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.t6 TSS g3235.t6 23941831 23941831
chr_3 g3235 g3235.t6 isoform g3235.t6 23941885 23944501
chr_3 g3235 g3235.t6 exon g3235.t6.exon1 23941885 23941944
chr_3 g3235 g3235.t6 cds g3235.t6.CDS1 23941885 23941944
chr_3 g3235 g3235.t6 exon g3235.t6.exon2 23942379 23942470
chr_3 g3235 g3235.t6 cds g3235.t6.CDS2 23942379 23942470
chr_3 g3235 g3235.t6 exon g3235.t6.exon3 23942755 23943335
chr_3 g3235 g3235.t6 cds g3235.t6.CDS3 23942755 23943335
chr_3 g3235 g3235.t6 exon g3235.t6.exon4 23943719 23943931
chr_3 g3235 g3235.t6 cds g3235.t6.CDS4 23943719 23943931
chr_3 g3235 g3235.t6 exon g3235.t6.exon5 23943995 23944206
chr_3 g3235 g3235.t6 cds g3235.t6.CDS5 23943995 23944206
chr_3 g3235 g3235.t6 exon g3235.t6.exon6 23944325 23944501
chr_3 g3235 g3235.t6 cds g3235.t6.CDS6 23944325 23944501
chr_3 g3235 g3235.t6 TTS g3235.t6 23944934 23944934

Sequences

>g3235.t6 Gene=g3235 Length=1335
ATGAGTTTTCTAACTAGATCAGCAATATTTGCAGGTTCATCCTTAAGAAATGGTGCAAAG
ATTCTCAGTGCCGCACAACAAAAACGTCAATTGAACGTTCAAGAGCACGTTTCGTACTCA
TTTTTAAATGAGGCCGGGATTCCAACACCAAAATTCGGTGTTGCAGGTTCAGCTGAAGAA
GCTCAACAGATTGCAAAGGATTTAAATACAAAGAATTTAGTTTTAAAAGCTCAAGTTTTG
GCTGGTGGTCGTGGAAAAGGTTCGTTTAAAAATGGTCTCAAAGGCGGTGTCAGAATCGTT
TACACACCAGAAGAAGCTAAAGAAATCTCGGGCAAAATGATAAATCAACTCTTGGTCACA
AAACAAACTGGTGCAGCAGGTCGAATCTGTAACCAAGTTATGGTTGCTGAACGAAAATTC
CCAAGACGTGAATTTTATTTTGCTGTGATGATGGAACGTGCTTTTAATGGCCCAGTACTT
ATTGCCTCATCGCAAGGAGGTGTAAATATTGAAGAAGTTGCTGCAGAAAATCCAGATGCA
ATTGTTTATGAACCAATCGATATCAATAAGGGACTCTCTAAAGATCAAGCAATGAAAATT
GCAAGAACAGTAGGTTTAGATGATCATTTGGAAACAACAACTCAAATGCTTTTGAACTTA
TATGATTTATTCGTCAAAAAAGATGCTCTTCTTGTAGAAATTAATCCATATGCTGAAGAT
GCTGGCGAAACCCACTTTGCTCTTGACGCTAAAATGCGTTTTGATGACAATGCCGAATTC
CGTCAAAAAGATTTGTTCGCAAAACGTGATTATTCTCAAGAAGATCCAAAAGAAGTTGCA
GCTGCAAAATTTGATTTGAATTACATCGCTTTAGATGGATCAATTGGTTGCATGGTAAAT
GGTGCAGGTTTGGCAATGGCTACAATGGACATCATTAAATTGCACGGAGGCGATCCCGCA
AATTTCTTGGACGTTGGTGGCGGTGCCACTGCAAATGCTGTCAAGGAGGCCTTCAAAATT
ATTACTGCAGATCCAAAAGTACATGTTATCCTCGTTAACATTTTTGGAGGTATTATGCGT
TGTGATGTGATTGCTGAAGGTATCATTGCTGCAACAAAAGAGCTTAATTTGACTTTACCC
ATCATTGTGCGTCTTCAGGGTACAAATGTCAATGAAGCAAAGGAGCTCATTCGCAAATCA
AAATTACGCATTTTACCTAAAGATGATCTTGACGAAGCTGCAATGCTTAGCGTTCACTTA
TCTCAAATTGTACATCTTGCACGCGAAGCTCATCTCAACGTTTTGTTCGAATTAGATCCA
GTTCATCATCATTAA

>g3235.t6 Gene=g3235 Length=444
MSFLTRSAIFAGSSLRNGAKILSAAQQKRQLNVQEHVSYSFLNEAGIPTPKFGVAGSAEE
AQQIAKDLNTKNLVLKAQVLAGGRGKGSFKNGLKGGVRIVYTPEEAKEISGKMINQLLVT
KQTGAAGRICNQVMVAERKFPRREFYFAVMMERAFNGPVLIASSQGGVNIEEVAAENPDA
IVYEPIDINKGLSKDQAMKIARTVGLDDHLETTTQMLLNLYDLFVKKDALLVEINPYAED
AGETHFALDAKMRFDDNAEFRQKDLFAKRDYSQEDPKEVAAAKFDLNYIALDGSIGCMVN
GAGLAMATMDIIKLHGGDPANFLDVGGGATANAVKEAFKIITADPKVHVILVNIFGGIMR
CDVIAEGIIAATKELNLTLPIIVRLQGTNVNEAKELIRKSKLRILPKDDLDEAAMLSVHL
SQIVHLAREAHLNVLFELDPVHHH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g3235.t6 Coils Coil Coil 58 78 -
9 g3235.t6 Gene3D G3DSA:3.30.470.20 - 31 267 4.1E-82
10 g3235.t6 Gene3D G3DSA:3.30.1490.20 - 51 146 4.1E-82
11 g3235.t6 Gene3D G3DSA:3.40.50.261 - 276 423 1.4E-55
6 g3235.t6 Hamap MF_03220 Succinate–CoA ligase [ADP-forming] subunit beta, mitochondrial [SUCLA2]. 28 440 55.327637
5 g3235.t6 Hamap MF_00558 Succinate–CoA ligase [ADP-forming] subunit beta [sucC]. 31 422 37.584812
3 g3235.t6 PANTHER PTHR11815:SF10 SUCCINATE–COA LIGASE [ADP-FORMING] SUBUNIT BETA, MITOCHONDRIAL 22 425 2.5E-195
4 g3235.t6 PANTHER PTHR11815 SUCCINYL-COA SYNTHETASE BETA CHAIN 22 425 2.5E-195
13 g3235.t6 PIRSF PIRSF001554 SucCS_beta 31 428 4.4E-139
2 g3235.t6 Pfam PF08442 ATP-grasp domain 32 238 1.9E-66
1 g3235.t6 Pfam PF00549 CoA-ligase 298 415 2.3E-26
14 g3235.t6 ProSitePatterns PS01217 ATP-citrate lyase / succinyl-CoA ligases family signature 3. 293 317 -
16 g3235.t6 ProSiteProfiles PS50975 ATP-grasp fold profile. 39 266 11.198
7 g3235.t6 SUPERFAMILY SSF56059 Glutathione synthetase ATP-binding domain-like 31 274 1.95E-71
8 g3235.t6 SUPERFAMILY SSF52210 Succinyl-CoA synthetase domains 275 420 1.16E-52
15 g3235.t6 TIGRFAM TIGR01016 sucCoAbeta: succinate-CoA ligase, beta subunit 32 421 1.2E-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. There were no conditions that were differentially expressed