Gene loci information

Transcript annotation

  • This transcript has been annotated as Succinate–CoA ligase [ADP-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_3 g3235 g3235.t1 TSS g3235.t1 23941831 23941831
chr_3 g3235 g3235.t1 isoform g3235.t1 23941885 23944501
chr_3 g3235 g3235.t1 exon g3235.t1.exon1 23941885 23941944
chr_3 g3235 g3235.t1 cds g3235.t1.CDS1 23941885 23941944
chr_3 g3235 g3235.t1 exon g3235.t1.exon2 23942379 23942470
chr_3 g3235 g3235.t1 cds g3235.t1.CDS2 23942379 23942470
chr_3 g3235 g3235.t1 exon g3235.t1.exon3 23942755 23943335
chr_3 g3235 g3235.t1 cds g3235.t1.CDS3 23942755 23943335
chr_3 g3235 g3235.t1 exon g3235.t1.exon4 23943481 23943489
chr_3 g3235 g3235.t1 cds g3235.t1.CDS4 23943481 23943489
chr_3 g3235 g3235.t1 exon g3235.t1.exon5 23943719 23943931
chr_3 g3235 g3235.t1 cds g3235.t1.CDS5 23943719 23943931
chr_3 g3235 g3235.t1 exon g3235.t1.exon6 23943995 23944206
chr_3 g3235 g3235.t1 cds g3235.t1.CDS6 23943995 23944206
chr_3 g3235 g3235.t1 exon g3235.t1.exon7 23944325 23944501
chr_3 g3235 g3235.t1 cds g3235.t1.CDS7 23944325 23944501
chr_3 g3235 g3235.t1 TTS g3235.t1 23944934 23944934

Sequences

>g3235.t1 Gene=g3235 Length=1344
ATGAGTTTTCTAACTAGATCAGCAATATTTGCAGGTTCATCCTTAAGAAATGGTGCAAAG
ATTCTCAGTGCCGCACAACAAAAACGTCAATTGAACGTTCAAGAGCACGTTTCGTACTCA
TTTTTAAATGAGGCCGGGATTCCAACACCAAAATTCGGTGTTGCAGGTTCAGCTGAAGAA
GCTCAACAGATTGCAAAGGATTTAAATACAAAGAATTTAGTTTTAAAAGCTCAAGTTTTG
GCTGGTGGTCGTGGAAAAGGTTCGTTTAAAAATGGTCTCAAAGGCGGTGTCAGAATCGTT
TACACACCAGAAGAAGCTAAAGAAATCTCGGGCAAAATGATAAATCAACTCTTGGTCACA
AAACAAACTGGTGCAGCAGGTCGAATCTGTAACCAAGTTATGGTTGCTGAACGAAAATTC
CCAAGACGTGAATTTTATTTTGCTGTGATGATGGAACGTGCTTTTAATGGCCCAGTACTT
ATTGCCTCATCGCAAGGAGGTGTAAATATTGAAGAAGTTGCTGCAGAAAATCCAGATGCA
ATTGTTTATGAACCAATCGATATCAATAAGGGACTCTCTAAAGATCAAGCAATGAAAATT
GCAAGAACAGTAGGTTTAGATGATCATTTGGAAACAACAACTCAAATGCTTTTGAACTTA
TATGATTTATTCGTCAAAAAAGATGCTCTTCTTGTAGAAATTAATCCATATGCTGAAGAT
GCTGGCGAAACCCGCGATCAGTACTTTGCTCTTGACGCTAAAATGCGTTTTGATGACAAT
GCCGAATTCCGTCAAAAAGATTTGTTCGCAAAACGTGATTATTCTCAAGAAGATCCAAAA
GAAGTTGCAGCTGCAAAATTTGATTTGAATTACATCGCTTTAGATGGATCAATTGGTTGC
ATGGTAAATGGTGCAGGTTTGGCAATGGCTACAATGGACATCATTAAATTGCACGGAGGC
GATCCCGCAAATTTCTTGGACGTTGGTGGCGGTGCCACTGCAAATGCTGTCAAGGAGGCC
TTCAAAATTATTACTGCAGATCCAAAAGTACATGTTATCCTCGTTAACATTTTTGGAGGT
ATTATGCGTTGTGATGTGATTGCTGAAGGTATCATTGCTGCAACAAAAGAGCTTAATTTG
ACTTTACCCATCATTGTGCGTCTTCAGGGTACAAATGTCAATGAAGCAAAGGAGCTCATT
CGCAAATCAAAATTACGCATTTTACCTAAAGATGATCTTGACGAAGCTGCAATGCTTAGC
GTTCACTTATCTCAAATTGTACATCTTGCACGCGAAGCTCATCTCAACGTTTTGTTCGAA
TTAGATCCAGTTCATCATCATTAA

