General information for g12073.t1
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.t1 | TTS | g12073.t1 | 20808417 | 20808417 |
| chr_1 | g12073 | g12073.t1 | isoform | g12073.t1 | 20808531 | 20809967 |
| chr_1 | g12073 | g12073.t1 | exon | g12073.t1.exon1 | 20808531 | 20809600 |
| chr_1 | g12073 | g12073.t1 | cds | g12073.t1.CDS1 | 20808531 | 20809600 |
| chr_1 | g12073 | g12073.t1 | exon | g12073.t1.exon2 | 20809658 | 20809805 |
| chr_1 | g12073 | g12073.t1 | cds | g12073.t1.CDS2 | 20809658 | 20809805 |
| chr_1 | g12073 | g12073.t1 | exon | g12073.t1.exon3 | 20809914 | 20809967 |
| chr_1 | g12073 | g12073.t1 | cds | g12073.t1.CDS3 | 20809914 | 20809967 |
| chr_1 | g12073 | g12073.t1 | TSS | g12073.t1 | 20810139 | 20810139 |
Sequences
>g12073.t1 Gene=g12073 Length=1272
ATGTCAAATTTGATTTTGCGACAATTCAATAACAAAATTCATAGAATAAGAAATACACTT
CTATCTTCATCTTCTATTCAAAAACGTCATTTAAATCTTCTAGAATTTCAAAGTAAGAAA
TTGCTCGATGAAGCAGGAGTTGCAATACAAAAATTTAGAGTGCTTGAATCAAGCAATGAT
AAAAATACATTATCGGACTTTAATGTTAAAGAGTATGTTGTGAAGGCTCAGATTCTAGCT
GGTGGTCGAGGTAAAGGCCATTTTGATAATGGCTTTAAAGGAGGTGTTCATTTGACAAAA
GATAAACAGGAAGTGTTTGAGCTTGTCAATAAAATGCTTGGACACAAATTGATAACAAAA
CAGACACCAAAAGAGGGAATTCCCGTAAAAAAAGTAATGGTAGCTGATTCAGTGAATATT
GTAAGAGAAACATATTTCTGCATCATTCTTGATCGAGAGCATAATGGTCCTGTTATAATC
TGTTCACCTGATGGTGGAATTGATATTGAAAAAGTAGCAGAAGAAACACCTGATCGAGTG
AAAACAGTAGCTGTTGATGTAATTAAAGGCCTATCAAATGAGACTGCTTTAGATTTAGCA
GAATTTCTTCAGTTCAAAGGCAATTTAAAAGAGAAAGCAGCGTATGAGATTAAAAAGCTT
TATGAACTTTTCAATAAAGTTGATGCAACACAAATTGAAATAAATCCATTAGCAGAAACC
GATGACGGTCGTGTGATTGCAGTCGATGCCAAATTAAACTTTGACGACAATGCTCAATTT
AGACAAAGACCAATCTTTGATATGGATGATACTTCAGAGAGCGATCCGAAAGAAGTTGAG
GCACAAAAATATAACTTAAATTACATATCAATGCAAGGTGGAAATATCGGTTGTATGGTC
AATGGTGCAGGTCTCGCAATGGGTACAATGGACATTATTAAATTGCATGGCGGTGAACCC
GCAAATTTCTTAGATGTCGGCGGTGGTGCAAATGAAGAACAAGTTTTAAAAGCATTTCAT
ATCATCACAAGCGATAAAAATGTAAAAGCGATTCTTGTCAATGTTTTTGGAGGAATTGTG
AATTGTGCCACAATTGCTAATGGAATTATAAAAGCTTCAAAATCAATCAACTTAAGTGTG
CCTTTAATTGTAAGATTAGAAGGAAATAATGTTGAGGCAGCAAAGAAGCTTTTAAAAGAT
TCTGGATTAAATATTCAAACTGCAGAAGATTTAGATGACGCTGCAAAGAAAGCTGTTGCT
GCAATTAAATAA
>g12073.t1 Gene=g12073 Length=423
MSNLILRQFNNKIHRIRNTLLSSSSIQKRHLNLLEFQSKKLLDEAGVAIQKFRVLESSND
KNTLSDFNVKEYVVKAQILAGGRGKGHFDNGFKGGVHLTKDKQEVFELVNKMLGHKLITK
