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.t1 TSS g10274.t1 8605526 8605526
chr_1 g10274 g10274.t1 isoform g10274.t1 8605625 8607395
chr_1 g10274 g10274.t1 exon g10274.t1.exon1 8605625 8605658
chr_1 g10274 g10274.t1 cds g10274.t1.CDS1 8605625 8605658
chr_1 g10274 g10274.t1 exon g10274.t1.exon2 8606258 8606481
chr_1 g10274 g10274.t1 cds g10274.t1.CDS2 8606258 8606481
chr_1 g10274 g10274.t1 exon g10274.t1.exon3 8606535 8606765
chr_1 g10274 g10274.t1 cds g10274.t1.CDS3 8606535 8606765
chr_1 g10274 g10274.t1 exon g10274.t1.exon4 8606837 8607121
chr_1 g10274 g10274.t1 cds g10274.t1.CDS4 8606837 8607121
chr_1 g10274 g10274.t1 exon g10274.t1.exon5 8607180 8607395
chr_1 g10274 g10274.t1 cds g10274.t1.CDS5 8607180 8607395
chr_1 g10274 g10274.t1 TTS g10274.t1 8608133 8608133

Sequences

>g10274.t1 Gene=g10274 Length=990
ATGGCTTCATCGAGAATGTTGTTGAAAGTGAAAGATGGTTTACAGCTGGGAAAATTCGGC
GTACGTTTTGCAAGTTATGAAGCAACGAGAAAGAATTTGAGACTTACGAAAGATACAAAA
GTAATCTGTCAAGGCTTTACCGGAAAACAGGGCACTTTCCATTCACAACAAGCTCTCGAA
TATGGAACAAAACTTATCGGAGGTGTCAGCCCAGGCAAAGGAGGCCGCACTCATTTGGAT
TTGCCAGTTTTTAATACTGTTGCTGAAGCCAGACAAGCGACTGGAGCGGAAGCAACTGTA
ATTTATGTACCACCTCCAGGCGCCGCGAAAGCCATTATGGAAGCTCTTGATGCAGAAATG
CCTTTAATTGTAGCAATCACTGAAGGAATTCCTCAACACGACATGGTGAAAGTTAAGAAT
CGTCTATTGAATCAAGATAAATCACGATTAGTTGGACCTAATTGTCCTGGGATCATTGCT
CCAGAAGCTTGTAAAATTGGCATTATGCCTGGTCATATTCATAAGAAAGGAGTCATTGGT
GTTGTCTCGCGTTCGGGAACTTTGACTTATGAGGCTGTGCATCAAACAACAGAAGTCGGT
TTAGGACAAACGTTATGCGTCGGAATTGGAGGTGATCCTTTCAATGGAACTGATTTCATC
GATTGTTTAGATATTTTCCTTAAAGACCCTGAAACTAAGGGTATCATTTTGATTGGTGAA
ATTGGTGGTGTTGCTGAGGAAAAGGCTGCTGACTTTTTGACTGAATATAATTCAGGTATC
AAAGCTAAGCCAGTTGTGTCATTTATTGCTGGTCTCTCTGCACCGCCTGGACGTAGAATG
GGTCATGCGGGTGCTATTATTTCTGGAGGAAAAGGAGGTGCTCAAGACAAAATTAATGCA
CTTGAGAAAGCTGGTGTTATTGTTACTAGAAGTCCTGCTCAAATGGGACGCGAATTATAT
AAAGAAATGAAACGACTTGAACTCGTTTAA

>g10274.t1 Gene=g10274 Length=329
MASSRMLLKVKDGLQLGKFGVRFASYEATRKNLRLTKDTKVICQGFTGKQGTFHSQQALE
YGTKLIGGVSPGKGGRTHLDLPVFNTVAEARQATGAEATVIYVPPPGAAKAIMEALDAEM
PLIVAITEGIPQHDMVKVKNRLLNQDKSRLVGPNCPGIIAPEACKIGIMPGHIHKKGVIG
VVSRSGTLTYEAVHQTTEVGLGQTLCVGIGGDPFNGTDFIDCLDIFLKDPETKGIILIGE
IGGVAEEKAADFLTEYNSGIKAKPVVSFIAGLSAPPGRRMGHAGAIISGGKGGAQDKINA
LEKAGVIVTRSPAQMGRELYKEMKRLELV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g10274.t1 Gene3D G3DSA:3.40.50.720 - 33 154 1.6E-49
13 g10274.t1 Gene3D G3DSA:3.40.50.261 - 155 324 3.0E-74
5 g10274.t1 Hamap MF_01988 Succinate–CoA ligase [ADP-forming] subunit alpha [sucD]. 31 323 41.197922
3 g10274.t1 PANTHER PTHR11117:SF2 SUCCINATE–COA LIGASE [ADP/GDP-FORMING] SUBUNIT ALPHA, MITOCHONDRIAL 21 325 3.8E-161
4 g10274.t1 PANTHER PTHR11117 SUCCINYL-COA LIGASE SUBUNIT ALPHA 21 325 3.8E-161
14 g10274.t1 PIRSF PIRSF001553 SucCS_alpha 28 326 1.6E-129
8 g10274.t1 PRINTS PR01798 Succinyl-CoA synthase signature 112 129 7.6E-38
7 g10274.t1 PRINTS PR01798 Succinyl-CoA synthase signature 208 226 7.6E-38
6 g10274.t1 PRINTS PR01798 Succinyl-CoA synthase signature 239 252 7.6E-38
9 g10274.t1 PRINTS PR01798 Succinyl-CoA synthase signature 275 292 7.6E-38
2 g10274.t1 Pfam PF02629 CoA binding domain 36 129 2.4E-29
1 g10274.t1 Pfam PF00549 CoA-ligase 182 306 8.6E-23
16 g10274.t1 ProSitePatterns PS01216 ATP-citrate lyase / succinyl-CoA ligases family signature 1. 183 212 -
15 g10274.t1 ProSitePatterns PS00399 ATP-citrate lyase / succinyl-CoA ligases family active site. 271 284 -
17 g10274.t1 SMART SM00881 CoA_binding_2 35 130 1.3E-29
10 g10274.t1 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 26 153 3.59E-41
11 g10274.t1 SUPERFAMILY SSF52210 Succinyl-CoA synthetase domains 154 321 4.19E-54
18 g10274.t1 TIGRFAM TIGR01019 sucCoAalpha: succinate-CoA ligase, alpha subunit 35 320 3.8E-132

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

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