Detailed information of OS493_008993-T1 in Lophelia pertusa

Genomic Location: scaffold_21:2531177...2542722
NR annotation: KAJ7380527.1, Cysteine and histidine-rich protein 1 [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
Q08CH8Zinc finger TRAF-type-containing protein 1 OS=Danio rerio OX=7955 GN=zftraf1 PE=2 SV=2
Q6GNX1Zinc finger TRAF-type-containing protein 1-A OS=Xenopus laevis OX=8355 GN=zftraf1-a PE=2 SV=2
P0DW87Zinc finger TRAF-type-containing protein 1 OS=Mus musculus OX=10090 GN=Zftraf1 PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0006932 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF02176
all species →		zf-TRAFTRAF-type zinc fingerFamilyInterproscan
PF21362
all species →		Sina_RINGE3 ubiquitin-protein ligase sina/sinah, RING fingerDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR013083
all species →		Homologous_superfamilyZinc finger, RING/FYVE/PHD-typeInterproscan
IPR039338
all species →		FamilyZinc finger TRAF-type-containing protein 1Interproscan
IPR001841
all species →		DomainZinc finger, RING-typeInterproscan
IPR001293
all species →		DomainZinc finger, TRAF-typeInterproscan
IPR049548
all species →		DomainE3 ubiquitin-protein ligase Sina-like, RING fingerInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR23059
all species →		CYSTEINE AND HISTIDINE-RICH PROTEIN 1Interproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005634
all species →		Cellular ComponentnucleusInterproscan
GO:0008270
all species →		Molecular Functionzinc ion 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
No KEGG orthology assignment for OS493_008993-T1.

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

Expression pattern (RNA-seq)

Transcript abundance of OS493_008993-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
241.4Max TPM
102.1Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
polyp at pH7 9 18 18 96.94 138.65
polyp at pH7 6 18 18 80.20 112.74
coral polyp · control treatment 16 16 112.02 167.67
coral polyp · oil and dispersant treatment 16 16 143.00 241.43
coral polyp · oil treatment 16 16 117.12 214.25
coral polyp · dispersant treatment 16 16 74.61 111.94
Polyp 10 10 89.80 176.09

