Detailed information of XP_074638984.1 in Acropora palmata

Genomic Location: NC_133892.1:13069205...13077577
NR annotation: XP_029198763.1, ATP synthase subunit d, 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
P31399ATP synthase peripheral stalk subunit d, mitochondrial OS=Rattus norvegicus OX=10116 GN=Atp5pd PE=1 SV=3
O75947ATP synthase peripheral stalk subunit d, mitochondrial OS=Homo sapiens OX=9606 GN=ATP5PD PE=1 SV=3
Q9DCX2ATP synthase peripheral stalk subunit d, mitochondrial OS=Mus musculus OX=10090 GN=Atp5pd PE=1 SV=3
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0007282 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF05873
all species →		Mt_ATP-synt_DATP synthase D chain, mitochondrial (ATP5H)FamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR036228
all species →		Homologous_superfamilyATP synthase, F0 complex, subunit D superfamily, mitochondrialInterproscan
IPR008689
all species →		FamilyATP synthase, F0 complex, subunit D, mitochondrialInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR12700
all species →		ATP SYNTHASE SUBUNIT D, MITOCHONDRIALInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0000276
all species →		Cellular Componentobsolete mitochondrial proton-transporting ATP synthase complex, coupling factor F(o)Interproscan
GO:0015078
all species →		Molecular Functionproton transmembrane transporter activityInterproscan
GO:0015986
all species →		Biological Processproton motive force-driven ATP synthesisInterproscan
GO:0000274
all species →		Cellular Componentobsolete mitochondrial proton-transporting ATP synthase, stator stalkInterproscan
GO:0046933
all species →		Molecular Functionproton-transporting ATP synthase activity, rotational mechanismInterproscan

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
K02138ATPeF0D, ATP5H, ATP7; F-type H+-transporting ATPase subunit d-Diabetic cardiomyopathyko05415deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of XP_074638984.1 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
81TPM > 0
2Conditions
1,530.3Max TPM
578.1Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
all_coral_tissue · exposed 46 45 630.15 1,530.35
all_coral_tissue · baseline 38 36 515.06 1,200.15

Per sample · hover a bar for the full sample record

Show the sample table (84 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR8800086 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 1,530.35
SRR8800027 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 1,320.05
SRR8800028 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 1,314.32
SRR8800088 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 1,273.50
SRR8800040 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 1,171.02
SRR8800107 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 1,105.49
SRR8800089 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 1,055.77
SRR8800087 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 1,046.85
SRR8800060 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 1,023.00
SRR8800058 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 1,011.59
SRR8800095 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 978.14
SRR8800091 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 935.74
SRR8800065 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 895.76
SRR8800063 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 864.86
SRR8800047 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 809.41
SRR8800062 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 771.33
SRR8800094 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 765.24
SRR8800061 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 741.75
SRR8800026 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 679.87
SRR8800092 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 584.56
SRR8800039 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 550.07
SRR8800029 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 544.97
SRR8800033 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 515.75
SRR8800038 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 482.35
SRR8800100 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 421.50
SRR8800083 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 411.78
SRR8800045 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 392.15
SRR8800068 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 385.09
SRR8800079 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 382.13
SRR8800042 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 379.57
SRR8800071 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 375.70
SRR8800105 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 370.43
SRR8800036 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 365.60
SRR8800099 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 346.72
SRR8800077 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 321.43
SRR8800073 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 321.16
SRR8800075 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 321.02
SRR8800097 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 315.89
SRR8800080 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 314.37
SRR8800051 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 302.85
SRR8800093 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 296.12
SRR8800034 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 268.24
SRR8800053 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 251.81
SRR8800056 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 239.45
SRR8800044 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 232.25
SRR8800066 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800084 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 1,200.15
SRR8800046 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 1,073.03
SRR8800102 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 1,067.15
SRR8800059 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 1,046.38
SRR8800031 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 1,008.73
SRR8800064 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 973.60
SRR8800055 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 942.95
SRR8800085 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 868.57
SRR8800030 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 845.14
SRR8800103 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 666.75
SRR8800070 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 610.97
SRR8800090 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 550.78
SRR8800049 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 473.14
SRR8800048 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 461.78
SRR8800104 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 441.76
SRR8800098 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 431.54
SRR8800106 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 422.93
SRR8800081 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 418.79
SRR8800072 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 413.74
SRR8800078 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 409.01
SRR8800037 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 404.13
SRR8800109 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 371.68
SRR8800101 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 370.99
SRR8800041 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 358.07
SRR8800032 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 357.76
SRR8800082 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 351.87
SRR8800050 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 343.88
SRR8800035 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 339.49
SRR8800043 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 303.92
SRR8800069 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 301.13
SRR8800067 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 300.23
SRR8800096 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 299.38
SRR8800074 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 293.12
SRR8800057 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 287.49
SRR8800108 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 283.83
SRR8800076 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 278.34
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

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 correlated30XP_074609999.10.891705620435944
Negatively correlated96XP_074619977.1-0.827562063367088

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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