General information for g3235.t20
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t20 | isoform | g3235.t20 | 23943700 | 23944729 |
| chr_3 | g3235 | g3235.t20 | exon | g3235.t20.exon1 | 23943700 | 23943904 |
| chr_3 | g3235 | g3235.t20 | cds | g3235.t20.CDS1 | 23943739 | 23943904 |
| chr_3 | g3235 | g3235.t20 | exon | g3235.t20.exon2 | 23943995 | 23944156 |
| chr_3 | g3235 | g3235.t20 | cds | g3235.t20.CDS2 | 23943995 | 23944156 |
| chr_3 | g3235 | g3235.t20 | exon | g3235.t20.exon3 | 23944383 | 23944729 |
| chr_3 | g3235 | g3235.t20 | cds | g3235.t20.CDS3 | 23944383 | 23944501 |
| chr_3 | g3235 | g3235.t20 | TTS | g3235.t20 | 23944934 | 23944934 |
| chr_3 | g3235 | g3235.t20 | TSS | g3235.t20 | NA | NA |
Sequences
>g3235.t20 Gene=g3235 Length=714
TTTCTTCGATGAATTTTAGACTTTGCTCTTGACGCTAAAATGCGTTTTGATGACAATGCC
GAATTCCGTCAAAAAGATTTGTTCGCAAAACGTGATTATTCTCAAGAAGATCCAAAAGAA
GTTGCAGCTGCAAAATTTGATTTGAATTACATCGCTTTAGATGGATCAATTGGTTGCATG
GTAAATGGTGCAGGTTTGGCAATGGGAGGCGATCCCGCAAATTTCTTGGACGTTGGTGGC
GGTGCCACTGCAAATGCTGTCAAGGAGGCCTTCAAAATTATTACTGCAGATCCAAAAGTA
CATGTTATCCTCGTTAACATTTTTGGAGGTATTATGCGTTGTGATGTGATTGCTGAAGGT
ATCATTGCTAAAGATGATCTTGACGAAGCTGCAATGCTTAGCGTTCACTTATCTCAAATT
GTACATCTTGCACGCGAAGCTCATCTCAACGTTTTGTTCGAATTAGATCCAGTTCATCAT
CATTAAATAAGACGTGAAAGAATTCGAAAATGATGAATAGGAATTATTCATATGTGTTAT
ACTATTAAATTTAAGAATGGTGTTAAATTATTGTCCTTATTTCATCAAACCATACAAAAA
CAAATATCCACGCTTCATCAATCTTATCTGTTTCGCACCAAAATTATTCTTATGTTCATC
AACTTCTTTTCTTTGTGTGTTATTTATGATCTTAGTTTTATCATATAAAAAAAT
>g3235.t20 Gene=g3235 Length=148
MRFDDNAEFRQKDLFAKRDYSQEDPKEVAAAKFDLNYIALDGSIGCMVNGAGLAMGGDPA
NFLDVGGGATANAVKEAFKIITADPKVHVILVNIFGGIMRCDVIAEGIIAKDDLDEAAML
SVHLSQIVHLAREAHLNVLFELDPVHHH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g3235.t20 | Gene3D | G3DSA:3.40.50.261 | - | 25 | 124 | 0 |
| 2 | g3235.t20 | PANTHER | PTHR11815:SF10 | SUCCINATE–COA LIGASE [ADP-FORMING] SUBUNIT BETA, MITOCHONDRIAL | 1 | 110 | 0 |
| 3 | g3235.t20 | PANTHER | PTHR11815 | SUCCINYL-COA SYNTHETASE BETA CHAIN | 1 | 110 | 0 |
| 1 | g3235.t20 | Pfam | PF00549 | CoA-ligase | 54 | 111 | 0 |
| 4 | g3235.t20 | SUPERFAMILY | SSF52210 | Succinyl-CoA synthetase domains | 24 | 110 | 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 |
| GO:0003824 | catalytic activity | 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.