Per sample · hover a bar for the full sample record

Show the sample table (110 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR11359521 polyp at pH7 9 not recorded not recorded not recorded - 138.65
SRR11359520 polyp at pH7 9 not recorded not recorded not recorded - 138.60
SRR11359510 polyp at pH7 9 not recorded not recorded not recorded - 112.27
SRR11359499 polyp at pH7 9 not recorded not recorded not recorded - 108.01
SRR11359511 polyp at pH7 9 not recorded not recorded not recorded - 107.13
SRR11359498 polyp at pH7 9 not recorded not recorded not recorded - 106.43
SRR11359523 polyp at pH7 9 not recorded not recorded not recorded - 101.66
SRR11359518 polyp at pH7 9 not recorded not recorded not recorded - 101.28
SRR11359496 polyp at pH7 9 not recorded not recorded not recorded - 98.05
SRR11359522 polyp at pH7 9 not recorded not recorded not recorded - 94.99
SRR11359519 polyp at pH7 9 not recorded not recorded not recorded - 93.98
SRR11359497 polyp at pH7 9 not recorded not recorded not recorded - 92.87
SRR11359508 polyp at pH7 9 not recorded not recorded not recorded - 87.06
SRR11359509 polyp at pH7 9 not recorded not recorded not recorded - 80.77
SRR11359495 polyp at pH7 9 not recorded not recorded not recorded - 79.09
SRR11359494 polyp at pH7 9 not recorded not recorded not recorded - 71.44
SRR11359506 polyp at pH7 9 not recorded not recorded not recorded - 67.63
SRR11359507 polyp at pH7 9 not recorded not recorded not recorded - 65.07
SRR11359501 polyp at pH7 6 not recorded not recorded not recorded - 112.74
SRR11359500 polyp at pH7 6 not recorded not recorded not recorded - 105.32
SRR11359503 polyp at pH7 6 not recorded not recorded not recorded - 92.77
SRR11359502 polyp at pH7 6 not recorded not recorded not recorded - 91.21
SRR11359504 polyp at pH7 6 not recorded not recorded not recorded - 87.78
SRR11359526 polyp at pH7 6 not recorded not recorded not recorded - 87.20
SRR11359515 polyp at pH7 6 not recorded not recorded not recorded - 87.13
SRR11359505 polyp at pH7 6 not recorded not recorded not recorded - 87.11
SRR11359527 polyp at pH7 6 not recorded not recorded not recorded - 85.62
SRR11359514 polyp at pH7 6 not recorded not recorded not recorded - 84.96
SRR11359517 polyp at pH7 6 not recorded not recorded not recorded - 78.56
SRR11359528 polyp at pH7 6 not recorded not recorded not recorded - 78.25
SRR11359516 polyp at pH7 6 not recorded not recorded not recorded - 76.87
SRR11359529 polyp at pH7 6 not recorded not recorded not recorded - 72.47
SRR11359524 polyp at pH7 6 not recorded not recorded not recorded - 62.82
SRR11359512 polyp at pH7 6 not recorded not recorded not recorded - 54.33
SRR11359513 polyp at pH7 6 not recorded not recorded not recorded - 53.58
SRR11359525 polyp at pH7 6 not recorded not recorded not recorded - 44.81
SRR16705970 coral polyp · control treatment coral polyp polyp control treatment SRP344271 167.67
SRR16705942 coral polyp · control treatment coral polyp polyp control treatment SRP344271 161.08
SRR16705971 coral polyp · control treatment coral polyp polyp control treatment SRP344271 153.94
SRR16705991 coral polyp · control treatment coral polyp polyp control treatment SRP344271 135.62
SRR16705943 coral polyp · control treatment coral polyp polyp control treatment SRP344271 135.02
SRR16705990 coral polyp · control treatment coral polyp polyp control treatment SRP344271 115.47
SRR16705974 coral polyp · control treatment coral polyp polyp control treatment SRP344271 115.12
SRR16705972 coral polyp · control treatment coral polyp polyp control treatment SRP344271 111.55
SRR16705973 coral polyp · control treatment coral polyp polyp control treatment SRP344271 109.34
SRR16705989 coral polyp · control treatment coral polyp polyp control treatment SRP344271 105.56
SRR16705975 coral polyp · control treatment coral polyp polyp control treatment SRP344271 98.88
SRR16705992 coral polyp · control treatment coral polyp polyp control treatment SRP344271 95.47
SRR16705965 coral polyp · control treatment coral polyp polyp control treatment SRP344271 77.92
SRR16705960 coral polyp · control treatment coral polyp polyp control treatment SRP344271 74.67
SRR16705946 coral polyp · control treatment coral polyp polyp control treatment SRP344271 68.14
SRR16705957 coral polyp · control treatment coral polyp polyp control treatment SRP344271 66.87
SRR16705947 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 241.43
SRR16705996 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 228.29
SRR16705994 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 205.12
SRR16705978 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 177.04
SRR16705945 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 171.30
SRR16705944 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 157.09
SRR16705977 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 145.57
SRR16705979 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 132.21
SRR16705976 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 128.08
SRR16705995 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 121.52
SRR16706004 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 121.41
SRR16705948 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 110.87
SRR16705997 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 98.86
SRR16705982 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 94.71
SRR16705993 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 83.95
SRR16706005 coral polyp · oil and dispersant treatment coral polyp polyp oil and dispersant treatment SRP344271 70.50
SRR16705962 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 214.25
SRR16705963 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 182.72
SRR16705961 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 168.99
SRR16705951 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 131.74
SRR16705980 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 126.71
SRR16705983 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 121.78
SRR16705981 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 117.23
SRR16705964 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 112.79
SRR16705952 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 110.78
SRR16705949 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 102.09
SRR16705998 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 99.57
SRR16705984 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 92.19
SRR16706001 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 79.18
SRR16706000 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 78.13
SRR16705999 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 72.93
SRR16705950 coral polyp · oil treatment coral polyp polyp oil treatment SRP344271 62.82
SRR16705985 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 111.94
SRR16705987 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 94.63
SRR16705959 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 91.97
SRR16706003 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 84.49
SRR16705986 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 80.49
SRR16705969 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 75.50
SRR16705955 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 75.44
SRR16705967 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 74.57
SRR16705954 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 72.40
SRR16705968 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 71.09
SRR16705958 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 70.69
SRR16705988 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 67.53
SRR16705956 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 59.84
SRR16705966 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 59.17
SRR16706002 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 52.37
SRR16705953 coral polyp · dispersant treatment coral polyp polyp dispersant treatment SRP344271 51.62
SRR23025711 Polyp not recorded not recorded not recorded - 176.09
SRR23025708 Polyp not recorded not recorded not recorded - 138.78
SRR23025710 Polyp not recorded not recorded not recorded - 105.83
SRR23025709 Polyp not recorded not recorded not recorded - 94.33
SRR23025712 Polyp not recorded not recorded not recorded - 87.09
SRR23025713 Polyp not recorded not recorded not recorded - 79.94
SRR7746666 Polyp not recorded not recorded not recorded - 64.78
SRR7746669 Polyp not recorded not recorded not recorded - 57.16
SRR7746667 Polyp not recorded not recorded not recorded - 49.89
SRR7746668 Polyp not recorded not recorded not recorded - 44.06

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 correlated10OS493_015086-T10.782668740928512
Negatively correlated13OS493_032702-T1-0.516135620350344

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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