General information for g3235.t10
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.t10 | TSS | g3235.t10 | 23941831 | 23941831 |
| chr_3 | g3235 | g3235.t10 | isoform | g3235.t10 | 23941885 | 23944729 |
| chr_3 | g3235 | g3235.t10 | exon | g3235.t10.exon1 | 23941885 | 23941944 |
| chr_3 | g3235 | g3235.t10 | cds | g3235.t10.CDS1 | 23941885 | 23941944 |
| chr_3 | g3235 | g3235.t10 | exon | g3235.t10.exon2 | 23942379 | 23942470 |
| chr_3 | g3235 | g3235.t10 | cds | g3235.t10.CDS2 | 23942379 | 23942470 |
| chr_3 | g3235 | g3235.t10 | exon | g3235.t10.exon3 | 23942755 | 23944206 |
| chr_3 | g3235 | g3235.t10 | cds | g3235.t10.CDS3 | 23942755 | 23943409 |
| chr_3 | g3235 | g3235.t10 | exon | g3235.t10.exon4 | 23944325 | 23944729 |
| chr_3 | g3235 | g3235.t10 | TTS | g3235.t10 | 23944934 | 23944934 |
Sequences
>g3235.t10 Gene=g3235 Length=2009
ATGAGTTTTCTAACTAGATCAGCAATATTTGCAGGTTCATCCTTAAGAAATGGTGCAAAG
ATTCTCAGTGCCGCACAACAAAAACGTCAATTGAACGTTCAAGAGCACGTTTCGTACTCA
TTTTTAAATGAGGCCGGGATTCCAACACCAAAATTCGGTGTTGCAGGTTCAGCTGAAGAA
GCTCAACAGATTGCAAAGGATTTAAATACAAAGAATTTAGTTTTAAAAGCTCAAGTTTTG
GCTGGTGGTCGTGGAAAAGGTTCGTTTAAAAATGGTCTCAAAGGCGGTGTCAGAATCGTT
TACACACCAGAAGAAGCTAAAGAAATCTCGGGCAAAATGATAAATCAACTCTTGGTCACA
AAACAAACTGGTGCAGCAGGTCGAATCTGTAACCAAGTTATGGTTGCTGAACGAAAATTC
CCAAGACGTGAATTTTATTTTGCTGTGATGATGGAACGTGCTTTTAATGGCCCAGTACTT
ATTGCCTCATCGCAAGGAGGTGTAAATATTGAAGAAGTTGCTGCAGAAAATCCAGATGCA
ATTGTTTATGAACCAATCGATATCAATAAGGGACTCTCTAAAGATCAAGCAATGAAAATT
GCAAGAACAGTAGGTTTAGATGATCATTTGGAAACAACAACTCAAATGCTTTTGAACTTA
TATGATTTATTCGTCAAAAAAGATGCTCTTCTTGTAGAAATTAATCCATATGCTGAAGAT
GCTGGCGAAACCCGTAAGTATTCTCTAATACAAAAATGCTCGTTTGACTATAATCTCATT
ATTCTGCTATTTACCTTTTTTGAATGATATTCACTATGTAAAAAGACATATAAATTGTAT
TTAACATTCACAAACTTCATTTTCTTTTCTCATTCAAGGCGATCAGTGTAAGTACAAACA
TCGATGATAGTTTCATTTTTTGGAAAGGAATGCAAAATTGATTTCATAAACCCTTCACAA
AAAAAATCCTGCTTCACTTAAGCGCTTAGTATCAAAAATTTATTTTTTTCTGCTGTACAA
TTGGCCAAAGCTGTCGTTTGTTTTTTTTCTCTTTTTTTATTTGACACTTTTACGTCATGC
TTATCTTAAAATATTTTTTTCTTCGATGAATTTTAGACTTTGCTCTTGACGCTAAAATGC
GTTTTGATGACAATGCCGAATTCCGTCAAAAAGATTTGTTCGCAAAACGTGATTATTCTC
AAGAAGATCCAAAAGAAGTTGCAGCTGCAAAATTTGATTTGAATTACATCGCTTTAGATG
GATCAATTGGTTGCATGGTAAATGGTGCAGGTTTGGCAATGGCTACAATGGACATCATTA
AATTGCACGGTGCTAACTAACTTTTGAGGAAATTAAAGCTTTTAAAAGCTATATGAAGTA
TTTATCTTACAGGAGGCGATCCCGCAAATTTCTTGGACGTTGGTGGCGGTGCCACTGCAA
ATGCTGTCAAGGAGGCCTTCAAAATTATTACTGCAGATCCAAAAGTACATGTTATCCTCG
TTAACATTTTTGGAGGTATTATGCGTTGTGATGTGATTGCTGAAGGTATCATTGCTGCAA
CAAAAGAGCTTAATTTGACTTTACCCATCATTGTGCGTCTTCAGGGTACAAATGTCAATG
AAGCAAAGGAGCTCATTCGCAAATCAAAATTACGCATTTTACCTAAAGATGATCTTGACG
AAGCTGCAATGCTTAGCGTTCACTTATCTCAAATTGTACATCTTGCACGCGAAGCTCATC
TCAACGTTTTGTTCGAATTAGATCCAGTTCATCATCATTAAATAAGACGTGAAAGAATTC
GAAAATGATGAATAGGAATTATTCATATGTGTTATACTATTAAATTTAAGAATGGTGTTA
AATTATTGTCCTTATTTCATCAAACCATACAAAAACAAATATCCACGCTTCATCAATCTT
ATCTGTTTCGCACCAAAATTATTCTTATGTTCATCAACTTCTTTTCTTTGTGTGTTATTT
ATGATCTTAGTTTTATCATATAAAAAAAT
>g3235.t10 Gene=g3235 Length=268
MSFLTRSAIFAGSSLRNGAKILSAAQQKRQLNVQEHVSYSFLNEAGIPTPKFGVAGSAEE
AQQIAKDLNTKNLVLKAQVLAGGRGKGSFKNGLKGGVRIVYTPEEAKEISGKMINQLLVT
KQTGAAGRICNQVMVAERKFPRREFYFAVMMERAFNGPVLIASSQGGVNIEEVAAENPDA
IVYEPIDINKGLSKDQAMKIARTVGLDDHLETTTQMLLNLYDLFVKKDALLVEINPYAED
AGETRKYSLIQKCSFDYNLIILLFTFFE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g3235.t10 | Coils | Coil | Coil | 58 | 78 | - |
| 5 | g3235.t10 | Gene3D | G3DSA:3.30.470.20 | - | 31 | 256 | 1.6E-70 |
| 6 | g3235.t10 | Gene3D | G3DSA:3.30.1490.20 | - | 51 | 146 | 1.6E-70 |
| 2 | g3235.t10 | PANTHER | PTHR11815:SF10 | SUCCINATE–COA LIGASE [ADP-FORMING] SUBUNIT BETA, MITOCHONDRIAL | 22 | 258 | 9.0E-90 |
| 3 | g3235.t10 | PANTHER | PTHR11815 | SUCCINYL-COA SYNTHETASE BETA CHAIN | 22 | 258 | 9.0E-90 |
| 1 | g3235.t10 | Pfam | PF08442 | ATP-grasp domain | 32 | 238 | 4.6E-67 |
| 8 | g3235.t10 | ProSiteProfiles | PS50975 | ATP-grasp fold profile. | 39 | 266 | 12.155 |
| 4 | g3235.t10 | SUPERFAMILY | SSF56059 | Glutathione synthetase ATP-binding domain-like | 31 | 259 | 4.91E-61 |
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.
