Detailed information of XP_074606270.1 in Acropora palmata

Genomic Location: NC_133893.1:17763638...17777226
NR annotation: XP_029201760.2, 26S proteasome non-ATPase regulatory subunit 14 [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
O0048726S proteasome non-ATPase regulatory subunit 14 OS=Homo sapiens OX=9606 GN=PSMD14 PE=1 SV=1
O3559326S proteasome non-ATPase regulatory subunit 14 OS=Mus musculus OX=10090 GN=Psmd14 PE=1 SV=2
Q9V3H226S proteasome non-ATPase regulatory subunit 14 OS=Drosophila melanogaster OX=7227 GN=Rpn11 PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0007033 (this species only) · gene tree & orthology
Ubiquitin familyUBD|Other|Jab_MPN · all ubiquitin genes in this species
Ubiquitin familyDUB|JAMM|JAMM · all ubiquitin genes in this species

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF01398
all species →		JABJAB1/Mov34/MPN/PAD-1 ubiquitin proteaseFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR050242
all species →		FamilyJAMM/MPN+ metalloenzymes, peptidase M67AInterproscan
IPR037518
all species →		DomainMPN domainInterproscan
IPR000555
all species →		DomainJAB1/MPN/MOV34 metalloenzyme domainInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR10410
all species →		EUKARYOTIC TRANSLATION INITIATION FACTOR 3 -RELATEDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0008237
all species →		Molecular Functionmetallopeptidase activityInterproscan
GO:0008541
all species →		Cellular Componentproteasome regulatory particle, lid subcomplexInterproscan
GO:0016579
all species →		Biological Processprotein deubiquitinationInterproscan
GO:0043161
all species →		Biological Processproteasome-mediated ubiquitin-dependent protein catabolic processInterproscan
GO:0070628
all species →		Molecular Functionproteasome bindingInterproscan
GO:0005515
all species →		Molecular Functionprotein bindingInterproscan
GO:0008233
all species →		Molecular Functionpeptidase activityInterproscan

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
K03030PSMD14, RPN11, POH1; 26S proteasome regulatory subunit N11-Proteasomeko03051deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of XP_074606270.1 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
70TPM > 0
2Conditions
104.8Max TPM
54.2Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
all_coral_tissue · exposed 46 38 47.73 99.10
all_coral_tissue · baseline 38 32 62.02 104.76

Per sample · hover a bar for the full sample record

Show the sample table (84 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR8800105 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 99.10
SRR8800068 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 86.71
SRR8800027 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 85.05
SRR8800044 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 81.52
SRR8800077 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 80.48
SRR8800100 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 78.13
SRR8800097 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 77.97
SRR8800051 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 77.27
SRR8800036 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 75.13
SRR8800099 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 74.63
SRR8800079 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 74.56
SRR8800092 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 71.20
SRR8800038 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 71.07
SRR8800080 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 70.01
SRR8800093 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 69.68
SRR8800071 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 68.66
SRR8800083 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 68.02
SRR8800045 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 64.27
SRR8800053 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 63.41
SRR8800034 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 62.82
SRR8800073 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 59.77
SRR8800033 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 56.84
SRR8800095 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 47.65
SRR8800058 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 46.73
SRR8800063 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 45.33
SRR8800060 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 43.19
SRR8800065 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 41.64
SRR8800094 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 39.19
SRR8800089 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 39.17
SRR8800040 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 38.39
SRR8800062 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 37.17
SRR8800047 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 33.76
SRR8800087 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 32.07
SRR8800026 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 30.36
SRR8800088 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 29.58
SRR8800091 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 26.76
SRR8800107 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 24.36
SRR8800061 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 23.78
SRR8800028 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
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
SRR8800056 all_coral_tissue · exposed all_coral_tissue not recorded exposed SRP189781 0.00
SRR8800066 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
SRR8800103 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 104.76
SRR8800041 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 95.48
SRR8800037 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 94.58
SRR8800101 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 93.59
SRR8800108 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 92.81
SRR8800035 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 92.34
SRR8800106 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 90.92
SRR8800043 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 85.71
SRR8800081 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 85.22
SRR8800049 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 83.44
SRR8800050 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 83.11
SRR8800057 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 82.96
SRR8800048 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 82.94
SRR8800078 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 82.48
SRR8800098 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 81.21
SRR8800074 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 81.13
SRR8800082 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 78.13
SRR8800096 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 77.82
SRR8800032 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 77.02
SRR8800072 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 74.79
SRR8800069 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 74.70
SRR8800076 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 73.91
SRR8800109 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 72.03
SRR8800104 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 63.90
SRR8800067 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 62.18
SRR8800031 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 51.75
SRR8800102 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 46.70
SRR8800070 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 46.01
SRR8800064 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 41.12
SRR8800090 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 40.54
SRR8800085 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 34.33
SRR8800084 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 29.18
SRR8800030 all_coral_tissue · baseline all_coral_tissue not recorded baseline SRP189781 0.00
SRR8800046 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
SRR8800059 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 correlated18XP_074613085.10.868275655102646
Negatively correlated3XP_074631570.1-0.630854274098244

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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