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.t3 TSS g3235.t3 23941831 23941831
chr_3 g3235 g3235.t3 isoform g3235.t3 23941885 23943904
chr_3 g3235 g3235.t3 exon g3235.t3.exon1 23941885 23942323
chr_3 g3235 g3235.t3 exon g3235.t3.exon2 23942379 23942470
chr_3 g3235 g3235.t3 exon g3235.t3.exon3 23942755 23943335
chr_3 g3235 g3235.t3 cds g3235.t3.CDS1 23942939 23943335
chr_3 g3235 g3235.t3 exon g3235.t3.exon4 23943719 23943904
chr_3 g3235 g3235.t3 cds g3235.t3.CDS2 23943719 23943903
chr_3 g3235 g3235.t3 TTS g3235.t3 NA NA

Sequences

>g3235.t3 Gene=g3235 Length=1298
ATGAGTTTTCTAACTAGATCAGCAATATTTGCAGGTTCATCCTTAAGAAATGGTGCAAAG
GTGAGTGCTCAAATTATCAAGACATACATAATAAGTGAAATAAGTGATACAAGTGTGTAA
AAAGTGAAAAAAATTTCTGAGAAAAAGATTGAATAATCACTCTCAGTCCTTGAAAGCGGT
CACGATAAAAATATTTTTATTAGCAAACAGTTTTAATGAACGTAAATTGGATAATATAAT
GTATGACATAGAAATTGAAAGTATGTTTTTCGACGTCATCAAAATTTTGATTTGACTGGA
TTTGCCAAATCACGCGTTTGTTTATAAAAAAATAAGAAGAGAAATATCGCTGAAATCATC
TGATTGCGTGAACTAAAAATAAGTAAAGAAAAGAAGCAATAGTGAAAATCAATCGGTGTC
TCAAAAAAAGAGTGAAACAATTCTCAGTGCCGCACAACAAAAACGTCAATTGAACGTTCA
AGAGCACGTTTCGTACTCATTTTTAAATGAGGCCGGGATTCCAACACCAAAATTCGGTGT
TGCAGGTTCAGCTGAAGAAGCTCAACAGATTGCAAAGGATTTAAATACAAAGAATTTAGT
TTTAAAAGCTCAAGTTTTGGCTGGTGGTCGTGGAAAAGGTTCGTTTAAAAATGGTCTCAA
AGGCGGTGTCAGAATCGTTTACACACCAGAAGAAGCTAAAGAAATCTCGGGCAAAATGAT
AAATCAACTCTTGGTCACAAAACAAACTGGTGCAGCAGGTCGAATCTGTAACCAAGTTAT
GGTTGCTGAACGAAAATTCCCAAGACGTGAATTTTATTTTGCTGTGATGATGGAACGTGC
TTTTAATGGCCCAGTACTTATTGCCTCATCGCAAGGAGGTGTAAATATTGAAGAAGTTGC
TGCAGAAAATCCAGATGCAATTGTTTATGAACCAATCGATATCAATAAGGGACTCTCTAA
AGATCAAGCAATGAAAATTGCAAGAACAGTAGGTTTAGATGATCATTTGGAAACAACAAC
TCAAATGCTTTTGAACTTATATGATTTATTCGTCAAAAAAGATGCTCTTCTTGTAGAAAT
TAATCCATATGCTGAAGATGCTGGCGAAACCCACTTTGCTCTTGACGCTAAAATGCGTTT
TGATGACAATGCCGAATTCCGTCAAAAAGATTTGTTCGCAAAACGTGATTATTCTCAAGA
AGATCCAAAAGAAGTTGCAGCTGCAAAATTTGATTTGAATTACATCGCTTTAGATGGATC
AATTGGTTGCATGGTAAATGGTGCAGGTTTGGCAATGG

>g3235.t3 Gene=g3235 Length=194
MINQLLVTKQTGAAGRICNQVMVAERKFPRREFYFAVMMERAFNGPVLIASSQGGVNIEE
VAAENPDAIVYEPIDINKGLSKDQAMKIARTVGLDDHLETTTQMLLNLYDLFVKKDALLV
EINPYAEDAGETHFALDAKMRFDDNAEFRQKDLFAKRDYSQEDPKEVAAAKFDLNYIALD
GSIGCMVNGAGLAM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g3235.t3 Gene3D G3DSA:3.30.470.20 - 14 163 0e+00
7 g3235.t3 Gene3D G3DSA:3.40.50.261 - 164 194 1e-07
2 g3235.t3 PANTHER PTHR11815:SF10 SUCCINATE–COA LIGASE [ADP-FORMING] SUBUNIT BETA, MITOCHONDRIAL 1 194 0e+00
3 g3235.t3 PANTHER PTHR11815 SUCCINYL-COA SYNTHETASE BETA CHAIN 1 194 0e+00
1 g3235.t3 Pfam PF08442 ATP-grasp domain 1 126 0e+00
4 g3235.t3 SUPERFAMILY SSF56059 Glutathione synthetase ATP-binding domain-like 1 162 0e+00
5 g3235.t3 SUPERFAMILY SSF52210 Succinyl-CoA synthetase domains 163 194 1e-07

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.

Raw TPM values