Gene detail

Detailed information of BRAKERXEIP00000046229.1 in Muricea muricata

Genomic Location: chr4:301576...319422
NR annotation: XP_028395907.1, protein jagged-1-like isoform X2 [Dendronephthya gigantea]
Species Muricea muricata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

BRAKERXEIT00000046229

ATGGCCTCGAAGTTTTTGCGCGGTTTGGCAGCGAAAAGACACAAgcgtaaaatcttagaattcgATCGCGTTTGTAGCATTGATTTCGAATTGAACTTTGCTCAGAATGTGTCGGGACTCGGTCAGTTTCAAGTACGTTTACTCGGAATCAAAAATATTAGAGGAGTTAAAAATGACGGATCGTGTTGCGATGGCTCACGCTCTATGATTCATGGATCCTATCTATGTCAGCCGGATAATTGCGATACCTTTTTTCGAATATGCTTACAACACTATCAGAAAGAGGTCCAGGAGAATGGAATGTGTACCCTGGGAAATTCTACAACTCCTGTACTAGGAAAAGATACATTCCTCATCGCAGATACTATAAATACTACAAATCCTGGCTTTCAGAATCCAATCTTGATACATTTCCAGTTCTGGTGGCTGATCGATTTCAATCTTATCATCGAGGCATGGGATAAAGACAATAAGACGTCTCCAGAACTAATCGAACGAGATAAACTTCAAGGAAAAATTGTAGCAGGTCTGAAATGGGAAAAACGAACTCACAATGGACAAGCAGCCGAAATACAATACGAATATCGCGTTGTATGTGATACCAACTACTATGGAAAAGAATGCAAGCATTACTGTAAACCTAGGGATGATCGTTATGGTCATTACAATTGTGACAGTTCTGGTTCACGTGTCTGCATGCCAGGCTGGACAGGAGATAAATGCGATGACGCCCAATGTAAAGCAGGATGTGACGAAGACCACGGCAAGTGTTCTGTGCCAGGTGAATGTAGGTGTAATGATGGTTGGCAAGGTGAACTTTGTGATCAGTGTATACCACATTCAAAGTGTAAACATGGCACGTGTTCTGTTCCCTATGAATGCCATTGTGATGAGTCCTGGGGAGGAACGTATTGTGATAAAGACCTCAACATGTGCTTACGTGCAAATTGGTGTAATGATCAGGGAACTTGTATTAATTCTGGTCCAGGGGAATATAGCTGTATTTGCAAAAATGGATTTACTGGGAAACACTGCGACCAAGACATTGACGAATGTCTATCGTCGCCTTGTCAAAACAATGGAACTTGTCAGAACAAGAAGAACGACTATTTTTGTGAATGTGTCCCAGGCTGGGAGGGCAGAGCCTGTGAAATCAACGTGGACGATTGCAAGAGCCATGCATGCAAAAACAATGCTGTATGTAAAGACAAGACAAATGATTACGAATGTCTTTGCGCTCCAGGATGGAAGGGAAAGTACTGTGAGACAGATATTGATGACTGTACTAACCCCTCTAACCCATGCGTGCACTCTACAAACTGTACAGATCTACAGCAAGATTTTGCTTGTGTTTGTAAACCTGGTTGGAAAGGAAAAACATGCAATGATAgTGTCAACGATTGCAAGGGACAGTGTTTACATGGAGCTTTCTGCACTGACTTGGAGAATGATTACCAATGCGATTGCCCGCAAGGGTTCATGGGTAAAAATTGTGAGAAAAATATCGACGATTGCATGAGTAACCCTTGTTTGAATAACGCTACATGTATTGATGGTATCCATGGATACCGTTGCGTGTGCCAGACCGGGTTCCTGGGCCCGCGTTGCGCAAACACGTCCGACGAATGCTCGCCAAATCCTTGCATCAATGGCAAGTGTGTAGACTTAGAAAATGATTATCGTTGTAACTGCAACACGAACTACTATGGTACAAACTGCAGCAAACTTGTGGGATCGTCTCCTGATGGGTGTTACCTAAACAACCAATGTAAACATGGGTCTTCTTGCGTCTTCGAGGCCAATGCAACCAAGTGTATTTGTTTGCCTGGCTTTACGGGTGACCTGTGTCAAACGGACATCAATGATTGCGTCAATAACCCATGTTTGAATTCCGGGGAGTGTGTGGATCGCGTCAGCGGTTTTGAATGTGTTTGTCTCGATGGCTTTAGTGGATCACGTTGTGAAGTCGACATTAACGAGTGCAATCTACGTCCTTGTCACCACAACGCGACGTGCGAAGACCTGCCAGGGAGCTACCGTTGTCACTGCCAAACCGGTTTTACAGGTCCACACTGTGATCACGATATTGATTACTGTTCCACAGGTAACCCTTGCAGGAATGGCGGAGTTTGTTTGGATGGCTTGGTTAACTATAGTTGTCAGTGCAGCCAAGATTTCGCTGGTGATCATTGCGATATCCCTGTTCAAAGATGTCTCAGTAATCCATGTCATAACGCGGGCAGGTGTGTTGACGTAACCAACGGATACATCTGCCAATGTCCAGTAGAGTTCACGGGCTCACACTGCGAGACGAAGATAAACCCGTGTGATTCCAGGCCTTGCATACACGGCACCTGCAAGCCAACGGATAGCGGCTATCATTGTAACTGTACCATGGGATATACGGGCGTAGTTTGTGGAACAAAGATAAAATACTGCGATTCAACGGTTTGTCAGAATGAAGGCATCTGTGTGGACGGTGATACATCTGCACGATGTCATTGTCGTCTTGGATACGATGGCGACCATTGTGAGAGAAACATTGATGACTGCCAATCAAATCCTTGTAAGAACAACGCGACATGTGTGGACGGAATTAATTCATTTCATTGTTCGTGTTTGCCTGGGACCAAGGGAAAATATTGCGACGAAGAAATAAACGTGTGTTTTCTGCCTCGTTCCTCGGGAGGTGATAATGATACGAGGATACCATCAAACGTCTGTGGCGATCACGGTGACTGTCATTCTTTACCTGGAGGAAATTTCTCATGTTCCTGTCATGATGGCTTCACTGGAGAACGATGCCGCGATGTTACGGACGAATGTTCATCGAATCCATGTCAAAATGGAGGGATTTGCATTGACGAACATCTGGCCTTCTCGTGTCAATGTCAGTCTGGGTGGCAGGGGAGTCTTTGCGAGAAAAAAATCGACCACTGTGCGTCACATCCATGTTTGAATAATGGCAACTGTACCAGTATCACGGAGACGTTTGTTTGCAAATGTCGTGACGGTTGGAAGGGACATACTTGTAATTCTCgAACATCCCAATGCGCAAAAATCAACCCATGTAAAAACTCCGGTACATGTAAAGATCTTGGGACGAGATTCTTCTGCAAATGCGCTGAAGGTTGGCGAGGAATTACGTGTGAAATACACGAGAAACTGTGTGAAAAGACGAATGCTTGTTATAATGGCGGCAAATGTATAGACATCCCTGGATCGTTTCGTTGCAACTGCGCCCCAGGCTTCACGGGGGTCAACTGTCGAGTCAATATCAATGAATGCGAGTCATCGCCTTGCTATGGTGGAGGCAAGTGCACTGATGGTGTTGATTTTTTCACTTGTACATGCACAAAGAACAGATATGGCGCTTTGTGTGAAAATAAGAAACCGGATAACTGTCAACGAAATCACATCGAGAGGCTGCATGGCAGCTCTTGGAGCGAGGACTGCAATACGTGTACATGCAGTGATAGTGCCGTGGAATGTACTCGTGTTGTGTGCCCGCCAAAGAATTGTATCTCGAGTGTGACAAACCGCGCTCAAGGCTGTGAGGAGCTGGGGTCTAGGTGTACAGAGATGAAGAACGTGAGCTGCTTACGTGATCCGTGCCCACGATTTGGTCAGTGCATGGTTGAAGGAGAGACACAGACCAACCGTTATCATGAATGCGATCCAGCAACCAACCACGTAACCGATGACTGTGTCAAGGTTCACCTAGTGTTTTGGAGGAAGAAATTACCACCAGGAACTCTGCTACCAGATTTTTGTCGTGACCTCAGTTCACTGGAGGTCTTTCAGCGTTATGCTAAGAAACATTACATTAAAGTCACGTGTGATGCCACCTCGCCAAACGAGCCGGCACGGAGCATGTCAAAGAGGAATGCAGAAGTCGCCGAAGTGACTGTCGCTGTCGGTAGCGACGAGGGCACTGGGGACGCTATAAAAGCGGCGACGGATTTGGCAAAGTATGTGAAATTGCAGTCAGAAGAAAAAGATGAGTTGAAAAATCAAACGATAACTAAAATAATCATCGCCATCACTAAAGTAACGGTTGAGAGACCTGTTGTTATCATGTACAGGAAGGAGAAAGAAACTCCTGTCTATCTTATTCCTGTGATAGCAGCCTTGGTCGTCATCGCTGCATTTGTTTTGCTGTTTGTTGTCATGTGTGAGAAACGTCGGCGTCGTCAGAGAGAACGACATCGCCGAAGAACGTACGAAGAAACAACGAAGTTGAAGCAGCGAAGAGACAGCGAAGATGTCGACGCAATAGAAACGGCAAGCGAAGCAAGTCGCGGCGTTCGCAAAGAACAGTCATTTGACGAACTACGAGACATTGAACCTGAAGAAATTGATGTCTCAGTCATTGAACAAACCGAGCGCGAAGTCTCGAGGTCTTCAATAGAGGTACTATCCCCTGCGCGTTCCCCACGCGAGCATGGCGCGCGTGACGAGTGGCGCAGGAGAGAAATTTTAAACTTGCAAAGAAAATCATCTCAAGAGATTGTAGTATAA

