Gene loci information

Transcript annotation

  • This transcript has been annotated as Succinate–CoA ligase [ADP-forming] subunit beta, 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_3 g3235 g3235.t4 TSS g3235.t4 23941831 23941831
chr_3 g3235 g3235.t4 isoform g3235.t4 23941885 23943919
chr_3 g3235 g3235.t4 exon g3235.t4.exon1 23941885 23941944
chr_3 g3235 g3235.t4 cds g3235.t4.CDS1 23941885 23941944
chr_3 g3235 g3235.t4 exon g3235.t4.exon2 23942379 23942470
chr_3 g3235 g3235.t4 cds g3235.t4.CDS2 23942379 23942470
chr_3 g3235 g3235.t4 exon g3235.t4.exon3 23942755 23943339
chr_3 g3235 g3235.t4 cds g3235.t4.CDS3 23942755 23943339
chr_3 g3235 g3235.t4 exon g3235.t4.exon4 23943719 23943919
chr_3 g3235 g3235.t4 cds g3235.t4.CDS4 23943719 23943731
chr_3 g3235 g3235.t4 TTS g3235.t4 23944934 23944934

Sequences

>g3235.t4 Gene=g3235 Length=938
ATGAGTTTTCTAACTAGATCAGCAATATTTGCAGGTTCATCCTTAAGAAATGGTGCAAAG
ATTCTCAGTGCCGCACAACAAAAACGTCAATTGAACGTTCAAGAGCACGTTTCGTACTCA
TTTTTAAATGAGGCCGGGATTCCAACACCAAAATTCGGTGTTGCAGGTTCAGCTGAAGAA
GCTCAACAGATTGCAAAGGATTTAAATACAAAGAATTTAGTTTTAAAAGCTCAAGTTTTG
GCTGGTGGTCGTGGAAAAGGTTCGTTTAAAAATGGTCTCAAAGGCGGTGTCAGAATCGTT
TACACACCAGAAGAAGCTAAAGAAATCTCGGGCAAAATGATAAATCAACTCTTGGTCACA
AAACAAACTGGTGCAGCAGGTCGAATCTGTAACCAAGTTATGGTTGCTGAACGAAAATTC
CCAAGACGTGAATTTTATTTTGCTGTGATGATGGAACGTGCTTTTAATGGCCCAGTACTT
ATTGCCTCATCGCAAGGAGGTGTAAATATTGAAGAAGTTGCTGCAGAAAATCCAGATGCA
ATTGTTTATGAACCAATCGATATCAATAAGGGACTCTCTAAAGATCAAGCAATGAAAATT
GCAAGAACAGTAGGTTTAGATGATCATTTGGAAACAACAACTCAAATGCTTTTGAACTTA
TATGATTTATTCGTCAAAAAAGATGCTCTTCTTGTAGAAATTAATCCATATGCTGAAGAT
GCTGGCGAAACCCGTAAACTTTGCTCTTGACGCTAAAATGCGTTTTGATGACAATGCCGA
ATTCCGTCAAAAAGATTTGTTCGCAAAACGTGATTATTCTCAAGAAGATCCAAAAGAAGT
TGCAGCTGCAAAATTTGATTTGAATTACATCGCTTTAGATGGATCAATTGGTTGCATGGT
AAATGGTGCAGGTTTGGCAATGGCTACAATGGACATCA

>g3235.t4 Gene=g3235 Length=249
MSFLTRSAIFAGSSLRNGAKILSAAQQKRQLNVQEHVSYSFLNEAGIPTPKFGVAGSAEE
AQQIAKDLNTKNLVLKAQVLAGGRGKGSFKNGLKGGVRIVYTPEEAKEISGKMINQLLVT
KQTGAAGRICNQVMVAERKFPRREFYFAVMMERAFNGPVLIASSQGGVNIEEVAAENPDA
IVYEPIDINKGLSKDQAMKIARTVGLDDHLETTTQMLLNLYDLFVKKDALLVEINPYAED
AGETRKLCS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g3235.t4 Coils Coil Coil 58 78 -
5 g3235.t4 Gene3D G3DSA:3.30.470.20 - 31 241 2.7E-70
6 g3235.t4 Gene3D G3DSA:3.30.1490.20 - 51 146 2.7E-70
2 g3235.t4 PANTHER PTHR11815:SF10 SUCCINATE–COA LIGASE [ADP-FORMING] SUBUNIT BETA, MITOCHONDRIAL 22 242 5.5E-89
3 g3235.t4 PANTHER PTHR11815 SUCCINYL-COA SYNTHETASE BETA CHAIN 22 242 5.5E-89
1 g3235.t4 Pfam PF08442 ATP-grasp domain 32 238 3.5E-67
8 g3235.t4 ProSiteProfiles PS50975 ATP-grasp fold profile. 39 85 9.541
4 g3235.t4 SUPERFAMILY SSF56059 Glutathione synthetase ATP-binding domain-like 31 241 1.96E-60

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:0006099 tricarboxylic acid cycle BP
GO:0046872 metal ion binding MF
GO:0005524 ATP binding 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