Detailed information of OS493_010673-T1 in Lophelia pertusa

Genomic Location: scaffold_26:2105436...2110001
NR annotation: KAJ7386269.1, hypothetical protein OS493_010673 [Desmophyllum pertusum]
Species Lophelia pertusa · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
P51128Retinoic acid receptor RXR-alpha OS=Xenopus laevis OX=8355 GN=rxra PE=1 SV=1
P28700Retinoic acid receptor RXR-alpha OS=Mus musculus OX=10090 GN=Rxra PE=1 SV=1
Q05343Retinoic acid receptor RXR-alpha OS=Rattus norvegicus OX=10116 GN=Rxra PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0000188 (this species only) · gene tree & orthology
Transcription factor familyESR-like · all TF in this species
Transcription factor familyNGFIB-like · all TF in this species
Transcription factor familyRXR-like · all TF in this species
Transcription factor familySF-like · all TF in this species
Transcription factor familyTHR-like · all TF in this species
Transcription factor familyGCNF-like · all TF in this species

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00105
all species →		zf-C4Zinc finger, C4 type (two domains)DomainInterproscan
PF00104
all species →		Hormone_recepLigand-binding domain of nuclear hormone receptorDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR001628
all species →		DomainZinc finger, nuclear hormone receptor-typeInterproscan
IPR001723
all species →		FamilyNuclear hormone receptorInterproscan
IPR035500
all species →		Homologous_superfamilyNuclear hormone receptor-like domain superfamilyInterproscan
IPR000536
all species →		DomainNuclear hormone receptor, ligand-binding domainInterproscan
IPR013088
all species →		Homologous_superfamilyZinc finger, NHR/GATA-typeInterproscan
IPR050200
all species →		FamilyNuclear hormone receptor family NR3 subfamilyInterproscan
IPR003070
all species →		FamilyNuclear receptor subfamily 4 group A member 1-3Interproscan

 PANTHER
PANTHER termDescriptionSource
PTHR48092
all species →		KNIRPS-RELATED PROTEIN-RELATEDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0003700
all species →		Molecular FunctionDNA-binding transcription factor activityInterproscan
GO:0006355
all species →		Biological Processregulation of DNA-templated transcriptionInterproscan
GO:0008270
all species →		Molecular Functionzinc ion bindingInterproscan
GO:0043565
all species →		Molecular Functionsequence-specific DNA bindingInterproscan
GO:0000790
all species →		Cellular ComponentchromatinInterproscan
GO:0004879
all species →		Molecular Functionnuclear receptor activityInterproscan
GO:0005634
all species →		Cellular ComponentnucleusInterproscan
GO:0006357
all species →		Biological Processregulation of transcription by RNA polymerase IIInterproscan
GO:0034056
all species →		Molecular Functionestrogen response element bindingInterproscan
GO:0003677
all species →		Molecular FunctionDNA 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
K08554NR3B3, ESRRG; estrogen-related receptor gamma-Nuclear receptorsko03310deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of OS493_010673-T1 across 110 RNA-seq samples of Lophelia pertusa. 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.

110Samples
110TPM > 0
7Conditions
23.3Max TPM
8.7Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
polyp at pH7 9 18 18 7.26 11.33
polyp at pH7 6 18 18 7.25 12.46
coral polyp · control treatment 16 16 11.18 23.31
coral polyp · oil and dispersant treatment 16 16 10.00 16.46
coral polyp · oil treatment 16 16 9.04 15.68
coral polyp · dispersant treatment 16 16 9.55 21.78
Polyp 10 10 6.16 8.60

