General information for g3235.t13
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Succinate–CoA ligase [ADP-forming] subunit beta, mitochondrial.
Parent gene
- The parent gene g3235 is located on chr_3: 23944038..23944729 (+ strand)
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.t13 | TSS | g3235.t13 | 23941831 | 23941831 |
| chr_3 | g3235 | g3235.t13 | isoform | g3235.t13 | 23942786 | 23943904 |
| chr_3 | g3235 | g3235.t13 | exon | g3235.t13.exon1 | 23942786 | 23943335 |
| chr_3 | g3235 | g3235.t13 | cds | g3235.t13.CDS1 | 23942939 | 23943335 |
| chr_3 | g3235 | g3235.t13 | exon | g3235.t13.exon2 | 23943719 | 23943904 |
| chr_3 | g3235 | g3235.t13 | cds | g3235.t13.CDS2 | 23943719 | 23943903 |
| chr_3 | g3235 | g3235.t13 | TTS | g3235.t13 | NA | NA |
Sequences
>g3235.t13 Gene=g3235 Length=736
CAACAGATTGCAAAGGATTTAAATACAAAGAATTTAGTTTTAAAAGCTCAAGTTTTGGCT
GGTGGTCGTGGAAAAGGTTCGTTTAAAAATGGTCTCAAAGGCGGTGTCAGAATCGTTTAC
ACACCAGAAGAAGCTAAAGAAATCTCGGGCAAAATGATAAATCAACTCTTGGTCACAAAA
CAAACTGGTGCAGCAGGTCGAATCTGTAACCAAGTTATGGTTGCTGAACGAAAATTCCCA
AGACGTGAATTTTATTTTGCTGTGATGATGGAACGTGCTTTTAATGGCCCAGTACTTATT
GCCTCATCGCAAGGAGGTGTAAATATTGAAGAAGTTGCTGCAGAAAATCCAGATGCAATT
GTTTATGAACCAATCGATATCAATAAGGGACTCTCTAAAGATCAAGCAATGAAAATTGCA
AGAACAGTAGGTTTAGATGATCATTTGGAAACAACAACTCAAATGCTTTTGAACTTATAT
GATTTATTCGTCAAAAAAGATGCTCTTCTTGTAGAAATTAATCCATATGCTGAAGATGCT
GGCGAAACCCACTTTGCTCTTGACGCTAAAATGCGTTTTGATGACAATGCCGAATTCCGT
CAAAAAGATTTGTTCGCAAAACGTGATTATTCTCAAGAAGATCCAAAAGAAGTTGCAGCT
GCAAAATTTGATTTGAATTACATCGCTTTAGATGGATCAATTGGTTGCATGGTAAATGGT
GCAGGTTTGGCAATGG
>g3235.t13 Gene=g3235 Length=194
MINQLLVTKQTGAAGRICNQVMVAERKFPRREFYFAVMMERAFNGPVLIASSQGGVNIEE
VAAENPDAIVYEPIDINKGLSKDQAMKIARTVGLDDHLETTTQMLLNLYDLFVKKDALLV
EINPYAEDAGETHFALDAKMRFDDNAEFRQKDLFAKRDYSQEDPKEVAAAKFDLNYIALD
GSIGCMVNGAGLAM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g3235.t13 | Gene3D | G3DSA:3.30.470.20 | - | 14 | 163 | 0e+00 |
| 7 | g3235.t13 | Gene3D | G3DSA:3.40.50.261 | - | 164 | 194 | 1e-07 |
| 2 | g3235.t13 | PANTHER | PTHR11815:SF10 | SUCCINATE–COA LIGASE [ADP-FORMING] SUBUNIT BETA, MITOCHONDRIAL | 1 | 194 | 0e+00 |
| 3 | g3235.t13 | PANTHER | PTHR11815 | SUCCINYL-COA SYNTHETASE BETA CHAIN | 1 | 194 | 0e+00 |
| 1 | g3235.t13 | Pfam | PF08442 | ATP-grasp domain | 1 | 126 | 0e+00 |
| 4 | g3235.t13 | SUPERFAMILY | SSF56059 | Glutathione synthetase ATP-binding domain-like | 1 | 162 | 0e+00 |
| 5 | g3235.t13 | 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.
