Detailed information of XP_068698886.1 in Montipora foliosa

Genomic Location: chr3:20856575...20873434
NR annotation: XP_027040351.1, zinc finger CCHC-type and RNA-binding motif-containing protein 1-like [Pocillopora damicornis]
Species Montipora foliosa · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q56JZ7Zinc finger CCHC-type and RNA-binding motif-containing protein 1 OS=Bos taurus OX=9913 GN=ZCRB1 PE=2 SV=1
Q8TBF4Zinc finger CCHC-type and RNA-binding motif-containing protein 1 OS=Homo sapiens OX=9606 GN=ZCRB1 PE=1 SV=2
Q499V6Zinc finger CCHC-type and RNA-binding motif-containing protein 1 OS=Rattus norvegicus OX=10116 GN=Zcrb1 PE=2 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0007054 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00098
all species →		zf-CCHCZinc knuckleDomainInterproscan
PF00076
all species →		RRM_1RNA recognition motifDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR001878
all species →		DomainZinc finger, CCHC-typeInterproscan
IPR035979
all species →		Homologous_superfamilyRNA-binding domain superfamilyInterproscan
IPR000504
all species →		DomainRNA recognition motif domainInterproscan
IPR034219
all species →		DomainZCRB1, RNA recognition motifInterproscan
IPR036875
all species →		Homologous_superfamilyZinc finger, CCHC-type superfamilyInterproscan
IPR044598
all species →		FamilyZinc finger CCHC-type and RNA-binding motif-containing protein 1Interproscan
IPR012677
all species →		Homologous_superfamilyNucleotide-binding alpha-beta plait domain superfamilyInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR46259
all species →		ZINC FINGER CCHC-TYPE AND RNA-BINDING MOTIF-CONTAINING PROTEIN 1Interproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0003676
all species →		Molecular Functionnucleic acid bindingInterproscan
GO:0008270
all species →		Molecular Functionzinc ion bindingInterproscan
GO:0003723
all species →		Molecular FunctionRNA bindingInterproscan
GO:0000398
all species →		Biological ProcessmRNA splicing, via spliceosomeInterproscan
GO:0005689
all species →		Cellular ComponentU12-type spliceosomal complexInterproscan

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
K13154ZCRB1; U11/U12 small nuclear ribonucleoprotein 31 kDa protein-Spliceosomeko03041deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of XP_068698886.1 across 36 RNA-seq samples of Montipora foliosa. 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.

36Samples
30TPM > 0
1Conditions
155.6Max TPM
63.7Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Polyps 36 30 63.71 155.56

Per sample · hover a bar for the full sample record

Show the sample table (36 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR12786903 Polyps Polyps OA4 day0 not recorded SRP199550 155.56
SRR12904780 Polyps Polyps not recorded not recorded SRP199550 119.79
SRR27940180 Polyps Polyps not recorded not recorded SRP199550 119.14
SRR12904792 Polyps Polyps not recorded not recorded SRP199550 102.69
SRR27940179 Polyps Polyps not recorded not recorded SRP199550 102.56
SRR27940177 Polyps Polyps not recorded not recorded SRP199550 94.19
SRR12904791 Polyps Polyps not recorded not recorded SRP199550 93.51
SRR12959237 Polyps Polyps E4 day0 not recorded SRP199550 85.32
SRR12959185 Polyps Polyps E4 day21 not recorded SRP199550 83.83
SRR12959224 Polyps Polyps E4 day3 not recorded SRP199550 79.16
SRR12959181 Polyps Polyps E4 day0 not recorded SRP199550 77.32
SRR12959211 Polyps Polyps E4 day9 not recorded SRP199550 76.61
SRR12959238 Polyps Polyps E4 day0 not recorded SRP199550 75.92
SRR12786904 Polyps Polyps OA4 day0 not recorded SRP199550 74.25
SRR12959225 Polyps Polyps E4 day3 not recorded SRP199550 73.54
SRR12959213 Polyps Polyps E4 day9 not recorded SRP199550 71.76
SRR12710854 Polyps Polyps OA4 day9 not recorded SRP199550 71.41
SRR12786895 Polyps Polyps OA4 day0 not recorded SRP199550 71.05
SRR12710865 Polyps Polyps OA4 day3 not recorded SRP199550 71.00
SRR12959212 Polyps Polyps E4 day9 not recorded SRP199550 69.45
SRR12959226 Polyps Polyps E4 day3 not recorded SRP199550 68.62
SRR12710866 Polyps Polyps OA4 day3 not recorded SRP199550 68.39
SRR12959200 Polyps Polyps E4 day15 not recorded SRP199550 63.59
SRR12959198 Polyps Polyps E4 day15 not recorded SRP199550 61.73
SRR12959199 Polyps Polyps E4 day15 not recorded SRP199550 56.92
SRR12959187 Polyps Polyps E4 day21 not recorded SRP199550 52.10
SRR12959186 Polyps Polyps E4 day21 not recorded SRP199550 50.48
SRR12710852 Polyps Polyps OA4 day9 not recorded SRP199550 37.16
SRR12710845 Polyps Polyps OA4 day3 not recorded SRP199550 33.67
SRR12710853 Polyps Polyps OA4 day9 not recorded SRP199550 32.76
SRR12807380 Polyps Polyps OA4 day0 not recorded SRP199550 0.00
SRR12849112 Polyps Polyps OA4 day0 not recorded SRP199550 0.00
SRR12927879 Polyps Polyps E4 day0 not recorded SRP199550 0.00
SRR12963483 Polyps Polyps E4 day0 not recorded SRP199550 0.00
SRR9129315 Polyps Polyps not recorded not recorded SRP199550 0.00
SRR9613518 Polyps Polyps not recorded not recorded SRP199550 0.00

Source: CnidoSite RNA-seq expression matrices (MFOLI_TPM, StringTie quantification over 36 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 Montipora foliosa 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 correlated19XP_068702571.10.939003994669916
Negatively correlated3XP_068681185.1-0.481337993182329

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 Montipora foliosa, 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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