Per sample · hover a bar for the full sample record

Show the sample table (110 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR11359523 polyp at pH7 9 not recorded not recorded not recorded - 11.33
SRR11359494 polyp at pH7 9 not recorded not recorded not recorded - 10.78
SRR11359519 polyp at pH7 9 not recorded not recorded not recorded - 10.52
SRR11359522 polyp at pH7 9 not recorded not recorded not recorded - 9.79
SRR11359495 polyp at pH7 9 not recorded not recorded not recorded - 8.61
SRR11359498 polyp at pH7 9 not recorded not recorded not recorded - 7.85
SRR11359497 polyp at pH7 9 not recorded not recorded not recorded - 7.34
SRR11359521 polyp at pH7 9 not recorded not recorded not recorded - 7.01
SRR11359520 polyp at pH7 9 not recorded not recorded not recorded - 6.78
SRR11359499 polyp at pH7 9 not recorded not recorded not recorded - 6.67
SRR11359506 polyp at pH7 9 not recorded not recorded not recorded - 6.36
SRR11359511 polyp at pH7 9 not recorded not recorded not recorded - 6.22
SRR11359510 polyp at pH7 9 not recorded not recorded not recorded - 6.07
SRR11359496 polyp at pH7 9 not recorded not recorded not recorded - 6.06
SRR11359508 polyp at pH7 9 not recorded not recorded not recorded - 5.30
SRR11359507 polyp at pH7 9 not recorded not recorded not recorded - 5.24
SRR11359509 polyp at pH7 9 not recorded not recorded not recorded - 4.93
SRR11359518 polyp at pH7 9 not recorded not recorded not recorded - 3.78
SRR11359527 polyp at pH7 6 not recorded not recorded not recorded - 12.46
SRR11359526 polyp at pH7 6 not recorded not recorded not recorded - 11.89
SRR11359515 polyp at pH7 6 not recorded not recorded not recorded - 10.08
SRR11359514 polyp at pH7 6 not recorded not recorded not recorded - 9.61
SRR11359528 polyp at pH7 6 not recorded not recorded not recorded - 9.09
SRR11359513 polyp at pH7 6 not recorded not recorded not recorded - 8.89
SRR11359529 polyp at pH7 6 not recorded not recorded not recorded - 7.04
SRR11359503 polyp at pH7 6 not recorded not recorded not recorded - 6.99
SRR11359524 polyp at pH7 6 not recorded not recorded not recorded - 6.51
SRR11359525 polyp at pH7 6 not recorded not recorded not recorded - 6.48
SRR11359512 polyp at pH7 6 not recorded not recorded not recorded - 6.32
SRR11359502 polyp at pH7 6 not recorded not recorded not recorded - 6.09
SRR11359504 polyp at pH7 6 not recorded not recorded not recorded - 5.67
SRR11359505 polyp at pH7 6 not recorded not recorded not recorded - 5.44
SRR11359516 polyp at pH7 6 not recorded not recorded not recorded - 5.34
SRR11359517 polyp at pH7 6 not recorded not recorded not recorded - 5.08
SRR11359500 polyp at pH7 6 not recorded not recorded not recorded - 4.82
SRR11359501 polyp at pH7 6 not recorded not recorded not recorded - 2.70
SRR16705957 coral polyp · control treatment coral polyp polyp control treatment SRP344271 23.31
SRR16705965 coral polyp · control treatment coral polyp polyp control treatment SRP344271 17.92
SRR16705946 coral polyp · control treatment coral polyp polyp control treatment SRP344271 14.27
SRR16705960 coral polyp · control treatment coral polyp polyp control treatment SRP344271 14.06
SRR16705942 coral polyp · control treatment coral polyp polyp control treatment SRP344271 12.39
SRR16705974 coral polyp · control treatment coral polyp polyp control treatment SRP344271 12.20
SRR16705972 coral polyp · control treatment coral polyp polyp control treatment SRP344271 11.79
SRR16705990 coral polyp · control treatment coral polyp polyp control treatment SRP344271 11.06
SRR16705943 coral polyp · control treatment coral polyp polyp control treatment SRP344271 10.97
SRR16705975 coral polyp · control treatment coral polyp polyp control treatment SRP344271 9.88
SRR16705971 coral polyp · control treatment coral polyp polyp control treatment SRP344271 9.82
SRR16705991 coral polyp · control treatment coral polyp polyp control treatment SRP344271 9.06
SRR16705973 coral polyp · control treatment coral polyp polyp control treatment SRP344271 8.93
SRR16705989 coral polyp · control treatment coral polyp polyp control treatment SRP344271 5.99
SRR16705970 coral polyp · control treatment coral polyp polyp control treatment SRP344271 4.75
SRR16705992 coral polyp · control treatment coral polyp polyp control treatment SRP344271 2.41
SRR16705995 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 16.46
SRR16706004 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 15.57
SRR16705976 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 12.72
SRR16705944 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 12.52
SRR16705979 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 10.71
SRR16705997 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 10.45
SRR16705977 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 10.22
SRR16705945 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 9.92
SRR16706005 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 9.35
SRR16705948 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 8.97
SRR16705947 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 8.85
SRR16705978 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 8.30
SRR16705993 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 8.21
SRR16705996 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 7.14
SRR16705982 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 6.88
SRR16705994 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 3.76
SRR16706001 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 15.68
SRR16705949 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 14.73
SRR16705998 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 11.64
SRR16705950 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 11.36
SRR16705999 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 11.17
SRR16705952 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 11.08
SRR16706000 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 10.87
SRR16705981 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 10.70
SRR16705951 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 8.88
SRR16705983 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 8.85
SRR16705980 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 7.88
SRR16705961 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 6.91
SRR16705984 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 6.32
SRR16705963 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 3.99
SRR16705964 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 2.94
SRR16705962 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 1.62
SRR16706003 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 21.78
SRR16705988 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 14.00
SRR16705969 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 12.21
SRR16705958 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 11.39
SRR16706002 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 11.34
SRR16705967 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 10.83
SRR16705966 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 10.30
SRR16705954 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 10.01
SRR16705987 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 8.91
SRR16705959 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 8.91
SRR16705956 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 8.35
SRR16705955 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 8.31
SRR16705968 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 6.82
SRR16705953 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 3.29
SRR16705986 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 3.23
SRR16705985 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 3.05
SRR7746668 Polyp not recorded not recorded not recorded - 8.60
SRR23025710 Polyp not recorded not recorded not recorded - 8.43
SRR23025713 Polyp not recorded not recorded not recorded - 8.33
SRR7746669 Polyp not recorded not recorded not recorded - 7.14
SRR7746667 Polyp not recorded not recorded not recorded - 5.99
SRR23025711 Polyp not recorded not recorded not recorded - 5.35
SRR23025709 Polyp not recorded not recorded not recorded - 5.01
SRR7746666 Polyp not recorded not recorded not recorded - 4.49
SRR23025712 Polyp not recorded not recorded not recorded - 4.43
SRR23025708 Polyp not recorded not recorded not recorded - 3.82

Source: CnidoSite RNA-seq expression matrices (LPERT_TPM, StringTie quantification over 110 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 Lophelia pertusa 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 correlated4OS493_027447-T10.736787853526013
Negatively correlated3OS493_013112-T1-0.594886233189061

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 Lophelia pertusa, 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.

No epigenomic data has been deposited for this species. The assays that exist across the site are described in the Epigenomic Data module.

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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