Detailed information of XP_074633129.1 in Acropora palmata

Genomic Location: NC_133890.1:3800683...3809881
NR annotation: XP_029183973.2, succinate--CoA ligase [ADP-forming] subunit beta, mitochondrial-like [Acropora millepora]
Species Acropora palmata · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q9YI37Succinate--CoA ligase [ADP-forming] subunit beta, mitochondrial (Fragment) OS=Columba livia OX=8932 GN=SUCLA2 PE=1 SV=1
O97580Succinate--CoA ligase [ADP-forming] subunit beta, mitochondrial (Fragment) OS=Sus scrofa OX=9823 GN=SUCLA2 PE=2 SV=1
Q148D5Succinate--CoA ligase [ADP-forming] subunit beta, mitochondrial OS=Bos taurus OX=9913 GN=SUCLA2 PE=2 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0001647 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00549
all species →		Ligase_CoACoA-ligaseDomainInterproscan
PF08442
all species →		ATP-grasp_2ATP-grasp domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR005809
all species →		FamilySuccinate--CoA ligase-like, beta subunitInterproscan
IPR005811
all species →		DomainATP-citrate synthase/succinyl-CoA ligase, C-terminal domainInterproscan
IPR013650
all species →		DomainATP-grasp fold, succinyl-CoA synthetase-typeInterproscan
IPR034723
all species →		FamilySuccinate--CoA ligase [ADP-forming] subunit beta, mitochondrialInterproscan
IPR016102
all species →		Homologous_superfamilySuccinyl-CoA synthetase-likeInterproscan
IPR017866
all species →		Conserved_siteSuccinyl-CoA synthetase, beta subunit, conserved siteInterproscan
IPR013815
all species →		Homologous_superfamilyATP-grasp fold, subdomain 1Interproscan

 PANTHER
PANTHER termDescriptionSource
PTHR11815
all species →		SUCCINYL-COA SYNTHETASE BETA CHAINInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0004775
all species →		Molecular Functionsuccinate-CoA ligase (ADP-forming) activityInterproscan
GO:0005739
all species →		Cellular ComponentmitochondrionInterproscan
GO:0006099
all species →		Biological Processtricarboxylic acid cycleInterproscan
GO:0006104
all species →		Biological Processsuccinyl-CoA metabolic processInterproscan
GO:0042709
all species →		Cellular Componentsuccinate-CoA ligase complexInterproscan
GO:0003824
all species →		Molecular Functioncatalytic activityInterproscan
GO:0005524
all species →		Molecular FunctionATP bindingInterproscan

Search by domain instead of by gene. Any accession above (InterPro, Pfam, PANTHER, GO, KEGG) can be used as a query on the Functional Domain Search page, which searches all 148 annotated genomes at once.
 KEGG pathway
KOEnzymeEnzyme IDPathwayMap IDSource
K01900LSC2; succinyl-CoA synthetase beta subunitEC:6.2.1.4
EC:6.2.1.5
Exosomeko04147deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of XP_074633129.1 across 84 RNA-seq samples of Acropora palmata. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.

84Samples
75TPM > 0
2Conditions
147.2Max TPM
67.7Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
all_coral_tissue · exposed 46 41 60.30 124.28
all_coral_tissue · baseline 38 34 76.56 147.16

