Detailed information of amic_s0002.g307.t1 in Acropora microphthalma

Genomic Location: sc0000002_pilon:4098706...4104550
NR annotation: XP_044175832.1, pre-mRNA-splicing factor CWC2-like isoform X1 [Acropora millepora]
Species Acropora microphthalma · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q54PH5Pre-mRNA-splicing factor cwc2 OS=Dictyostelium discoideum OX=44689 GN=cwc2 PE=3 SV=1
Q6T412Pre-mRNA-splicing factor CWC2 OS=Leptosphaeria maculans OX=5022 GN=CWC2 PE=3 SV=1
Q5BB35Pre-mRNA-splicing factor cwc2 OS=Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) OX=227321 GN=cwc2 PE=3 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0002327 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00076
all species →
RRM_1RNA recognition motifDomainInterproscan
PF16131
all species →
TorusTorus domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR001202
all species →
DomainWW domainInterproscan
IPR000504
all species →
DomainRNA recognition motif domainInterproscan
IPR000571
all species →
DomainZinc finger, CCCH-typeInterproscan
IPR032297
all species →
DomainTorus domainInterproscan
IPR035979
all species →
Homologous_superfamilyRNA-binding domain superfamilyInterproscan
IPR034181
all species →
DomainPre-mRNA-splicing factor Cwc2, RNA recognition motifInterproscan
IPR012677
all species →
Homologous_superfamilyNucleotide-binding alpha-beta plait domain superfamilyInterproscan
IPR039171
all species →
FamilyPre-mRNA-splicing factor Cwc2/Slt11Interproscan

 PANTHER
PANTHER termDescriptionSource
PTHR14089
all species →
PRE-MRNA-SPLICING FACTOR RBM22Interproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005515
all species →
Molecular Functionprotein bindingInterproscan
GO:0003723
all species →
Molecular FunctionRNA bindingInterproscan
GO:0046872
all species →
Molecular Functionmetal ion bindingInterproscan
GO:0003676
all species →
Molecular Functionnucleic acid bindingInterproscan
GO:0000974
all species →
Cellular ComponentPrp19 complexInterproscan
GO:0017070
all species →
Molecular FunctionU6 snRNA bindingInterproscan
GO:0036002
all species →
Molecular Functionpre-mRNA bindingInterproscan
GO:0071006
all species →
Cellular ComponentU2-type catalytic step 1 spliceosomeInterproscan
GO:0071007
all species →
Cellular ComponentU2-type catalytic step 2 spliceosomeInterproscan

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
K27398CWC2; pre-mRNA-splicing factor CWC2-Spliceosomeko03041deepkoala

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

Co-expression network

Genes whose expression across the transcriptome samples of Acropora microphthalma 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.

No co-expression network has been built for this species, so this gene has no partners to show. Networks are available for the species listed on the Network Analysis page.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Acropora microphthalma, 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.no expression matrix
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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