Transcript

BRAKERXEIT00000046229

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9NR61	Delta-like protein 4 OS=Homo sapiens OX=9606 GN=DLL4 PE=1 SV=1
Q9IAT6	Delta-like protein C OS=Danio rerio OX=7955 GN=dlc PE=2 SV=1
P97607	Protein jagged-2 (Fragment) OS=Rattus norvegicus OX=10116 GN=Jag2 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000330 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF12661 all species →	hEGF	Human growth factor-like EGF	Domain	Interproscan
PF01414 all species →	DSL	Delta serrate ligand	Domain	Interproscan
PF07645 all species →	EGF_CA	Calcium-binding EGF domain	Domain	Interproscan
PF07657 all species →	MNNL	N terminus of Notch ligand C2-like domain	Domain	Interproscan
PF21700 all species →	DL-JAG_EGF-like	Delta-like/Jagged, EGF-like domain	Domain	Interproscan
PF00008 all species →	EGF	EGF-like domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001774 all species →	Domain	Delta/Serrate/lag-2 (DSL) protein	Interproscan
IPR000742 all species →	Domain	EGF-like domain	Interproscan
IPR013032 all species →	Conserved_site	EGF-like, conserved site	Interproscan
IPR000152 all species →	PTM	EGF-type aspartate/asparagine hydroxylation site	Interproscan
IPR050906 all species →	Family	Notch signaling pathway	Interproscan
IPR018097 all species →	Conserved_site	EGF-like calcium-binding, conserved site	Interproscan
IPR009030 all species →	Homologous_superfamily	Growth factor receptor cysteine-rich domain superfamily	Interproscan
IPR001881 all species →	Domain	EGF-like calcium-binding domain	Interproscan
IPR049883 all species →	Domain	NOTCH1 EGF-like calcium-binding domain	Interproscan
IPR001007 all species →	Domain	VWFC domain	Interproscan
IPR011651 all species →	Domain	Notch ligand, N-terminal domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR24044 all species →	NOTCH LIGAND FAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0007154 all species →	Biological Process	cell communication	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0005112 all species →	Molecular Function	Notch binding	Interproscan
GO:0005509 all species →	Molecular Function	calcium ion binding	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0007219 all species →	Biological Process	Notch signaling pathway	Interproscan
GO:0007275 all species →	Biological Process	multicellular organism development	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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K06052	JAG1, CD339; jagged-1	-	CD molecules	ko04090	deepkoala

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 Muricea muricata 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 Muricea muricata, 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 →