General information for g12073.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Succinate–CoA ligase [ADP-forming] subunit beta.
Parent gene
- The parent gene g12073 is located on chr_1: 20809245..20809967 (- 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_1 | g12073 | g12073.t3 | TTS | g12073.t3 | 20808417 | 20808417 |
| chr_1 | g12073 | g12073.t3 | isoform | g12073.t3 | 20808531 | 20809967 |
| chr_1 | g12073 | g12073.t3 | exon | g12073.t3.exon1 | 20808531 | 20809162 |
| chr_1 | g12073 | g12073.t3 | cds | g12073.t3.CDS1 | 20808531 | 20809001 |
| chr_1 | g12073 | g12073.t3 | exon | g12073.t3.exon2 | 20809245 | 20809600 |
| chr_1 | g12073 | g12073.t3 | exon | g12073.t3.exon3 | 20809658 | 20809805 |
| chr_1 | g12073 | g12073.t3 | exon | g12073.t3.exon4 | 20809914 | 20809967 |
| chr_1 | g12073 | g12073.t3 | TSS | g12073.t3 | 20810139 | 20810139 |
Sequences
>g12073.t3 Gene=g12073 Length=1190
ATGTCAAATTTGATTTTGCGACAATTCAATAACAAAATTCATAGAATAAGAAATACACTT
CTATCTTCATCTTCTATTCAAAAACGTCATTTAAATCTTCTAGAATTTCAAAGTAAGAAA
TTGCTCGATGAAGCAGGAGTTGCAATACAAAAATTTAGAGTGCTTGAATCAAGCAATGAT
AAAAATACATTATCGGACTTTAATGTTAAAGAGTATGTTGTGAAGGCTCAGATTCTAGCT
GGTGGTCGAGGTAAAGGCCATTTTGATAATGGCTTTAAAGGAGGTGTTCATTTGACAAAA
GATAAACAGGAAGTGTTTGAGCTTGTCAATAAAATGCTTGGACACAAATTGATAACAAAA
CAGACACCAAAAGAGGGAATTCCCGTAAAAAAAGTAATGGTAGCTGATTCAGTGAATATT
GTAAGAGAAACATATTTCTGCATCATTCTTGATCGAGAGCATAATGGTCCTGTTATAATC
TGTTCACCTGATGGTGGAATTGATATTGAAAAAGTAGCAGAAGAAACACCTGATCGAGTG
AAAACAGTAGCTGTTGATCGTATGAGATTAAAAAGCTTTATGAACTTTTCAATAAAGTTG
ATGCAACACAAATTGAAATAAATCCATTAGCAGAAACCGATGACGGTCGTGTGATTGCAG
TCGATGCCAAATTAAACTTTGACGACAATGCTCAATTTAGACAAAGACCAATCTTTGATA
TGGATGATACTTCAGAGAGCGATCCGAAAGAAGTTGAGGCACAAAAATATAACTTAAATT
ACATATCAATGCAAGGTGGAAATATCGGTTGTATGGTCAATGGTGCAGGTCTCGCAATGG
GTACAATGGACATTATTAAATTGCATGGCGGTGAACCCGCAAATTTCTTAGATGTCGGCG
GTGGTGCAAATGAAGAACAAGTTTTAAAAGCATTTCATATCATCACAAGCGATAAAAATG
TAAAAGCGATTCTTGTCAATGTTTTTGGAGGAATTGTGAATTGTGCCACAATTGCTAATG
GAATTATAAAAGCTTCAAAATCAATCAACTTAAGTGTGCCTTTAATTGTAAGATTAGAAG
GAAATAATGTTGAGGCAGCAAAGAAGCTTTTAAAAGATTCTGGATTAAATATTCAAACTG
CAGAAGATTTAGATGACGCTGCAAAGAAAGCTGTTGCTGCAATTAAATAA
>g12073.t3 Gene=g12073 Length=156
MDDTSESDPKEVEAQKYNLNYISMQGGNIGCMVNGAGLAMGTMDIIKLHGGEPANFLDVG
GGANEEQVLKAFHIITSDKNVKAILVNVFGGIVNCATIANGIIKASKSINLSVPLIVRLE
GNNVEAAKKLLKDSGLNIQTAEDLDDAAKKAVAAIK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g12073.t3 | Gene3D | G3DSA:3.40.50.261 | - | 9 | 156 | 5.9E-57 |
| 2 | g12073.t3 | PANTHER | PTHR11815:SF17 | SUCCINATE–COA LIGASE [GDP-FORMING] SUBUNIT BETA, MITOCHONDRIAL | 1 | 156 | 8.5E-76 |
| 3 | g12073.t3 | PANTHER | PTHR11815 | SUCCINYL-COA SYNTHETASE BETA CHAIN | 1 | 156 | 8.5E-76 |
| 1 | g12073.t3 | Pfam | PF00549 | CoA-ligase | 32 | 152 | 6.8E-26 |
| 5 | g12073.t3 | ProSitePatterns | PS01217 | ATP-citrate lyase / succinyl-CoA ligases family signature 3. | 27 | 52 | - |
| 4 | g12073.t3 | SUPERFAMILY | SSF52210 | Succinyl-CoA synthetase domains | 8 | 155 | 7.72E-53 |
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. There were no conditions that were differentially expressed