Gene detail

Detailed information of BRAKERTYJP00000038263.1 in Cladopsammia gracilis

Genomic Location: JAJGOT010000281.1:218797...234549
NR annotation: no NCBI-NR hit recorded
Species Cladopsammia gracilis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

BRAKERTYJT00000038263

ATGGGTGCTGAACAGTCCCTTCATCTCCACCAGAGACGGATGAACGCGAGTCCTGTGGACTCACTGTTTGAACGCGCAGTTCTGGATGCTCTCCGCGAAATAGCCGAGGAATCCGAAGTGCCTTCTGAACAGTTTGAGCATGCGTGGGATCCTGAGGATTGCTCCCCGAGGTTTAGAGTGTTGAGTGACAGGCTGACAGCTAGAAGACTTCCCTCACCTCTTACCACGGATGCTGTAAGAGGGAAAAAAGGTTACAGACAAGGCCGGCATGTATGGGAGATAACATGGGAACAAGACGAGCGGGGGTCTCACGCAGTTATAGGAATAGCTACACCCCAGGCCCCTCTACAGTGCCTCGGTTACGTTCCACTCATAGGATCTAACGCACAATCGTGGGGCTGGAATCTAAGCAAGAAGGTGTCCTTTCACAAAGGGAATGAGGTCGCGTACCCCGCGAATTATCCAACGTTTGTTGTACCCGATACGGTGTATGTAATACTTGATATGGACAATGCCACACTAAGCTTTGCCACTGACGATACTCATCTGGGTGTGGCCTTTTGTAATTTACCTCGCAATCCCCTGATACCCTTGTGCCCATGCGCCAGTGCCGTGTACGGTAACTGCGACATTAAAATGAAGTATCTCGGACGAGGAGataatTTTCTAGCCAAGTTGGAGGCGTCTAAAAGGAAAGCATCTTCCTCGGCCCCACCTCCCAGAGTGACATCCCCGCCACAATCACCTGGAGTCAAATCACCGCCCCAGTCTCCGAGCGCCTCGTCACCAGGCCAGGTCGCACCGAATTCTGCTGATCCTGTGAAATCCTCGGAATCATACAAGTTTAACCACACCTGTGGGGCCAACATCGCTGTGATGTGCGCCGGGAAAAAAGCCAAGAGACTCGATCCCCTTCAGTGTTTCAATCATGGCGCCGTTTTAACAAGCCAGCCTCTACAAGATGAAGAGCTATTTGAAGTTCGTTTGGACAGCAAAGTGGGCAGATGGTTAGGCAGTTTAGATATTGGTGCCACGACTGTTTCTGCTGAAAACTTGCAGTTCCCTTCAACAATAACGTCCTGCTCACAAGGAACAACGTTTGTACTCAGCAGTGATCAGATCCTAAATAACGGCAAAAAAATGACAACCATTTccaaaaatttggaaaatttgtCGGTAGGAGATCGCGTGGGGGTGATGCGAAAGTCAGACAACACGTTGCATTTCTTCGTCAATGGCGTAGATGTTGGCAAACGGATAAAAACTATCCCGCCAGTGCTTTATGGAATAGTTGATGTGTTCGGCCAGGCTGAAGAAGTTACTATAACTGGTGGTACTGCGGAAACACAGAGCAGTAATCAGGACCAGGTAGATTCTGTCTCCGTGATGGTGCGCATGAACAACACCGTAAACATCCTAAAAGAAGGGTCGTATGGCGATATCTTGTCTGTAGTTGGTAAAGTGGCCAAGGATATTTTACAACCTTACGAAGAAACAGATAATCGAGAGCTTCGACAAAAGTACGGAGACCATTTGGCCGAGATCGATGCTCCATTGCACCTCACTAAACTCCTTCGTCGCCTGATGGATACCGGCATGGAGACTCGAGATGGCTGGCTGGGTATGTACGTGGTTCGTGGTGCATTCTGGAACTACTCAGATGCCAGTTTGAAAATGGGTAGAGGATTGGGACGGAGTGGTCTGTTGCAGATAGTGTTGAATGATCTGGACACGTATGGCATCAAAAGTTCCAAAAACGAGAAAAGGAAATACCTGGTGTCGTCTGCTATCAACATTCTACACAACTGTTCCAAAGCTTCAGAAAATCGACAGATTCTCCGCGATCTACGGGCACAGGAAAGGATCGCTCCATTTCTTAAGGCAGATGATATGGAAGTCGTTGTGACGGCCACATTAACGCTTTCATACATCACCCCTGATGAACAGAAAAAACTGTTGGAAGCCGAGAGTAGGGTATTAAGCTATCTTCTCGGCATGTTGCGCAATGCGCTGGATCAACCAAACCTACGCGGGAGATCAGAGGGTTCTACATGGTCGGCTCAGGAAATCGCAGACGGCCTGGGTAACTTGCTCATAAATAAACAGAACATGGAGACTATGTTGGACCGAGATGTTGTTTCGCTGTTGATTTCGCTCATTGGTAAAGGCGGAGCCACTGAAAAAGAATGCGCTGCTAACTCCCTGTGGGTTATCGCAAAGAACTCTAAAGGGAAGGCGAAAATAAAAGAGACAGCGAACGCGAAAGAAGAGCTGTTGCGCCTAAGCAGAAGTGATAACCAGGCAGTTCAAGAGGCTGCCAAAAGGGTTCTCTTAGAGCTAAAGGAAACTACAAACACTCGAGGTGCACCAAACGTGCAAAGACGAACAAGCTGTGACTATCAAGAAAAATGCCGCAGATTCAAGTCATCGCTCAAGTTGTCAGATATTTTCTTTGACCCACAATACGACAGATGTTTTTGTACGGAGTGCCACGCATCTCGAGGTGACAAACTCTATTACACTCGAGGAAAACCTCCAAAGGACTATGGGATTCCCATAGGATGGTGTCGATTTGGGCTAAAGGTCCACCATCGAGCTCTTGTTCTGGATGTTTTCAACAAGTGGCACGTAGCATTCCATGGCACAAAAGTAGAGAGCGTCAGTGCCATTTTGGAATGTGGTGATCTTCTCATACCAGGTGTGTCTTTGTTGCAAGGACAGTGTGTCCTCCTCACTGTAGCAGCGCTGATAGCGCACAATGCTTTTAGAAGTGTAGTATTCAGGTATTATATCCTTACATCAGATCGTTTGGGATTCCTCAATTCCTCTCTCCACTCAGGTGATGTGGCACTTGGGGGGAGAAAGCTGAGCGAGGAAGAAGGGCATTTTAATGACAACAGAAAACCTTCAGGATTTGACACAAAGCAGATCTTCGTATCACCGAGTGTTCGCTACTCAGGACACAACTGCTACGCGAAAACCAAAAGTTTTAGTGACCCTGTGACGACAAAGAAGTTGAATGCCAAAGCTGTGCTTCAGCTGTGTATCAACCCGGACAGCTACCAGGTTGGACCACAAACGATTGCTGCTACCTCCGAGATTGACCCTAAGTTTAGCAACCAGGAGATTGAATGGTCAACCAAGGAACGTGGATCCATCATTCTTTATGGACTTCTGGTTAAACTTGATGAAACCAGTTGA