Per sample · hover a bar for the full sample record

Show the sample table (84 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR8800066 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 124.28
SRR8800092 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 109.76
SRR8800071 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 107.07
SRR8800077 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 100.97
SRR8800068 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 100.52
SRR8800105 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 97.49
SRR8800044 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 94.68
SRR8800051 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 94.43
SRR8800053 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 94.07
SRR8800097 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 89.33
SRR8800080 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 85.28
SRR8800083 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 82.85
SRR8800100 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 81.57
SRR8800036 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 79.06
SRR8800079 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 77.66
SRR8800093 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 77.32
SRR8800034 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 73.63
SRR8800056 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 72.73
SRR8800047 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 72.50
SRR8800099 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 71.65
SRR8800028 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 71.23
SRR8800038 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 70.08
SRR8800063 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 65.50
SRR8800107 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 64.69
SRR8800033 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 62.83
SRR8800045 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 61.67
SRR8800073 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 58.72
SRR8800060 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 58.10
SRR8800058 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 52.56
SRR8800065 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 48.85
SRR8800091 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 46.75
SRR8800095 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 45.86
SRR8800089 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 41.25
SRR8800062 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 40.88
SRR8800061 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 38.99
SRR8800040 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 35.01
SRR8800027 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 29.97
SRR8800087 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 25.39
SRR8800094 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 25.26
SRR8800088 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 23.80
SRR8800026 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 19.39
SRR8800029 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800039 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800042 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800075 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800086 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800035 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 147.16
SRR8800046 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 118.42
SRR8800108 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 106.81
SRR8800050 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 105.45
SRR8800096 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 105.24
SRR8800049 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 99.04
SRR8800057 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 95.98
SRR8800078 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 94.94
SRR8800082 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 94.92
SRR8800109 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 94.59
SRR8800069 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 93.20
SRR8800072 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 92.43
SRR8800102 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 92.33
SRR8800076 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 91.42
SRR8800032 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 90.91
SRR8800048 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 90.59
SRR8800037 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 90.16
SRR8800043 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 89.23
SRR8800081 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 87.92
SRR8800067 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 86.77
SRR8800041 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 86.70
SRR8800070 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 83.76
SRR8800074 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 80.34
SRR8800101 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 79.96
SRR8800098 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 79.89
SRR8800106 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 75.88
SRR8800104 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 71.08
SRR8800059 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 70.66
SRR8800103 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 66.48
SRR8800031 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 64.63
SRR8800064 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 49.40
SRR8800090 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 48.54
SRR8800084 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 46.76
SRR8800085 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 37.58
SRR8800030 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800052 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800054 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800055 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00

Source: CnidoSite RNA-seq expression matrices (APALM_TPM, StringTie quantification over 84 runs), joined to SRA sample metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped by the descriptor carried in the expression matrix itself.

Co-expression network

Genes whose expression across the transcriptome samples of Acropora palmata tracks this one. Counts are over the whole network; the network view itself draws at most 100 partners per query gene (CNIDO_NET_TOP_K), so a hub gene can show fewer edges than the number below.

DirectionPartnersMost correlated partnerPCC
Positively correlated16XP_074624809.10.834769560072094
Negatively correlated4XP_074627945.1-0.596776942109304

Open this gene in Network Analysis → The network opens with the gene already entered and both directions selected. There you can add up to 9 more genes, switch between the positive and negative network, and export the edge list.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Acropora palmata, and in which cell types it is a marker. Expression is stored per cell, so the violin plot and the cell-type means are computed in the viewer — open a dataset to see them.

No single-cell dataset has been published for this species. The atlases that do exist are listed in the Cell Atlas.

Epigenetic marks

Chromatin and DNA-methylation data covering this gene. Peak calls are listed per sample with the genomic region the peak falls in; DNA methylation is listed as sample availability only, because those tables are queried by the DNA Methylation page itself.

DNA methylation (bisulphite samples)

SampleMethylation profile
Polyp_Underside_Control_2open
Polyp_Underside_Control_3open
Polyp_Underside_Treatment_1open
Polyp_Upperside_Control_1open
Polyp_Upperside_Treatment_3open
Polyp_Upperside_Treatment_4open

The DNA Methylation page locates this gene by scanning the bisulphite table, which holds one row per cytosine. For the largest datasets that scan takes a while to return; it does not mean the link is broken.

What you can do with this gene

Every tool below opens with this gene already entered, so you land on the analysis rather than on an empty form. Links open in a new tab.

AnalysisWhat it doesStatus
Primer designDesign PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.template foundopen →
BLASTSearch this gene’s sequence against the CnidoSite BLAST databases. The query is filled in and the species’ database is preselected — press Run to start.template foundopen →
Expression heatmapDraw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it.readyopen →
Gene family / orthogroupLook this gene up in the single-copy orthogroups built from the high-quality cnidarian genomes, and see which other species carry an orthologue.open →
Gene set analysisStart a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.open →
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