Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t12 TSS g3235.t12 23941831 23941831
chr_3 g3235 g3235.t12 isoform g3235.t12 23942753 23944501
chr_3 g3235 g3235.t12 exon g3235.t12.exon1 23942753 23943339
chr_3 g3235 g3235.t12 cds g3235.t12.CDS1 23942939 23943339
chr_3 g3235 g3235.t12 exon g3235.t12.exon2 23943719 23943931
chr_3 g3235 g3235.t12 cds g3235.t12.CDS2 23943719 23943731
chr_3 g3235 g3235.t12 exon g3235.t12.exon3 23943995 23944206
chr_3 g3235 g3235.t12 exon g3235.t12.exon4 23944325 23944501
chr_3 g3235 g3235.t12 TTS g3235.t12 23944934 23944934

Sequences

>g3235.t12 Gene=g3235 Length=1189
AGATTCGGTGTTGCAGGTTCAGCTGAAGAAGCTCAACAGATTGCAAAGGATTTAAATACA
AAGAATTTAGTTTTAAAAGCTCAAGTTTTGGCTGGTGGTCGTGGAAAAGGTTCGTTTAAA
AATGGTCTCAAAGGCGGTGTCAGAATCGTTTACACACCAGAAGAAGCTAAAGAAATCTCG
GGCAAAATGATAAATCAACTCTTGGTCACAAAACAAACTGGTGCAGCAGGTCGAATCTGT
AACCAAGTTATGGTTGCTGAACGAAAATTCCCAAGACGTGAATTTTATTTTGCTGTGATG
ATGGAACGTGCTTTTAATGGCCCAGTACTTATTGCCTCATCGCAAGGAGGTGTAAATATT
GAAGAAGTTGCTGCAGAAAATCCAGATGCAATTGTTTATGAACCAATCGATATCAATAAG
GGACTCTCTAAAGATCAAGCAATGAAAATTGCAAGAACAGTAGGTTTAGATGATCATTTG
GAAACAACAACTCAAATGCTTTTGAACTTATATGATTTATTCGTCAAAAAAGATGCTCTT
CTTGTAGAAATTAATCCATATGCTGAAGATGCTGGCGAAACCCGTAAACTTTGCTCTTGA
CGCTAAAATGCGTTTTGATGACAATGCCGAATTCCGTCAAAAAGATTTGTTCGCAAAACG
TGATTATTCTCAAGAAGATCCAAAAGAAGTTGCAGCTGCAAAATTTGATTTGAATTACAT
CGCTTTAGATGGATCAATTGGTTGCATGGTAAATGGTGCAGGTTTGGCAATGGCTACAAT
GGACATCATTAAATTGCACGGAGGCGATCCCGCAAATTTCTTGGACGTTGGTGGCGGTGC
CACTGCAAATGCTGTCAAGGAGGCCTTCAAAATTATTACTGCAGATCCAAAAGTACATGT
TATCCTCGTTAACATTTTTGGAGGTATTATGCGTTGTGATGTGATTGCTGAAGGTATCAT
TGCTGCAACAAAAGAGCTTAATTTGACTTTACCCATCATTGTGCGTCTTCAGGGTACAAA
TGTCAATGAAGCAAAGGAGCTCATTCGCAAATCAAAATTACGCATTTTACCTAAAGATGA
TCTTGACGAAGCTGCAATGCTTAGCGTTCACTTATCTCAAATTGTACATCTTGCACGCGA
AGCTCATCTCAACGTTTTGTTCGAATTAGATCCAGTTCATCATCATTAA

>g3235.t12 Gene=g3235 Length=137
MINQLLVTKQTGAAGRICNQVMVAERKFPRREFYFAVMMERAFNGPVLIASSQGGVNIEE
VAAENPDAIVYEPIDINKGLSKDQAMKIARTVGLDDHLETTTQMLLNLYDLFVKKDALLV
EINPYAEDAGETRKLCS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g3235.t12 Gene3D G3DSA:3.30.470.20 - 15 136 0
2 g3235.t12 PANTHER PTHR11815:SF10 SUCCINATE–COA LIGASE [ADP-FORMING] SUBUNIT BETA, MITOCHONDRIAL 1 130 0
3 g3235.t12 PANTHER PTHR11815 SUCCINYL-COA SYNTHETASE BETA CHAIN 1 130 0
1 g3235.t12 Pfam PF08442 ATP-grasp domain 1 126 0
4 g3235.t12 SUPERFAMILY SSF56059 Glutathione synthetase ATP-binding domain-like 1 129 0

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

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