General information for g12073.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Succinate–CoA ligase [GDP-forming] subunit beta, mitochondrial.
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.t4 | TTS | g12073.t4 | 20808417 | 20808417 |
| chr_1 | g12073 | g12073.t4 | isoform | g12073.t4 | 20808531 | 20809967 |
| chr_1 | g12073 | g12073.t4 | exon | g12073.t4.exon1 | 20808531 | 20809600 |
| chr_1 | g12073 | g12073.t4 | cds | g12073.t4.CDS1 | 20808531 | 20809469 |
| chr_1 | g12073 | g12073.t4 | exon | g12073.t4.exon2 | 20809658 | 20809967 |
| chr_1 | g12073 | g12073.t4 | TSS | g12073.t4 | 20810139 | 20810139 |
Sequences
>g12073.t4 Gene=g12073 Length=1380
ATGTCAAATTTGATTTTGCGACAATTCAATAACAAAATTCATAGAATAAGAAATGTAAGT
TGCCATTTACTGCTCTTATCTGGAAGTAAAATTTAACATTTTTATGATAAAAAGCAAAAT
ACAATAACCACGTTGTCTTTCTATTATCTTGTCTATTTTTAGACACTTCTATCTTCATCT
TCTATTCAAAAACGTCATTTAAATCTTCTAGAATTTCAAAGTAAGAAATTGCTCGATGAA
GCAGGAGTTGCAATACAAAAATTTAGAGTGCTTGAATCAAGCAATGATAAAAATACATTA
TCGGACTTTAATGTTAAAGAGTATGTTGTGAAGGCTCAGATTCTAGCTGGTGGTCGAGGT
AAAGGCCATTTTGATAATGGCTTTAAAGGAGGTGTTCATTTGACAAAAGATAAACAGGAA
GTGTTTGAGCTTGTCAATAAAATGCTTGGACACAAATTGATAACAAAACAGACACCAAAA
GAGGGAATTCCCGTAAAAAAAGTAATGGTAGCTGATTCAGTGAATATTGTAAGAGAAACA
TATTTCTGCATCATTCTTGATCGAGAGCATAATGGTCCTGTTATAATCTGTTCACCTGAT
GGTGGAATTGATATTGAAAAAGTAGCAGAAGAAACACCTGATCGAGTGAAAACAGTAGCT
GTTGATGTAATTAAAGGCCTATCAAATGAGACTGCTTTAGATTTAGCAGAATTTCTTCAG
TTCAAAGGCAATTTAAAAGAGAAAGCAGCGTATGAGATTAAAAAGCTTTATGAACTTTTC
AATAAAGTTGATGCAACACAAATTGAAATAAATCCATTAGCAGAAACCGATGACGGTCGT
GTGATTGCAGTCGATGCCAAATTAAACTTTGACGACAATGCTCAATTTAGACAAAGACCA
ATCTTTGATATGGATGATACTTCAGAGAGCGATCCGAAAGAAGTTGAGGCACAAAAATAT
AACTTAAATTACATATCAATGCAAGGTGGAAATATCGGTTGTATGGTCAATGGTGCAGGT
CTCGCAATGGGTACAATGGACATTATTAAATTGCATGGCGGTGAACCCGCAAATTTCTTA
GATGTCGGCGGTGGTGCAAATGAAGAACAAGTTTTAAAAGCATTTCATATCATCACAAGC
GATAAAAATGTAAAAGCGATTCTTGTCAATGTTTTTGGAGGAATTGTGAATTGTGCCACA
ATTGCTAATGGAATTATAAAAGCTTCAAAATCAATCAACTTAAGTGTGCCTTTAATTGTA
AGATTAGAAGGAAATAATGTTGAGGCAGCAAAGAAGCTTTTAAAAGATTCTGGATTAAAT
ATTCAAACTGCAGAAGATTTAGATGACGCTGCAAAGAAAGCTGTTGCTGCAATTAAATAA
>g12073.t4 Gene=g12073 Length=312
MLGHKLITKQTPKEGIPVKKVMVADSVNIVRETYFCIILDREHNGPVIICSPDGGIDIEK
VAEETPDRVKTVAVDVIKGLSNETALDLAEFLQFKGNLKEKAAYEIKKLYELFNKVDATQ
IEINPLAETDDGRVIAVDAKLNFDDNAQFRQRPIFDMDDTSESDPKEVEAQKYNLNYISM
QGGNIGCMVNGAGLAMGTMDIIKLHGGEPANFLDVGGGANEEQVLKAFHIITSDKNVKAI
LVNVFGGIVNCATIANGIIKASKSINLSVPLIVRLEGNNVEAAKKLLKDSGLNIQTAEDL
DDAAKKAVAAIK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g12073.t4 | Gene3D | G3DSA:3.30.470.20 | - | 13 | 164 | 1.0E-55 |
| 9 | g12073.t4 | Gene3D | G3DSA:3.40.50.261 | - | 165 | 312 | 5.0E-56 |
| 3 | g12073.t4 | PANTHER | PTHR11815:SF17 | SUCCINATE–COA LIGASE [GDP-FORMING] SUBUNIT BETA, MITOCHONDRIAL | 1 | 312 | 2.0E-152 |
| 4 | g12073.t4 | PANTHER | PTHR11815 | SUCCINYL-COA SYNTHETASE BETA CHAIN | 1 | 312 | 2.0E-152 |
| 11 | g12073.t4 | PIRSF | PIRSF001554 | SucCS_beta | 1 | 312 | 6.9E-117 |
| 2 | g12073.t4 | Pfam | PF08442 | ATP-grasp domain | 1 | 127 | 6.9E-44 |
| 1 | g12073.t4 | Pfam | PF00549 | CoA-ligase | 188 | 308 | 4.4E-25 |
| 7 | g12073.t4 | ProSitePatterns | PS01217 | ATP-citrate lyase / succinyl-CoA ligases family signature 3. | 183 | 208 | - |
| 5 | g12073.t4 | SUPERFAMILY | SSF56059 | Glutathione synthetase ATP-binding domain-like | 1 | 162 | 8.48E-42 |
| 6 | g12073.t4 | SUPERFAMILY | SSF52210 | Succinyl-CoA synthetase domains | 164 | 311 | 6.67E-52 |
| 10 | g12073.t4 | TIGRFAM | TIGR01016 | sucCoAbeta: succinate-CoA ligase, beta subunit | 1 | 311 | 6.5E-115 |
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