATG
TACCACCTCCAGGCGCCGCGAAAGCCATTATGGAAGCTCTTGATGCAGAAATGCCTTTAA
TTGTAGCAATCACTGAAGGAATTCCTCAACACGACATGGTGAAAGTTAAGAATCGTCTAT
TGAATCAAGATAAATCACGATTAGTTGGACCTAATTGTCCTGGGATCATTGCTCCAGAAG
CTTGTAAAATTGGCATTATGCCTGGTCATATTCATAAGAAAGGAGTCATTGGTGTTGTCT
CGCGTTCGGGAACTTTGACTTATGAGGCTGTGCATCAAACAACAGAAGTCGGTTTAGGAC
AAACGTTATGCGTCGGAATTGGAGGTGATCCTTTCAATGGAACTGATTTCATCGATTGTT
TAGATATTTTCCTTAAAGACCCTGAAACTAAGGGTATCATTTTGATTGGTGAAATTGGTG
GTGTTGCTGAGGAAAAGGCTGCTGACTTTTTGACTGAATATAATTCAGGTATCAAAGCTA
AGCCAGTTGTGTCATTTATTGCTGGTCTCTCTGCACCGCCTGGACGTAGAATGGGTCATG
CGGGTGCTATTATTTCTGGAGGAAAAGGAGGTGCTCAAGACAAAATTAATGCACTTGAGA
AAGCTGGTGTTATTGTTACTAGAAGTCCTGCTCAAATGGGACGCGAATTATATAAAGAAA
TGAAACGACTTGAACTCGTTTAAACATCCCTTTTGAACACTTGATCAATTCATCTCATCA
TTATAAATTACACTTCTAAACTTATAGTGTTTCAAGTTTATTTCCCTTCTTTTCGCGTAA
TTTATTTGAATTTTTACTAAATCATACAGTTCCTATGAAAAATTATATATGGAACAATTG
TAGCCAAGACAATTTAACTTAAAAATTATATCTGTTCTGAGTTTAGCTTTATTATTTTAT
TAAAATTTAAATGTCATTGTGAATGCATTGATTTTTAATAAGCATGATTCTACTTTGAAT
CTTGTTTTATGTTTAATTAGCTACAAATTATGTACTACTACTACATTACTTTAGGTAAGT
AAAGATTGGTGGTAAAGAACAAAAAAAAATAAATCGGCGGTGCTTTGAAAGAAGAAAAAA
AATTAAAGAGACCTTGAATTCATTTTCGATCGACAACAAAAAATAGAAATACTAAGCAAG
AAATCATAAACTGCCACACTTTTGGGTTGTTTCTCATTTCGTAAATAATTTGGTTTTTAA
AAAAACAATAATTATATTCAACTAAACATTCATATATGCTCGTATAACAGCAATTAGAGT
AATATGCTTAAATGCGTGTTTTAAATTTTTTGATGTTTTTTGCACTTACATCTATGATAA
TACTTACTCAAAAAAGCACCGCACTCTTATATGTAGATGTAAATAAACAAATGAATAAAT
AAATTAACTGCAATCATTTTGGTTGAGTTCAAGTTAAAGACAAAAATTTCATTTGCTCAT
AATTTGTTTTAATCTTTAATTTCACATAACTTTCAGAGTATTTTGATTAAGCACAATAAT
TCTTTTTTTCATGGTCGATGCGAGAGATTCATTTACAAACAATTAAAAATTATTGGAATG
TGTGCATATGAAATATGCAACAGGTCATT

>g10274.t9 Gene=g10274 Length=217
MEALDAEMPLIVAITEGIPQHDMVKVKNRLLNQDKSRLVGPNCPGIIAPEACKIGIMPGH
IHKKGVIGVVSRSGTLTYEAVHQTTEVGLGQTLCVGIGGDPFNGTDFIDCLDIFLKDPET
KGIILIGEIGGVAEEKAADFLTEYNSGIKAKPVVSFIAGLSAPPGRRMGHAGAIISGGKG
GAQDKINALEKAGVIVTRSPAQMGRELYKEMKRLELV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g10274.t9 Gene3D G3DSA:3.40.50.720 - 1 42 2.3E-11
12 g10274.t9 Gene3D G3DSA:3.40.50.261 - 43 212 8.8E-75
2 g10274.t9 PANTHER PTHR11117:SF2 SUCCINATE–COA LIGASE [ADP/GDP-FORMING] SUBUNIT ALPHA, MITOCHONDRIAL 1 213 8.2E-114
3 g10274.t9 PANTHER PTHR11117 SUCCINYL-COA LIGASE SUBUNIT ALPHA 1 213 8.2E-114
4 g10274.t9 PRINTS PR01798 Succinyl-CoA synthase signature 96 114 3.7E-28
6 g10274.t9 PRINTS PR01798 Succinyl-CoA synthase signature 127 140 3.7E-28
5 g10274.t9 PRINTS PR01798 Succinyl-CoA synthase signature 163 180 3.7E-28
1 g10274.t9 Pfam PF00549 CoA-ligase 70 194 3.1E-23
10 g10274.t9 ProSitePatterns PS01216 ATP-citrate lyase / succinyl-CoA ligases family signature 1. 71 100 -
9 g10274.t9 ProSitePatterns PS00399 ATP-citrate lyase / succinyl-CoA ligases family active site. 159 172 -
7 g10274.t9 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 1 41 3.15E-5
8 g10274.t9 SUPERFAMILY SSF52210 Succinyl-CoA synthetase domains 42 209 1.2E-54

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