QTPKEGIPVKKVMVADSVNIVRETYFCIILDREHNGPVIICSPDGGIDIEKVAEETPDRV
KTVAVDVIKGLSNETALDLAEFLQFKGNLKEKAAYEIKKLYELFNKVDATQIEINPLAET
DDGRVIAVDAKLNFDDNAQFRQRPIFDMDDTSESDPKEVEAQKYNLNYISMQGGNIGCMV
NGAGLAMGTMDIIKLHGGEPANFLDVGGGANEEQVLKAFHIITSDKNVKAILVNVFGGIV
NCATIANGIIKASKSINLSVPLIVRLEGNNVEAAKKLLKDSGLNIQTAEDLDDAAKKAVA
AIK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g12073.t1 | Gene3D | G3DSA:3.30.470.20 | - | 31 | 268 | 4.6E-88 |
| 10 | g12073.t1 | Gene3D | G3DSA:3.30.1490.20 | - | 51 | 145 | 4.6E-88 |
| 11 | g12073.t1 | Gene3D | G3DSA:3.40.50.261 | - | 276 | 423 | 9.9E-56 |
| 6 | g12073.t1 | Hamap | MF_03221 | Succinate–CoA ligase [GDP-forming] subunit beta, mitochondrial [SUCLG2]. | 21 | 423 | 54.318253 |
| 5 | g12073.t1 | Hamap | MF_00558 | Succinate–CoA ligase [ADP-forming] subunit beta [sucC]. | 31 | 423 | 37.525612 |
| 3 | g12073.t1 | PANTHER | PTHR11815:SF17 | SUCCINATE–COA LIGASE [GDP-FORMING] SUBUNIT BETA, MITOCHONDRIAL | 6 | 423 | 1.8E-194 |
| 4 | g12073.t1 | PANTHER | PTHR11815 | SUCCINYL-COA SYNTHETASE BETA CHAIN | 6 | 423 | 1.8E-194 |
| 12 | g12073.t1 | PIRSF | PIRSF001554 | SucCS_beta | 31 | 423 | 3.0E-140 |
| 2 | g12073.t1 | Pfam | PF08442 | ATP-grasp domain | 32 | 238 | 1.1E-68 |
| 1 | g12073.t1 | Pfam | PF00549 | CoA-ligase | 299 | 419 | 8.2E-25 |
| 13 | g12073.t1 | ProSitePatterns | PS01217 | ATP-citrate lyase / succinyl-CoA ligases family signature 3. | 294 | 319 | - |
| 15 | g12073.t1 | ProSiteProfiles | PS50975 | ATP-grasp fold profile. | 39 | 266 | 10.057 |
| 7 | g12073.t1 | SUPERFAMILY | SSF56059 | Glutathione synthetase ATP-binding domain-like | 31 | 273 | 3.28E-66 |
| 8 | g12073.t1 | SUPERFAMILY | SSF52210 | Succinyl-CoA synthetase domains | 275 | 422 | 1.31E-51 |
| 14 | g12073.t1 | TIGRFAM | TIGR01016 | sucCoAbeta: succinate-CoA ligase, beta subunit | 32 | 422 | 2.1E-133 |
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:0006104 | succinyl-CoA metabolic process | BP |
| GO:0005524 | ATP binding | MF |
| GO:0003824 | catalytic activity | MF |
| GO:0004776 | succinate-CoA ligase (GDP-forming) activity | MF |
KEGG
Orthology
- This transcript has been annotated with K01900 (succinyl-CoA synthetase beta subunit)
Pathway
- This transcript belongs to the following pathways
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.