>g3235.t1 Gene=g3235 Length=447
MSFLTRSAIFAGSSLRNGAKILSAAQQKRQLNVQEHVSYSFLNEAGIPTPKFGVAGSAEE
AQQIAKDLNTKNLVLKAQVLAGGRGKGSFKNGLKGGVRIVYTPEEAKEISGKMINQLLVT
KQTGAAGRICNQVMVAERKFPRREFYFAVMMERAFNGPVLIASSQGGVNIEEVAAENPDA
IVYEPIDINKGLSKDQAMKIARTVGLDDHLETTTQMLLNLYDLFVKKDALLVEINPYAED
AGETRDQYFALDAKMRFDDNAEFRQKDLFAKRDYSQEDPKEVAAAKFDLNYIALDGSIGC
MVNGAGLAMATMDIIKLHGGDPANFLDVGGGATANAVKEAFKIITADPKVHVILVNIFGG
IMRCDVIAEGIIAATKELNLTLPIIVRLQGTNVNEAKELIRKSKLRILPKDDLDEAAMLS
VHLSQIVHLAREAHLNVLFELDPVHHH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g3235.t1 Coils Coil Coil 58 78 -
9 g3235.t1 Gene3D G3DSA:3.30.470.20 - 31 270 5.7E-81
10 g3235.t1 Gene3D G3DSA:3.30.1490.20 - 51 146 5.7E-81
11 g3235.t1 Gene3D G3DSA:3.40.50.261 - 279 426 1.4E-55
6 g3235.t1 Hamap MF_03220 Succinate–CoA ligase [ADP-forming] subunit beta, mitochondrial [SUCLA2]. 28 443 55.384876
5 g3235.t1 Hamap MF_00558 Succinate–CoA ligase [ADP-forming] subunit beta [sucC]. 31 425 37.625511
3 g3235.t1 PANTHER PTHR11815:SF10 SUCCINATE–COA LIGASE [ADP-FORMING] SUBUNIT BETA, MITOCHONDRIAL 22 428 3.5E-194
4 g3235.t1 PANTHER PTHR11815 SUCCINYL-COA SYNTHETASE BETA CHAIN 22 428 3.5E-194
13 g3235.t1 PIRSF PIRSF001554 SucCS_beta 31 431 5.8E-139
2 g3235.t1 Pfam PF08442 ATP-grasp domain 32 238 2.0E-66
1 g3235.t1 Pfam PF00549 CoA-ligase 301 418 2.3E-26
14 g3235.t1 ProSitePatterns PS01217 ATP-citrate lyase / succinyl-CoA ligases family signature 3. 296 320 -
16 g3235.t1 ProSiteProfiles PS50975 ATP-grasp fold profile. 39 262 10.94
7 g3235.t1 SUPERFAMILY SSF56059 Glutathione synthetase ATP-binding domain-like 31 277 9.56E-71
8 g3235.t1 SUPERFAMILY SSF52210 Succinyl-CoA synthetase domains 278 423 1.18E-52
15 g3235.t1 TIGRFAM TIGR01016 sucCoAbeta: succinate-CoA ligase, beta subunit 32 424 6.8E-125

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:0005524 ATP binding MF
GO:0005739 mitochondrion CC
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