Gene loci information

Transcript annotation

  • This transcript has been annotated as Succinate–CoA ligase [GDP-forming] subunit beta, mitochondrial.

Parent gene

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.t5 TTS g12073.t5 20808417 20808417
chr_1 g12073 g12073.t5 isoform g12073.t5 20808531 20809967
chr_1 g12073 g12073.t5 exon g12073.t5.exon1 20808531 20809600
chr_1 g12073 g12073.t5 cds g12073.t5.CDS1 20808531 20809600
chr_1 g12073 g12073.t5 exon g12073.t5.exon2 20809654 20809805
chr_1 g12073 g12073.t5 cds g12073.t5.CDS2 20809654 20809732
chr_1 g12073 g12073.t5 exon g12073.t5.exon3 20809914 20809967
chr_1 g12073 g12073.t5 TSS g12073.t5 20810139 20810139

Sequences

>g12073.t5 Gene=g12073 Length=1276
ATGTCAAATTTGATTTTGCGACAATTCAATAACAAAATTCATAGAATAAGAAATACACTT
CTATCTTCATCTTCTATTCAAAAACGTCATTTAAATCTTCTAGAATTTCAAAGTAAGAAA
TTGCTCGATGAAGCAGGAGTTGCAATACAAAAATTTAGAGTGCTTGAATCAAGCAATGAT
AAAAATACATTATCGGACTTTAGTAAATGTTAAAGAGTATGTTGTGAAGGCTCAGATTCT
AGCTGGTGGTCGAGGTAAAGGCCATTTTGATAATGGCTTTAAAGGAGGTGTTCATTTGAC
AAAAGATAAACAGGAAGTGTTTGAGCTTGTCAATAAAATGCTTGGACACAAATTGATAAC
AAAACAGACACCAAAAGAGGGAATTCCCGTAAAAAAAGTAATGGTAGCTGATTCAGTGAA
TATTGTAAGAGAAACATATTTCTGCATCATTCTTGATCGAGAGCATAATGGTCCTGTTAT
AATCTGTTCACCTGATGGTGGAATTGATATTGAAAAAGTAGCAGAAGAAACACCTGATCG
AGTGAAAACAGTAGCTGTTGATGTAATTAAAGGCCTATCAAATGAGACTGCTTTAGATTT
AGCAGAATTTCTTCAGTTCAAAGGCAATTTAAAAGAGAAAGCAGCGTATGAGATTAAAAA
GCTTTATGAACTTTTCAATAAAGTTGATGCAACACAAATTGAAATAAATCCATTAGCAGA
AACCGATGACGGTCGTGTGATTGCAGTCGATGCCAAATTAAACTTTGACGACAATGCTCA
ATTTAGACAAAGACCAATCTTTGATATGGATGATACTTCAGAGAGCGATCCGAAAGAAGT
TGAGGCACAAAAATATAACTTAAATTACATATCAATGCAAGGTGGAAATATCGGTTGTAT
GGTCAATGGTGCAGGTCTCGCAATGGGTACAATGGACATTATTAAATTGCATGGCGGTGA
ACCCGCAAATTTCTTAGATGTCGGCGGTGGTGCAAATGAAGAACAAGTTTTAAAAGCATT
TCATATCATCACAAGCGATAAAAATGTAAAAGCGATTCTTGTCAATGTTTTTGGAGGAAT
TGTGAATTGTGCCACAATTGCTAATGGAATTATAAAAGCTTCAAAATCAATCAACTTAAG
TGTGCCTTTAATTGTAAGATTAGAAGGAAATAATGTTGAGGCAGCAAAGAAGCTTTTAAA
AGATTCTGGATTAAATATTCAAACTGCAGAAGATTTAGATGACGCTGCAAAGAAAGCTGT
TGCTGCAATTAAATAA

>g12073.t5 Gene=g12073 Length=382
MKQELQYKNLECLNQAMIKIHYRTLVNVKEYVVKAQILAGGRGKGHFDNGFKGGVHLTKD
KQEVFELVNKMLGHKLITKQTPKEGIPVKKVMVADSVNIVRETYFCIILDREHNGPVIIC
SPDGGIDIEKVAEETPDRVKTVAVDVIKGLSNETALDLAEFLQFKGNLKEKAAYEIKKLY
ELFNKVDATQIEINPLAETDDGRVIAVDAKLNFDDNAQFRQRPIFDMDDTSESDPKEVEA
QKYNLNYISMQGGNIGCMVNGAGLAMGTMDIIKLHGGEPANFLDVGGGANEEQVLKAFHI
ITSDKNVKAILVNVFGGIVNCATIANGIIKASKSINLSVPLIVRLEGNNVEAAKKLLKDS
GLNIQTAEDLDDAAKKAVAAIK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g12073.t5 Gene3D G3DSA:3.30.1490.20 - 26 104 3.9E-78
8 g12073.t5 Gene3D G3DSA:3.30.470.20 - 105 227 3.9E-78
10 g12073.t5 Gene3D G3DSA:3.40.50.261 - 235 382 7.9E-56
5 g12073.t5 Hamap MF_00558 Succinate–CoA ligase [ADP-forming] subunit beta [sucC]. 2 382 35.209476
3 g12073.t5 PANTHER PTHR11815:SF17 SUCCINATE–COA LIGASE [GDP-FORMING] SUBUNIT BETA, MITOCHONDRIAL 25 382 1.5E-177
4 g12073.t5 PANTHER PTHR11815 SUCCINYL-COA SYNTHETASE BETA CHAIN 25 382 1.5E-177
11 g12073.t5 PIRSF PIRSF001554 SucCS_beta 5 382 3.1E-132
2 g12073.t5 Pfam PF08442 ATP-grasp domain 26 197 2.7E-61
1 g12073.t5 Pfam PF00549 CoA-ligase 258 378 6.7E-25
12 g12073.t5 ProSitePatterns PS01217 ATP-citrate lyase / succinyl-CoA ligases family signature 3. 253 278 -
6 g12073.t5 SUPERFAMILY SSF56059 Glutathione synthetase ATP-binding domain-like 27 232 4.95E-60
7 g12073.t5 SUPERFAMILY SSF52210 Succinyl-CoA synthetase domains 234 381 1.09E-51
13 g12073.t5 TIGRFAM TIGR01016 sucCoAbeta: succinate-CoA ligase, beta subunit 27 381 1.0E-126

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:0005524 ATP binding MF
GO:0003824 catalytic activity MF

KEGG

Orthology

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.

Raw TPM values