Transcript

BRAKERTYJT00000038263

Protein

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003242 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00622 all species →	SPRY	SPRY domain	Family	Interproscan
PF07177 all species →	Neuralized	Neuralized	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR016024 all species →	Homologous_superfamily	Armadillo-type fold	Interproscan
IPR006573 all species →	Domain	Neuralized homology repeat (NHR) domain	Interproscan
IPR003877 all species →	Domain	SPRY domain	Interproscan
IPR013320 all species →	Homologous_superfamily	Concanavalin A-like lectin/glucanase domain superfamily	Interproscan
IPR043136 all species →	Homologous_superfamily	B30.2/SPRY domain superfamily	Interproscan
IPR001870 all species →	Domain	B30.2/SPRY domain	Interproscan
IPR050672 all species →	Family	F-box/SPRY and SOCS box protein families	Interproscan
IPR011989 all species →	Homologous_superfamily	Armadillo-like helical	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12245 all species →	SPRY DOMAIN CONTAINING SOCS BOX PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0019005 all species →	Cellular Component	SCF ubiquitin ligase complex	Interproscan
GO:0043161 all species →	Biological Process	proteasome-mediated ubiquitin-dependent protein catabolic process	Interproscan

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 BRAKERTYJP00000038263.1.

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 Cladopsammia gracilis 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 Cladopsammia gracilis, 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.

Analysis	What it does	Status
Primer design	Design PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.	template found	open →
BLAST	Search 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 found	open →
Expression heatmap	Draw 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 / orthogroup	Look 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 analysis	Start a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.		open →