Gene detail

Detailed information of FUN_003818-T1 in Colpophyllia natans

Genomic Location: contig_4:8996985...9060872
NR annotation: CAH3043325.1, unnamed protein product [Porites lobata]
Species Colpophyllia natans · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

FUN_003818-T1

ATGGGGTTGTTCCAAGGTGCTCAACTATTGGCTGTACTTTTGGTTTTGTGCAAACTCTCGGTCCTAGCTGAAGGACAAAATCTGCTCCAAAATGGAAAGGTTAACTTCACGGTGACATATGGAGACTTCCTTTATTGCACAACCGTGAATTACCCTCGTGCATTTTCTAGCTCTAGAAATGTACGTGTCCTTGCATCGATCAGCCACGGAAAAGAATCTGTCAGTGTGCATGATTCAGCAGTTGTCTGGACATCAGACGTGACTCAGAGCAGTTTTCGTGTATGTTTGTTAGAATCGGGTCTTGGTGCAAATGGATCCTCTATCGTGAACTGGATCGCGTTTCGGAGCACACCCTCTGGAATGTTGGACGGTGCCGCCGCCTTTAATACATTCACCAGTGGTACAAAATGTGAAAGAGTTAACTTTGCTCAGCGCTTTTCTTCTGTCCCAAAAGTTCTCGCCACAGTACGTCACACAGTCAGCAACAGGCCACAGGACGCCGTGAATATATGGATCGAAGAGCTGAAGGAAGATTATTTCAGAATCTGTCTCCGAGAAGTAAAAACATTTGACGGCAAGCATGAGAACTTGAAAGTGgacTGGCTGGCATTTACTCAGGGAGGCGTTCAACTTACATTCCAAGGAAAACTACAATTTGAAAATGGCGGTGCTCCTCTTGAACAAGATAATTTCGCCTTTTGTAAGATGTATAATTTTACTGAAGAGTTTTATGCACCCCCAGTTGTTATAGTCACAGCTAACCATCTTTATGATAGCAACAATGTGCATTCTATCAAACCAGAGAACAATGTCCTTAACACGTGGATTGAGGCAATAACGACTTCATCTTTTCGTGTGTGCGTAAAAGACTTGGCAGGAATGGAAAGTCAGCATGATCCTGTTACTGTTGATTATGCAGTTATTGGAGctCTTGATCCATGTATCAACGTCTCCTGTAACTACTTCGCTGTTTGCAAGGCGTTTGGACCCAGGGATGCCCGGTGTATTTGTGTGAATAACTGTCCATCATACGAAGAGCCCGTATGTTCCTCAAATGGAACCACATATGACAACGAGTGTGTTTTCCAGCGAGAAATGTGCCACCTGAAAGCTAACTTCACTCTGTATCATCCAGGTGACTGTACAGGATTCCCTTCTCAAAAAGGCCGTCATCGACTCCGTCGCTCGCCAAGCTGGGCTGAAGCAGTTTGTGAACAGGTTCCACTAGCTCCTTATGTCTTCTATCCTGACAAACCGGTTCACATACAAGTTTCCGTCAATCACGTCAACTTCTCAGATCCCAGCTACGTTCATGAAGCCGTAGTGCTCTGGGTTGAAGACATTAGAGAGAACAATTTTACAGTTTGTGTGACACAGGAGGGAAggaacgaaaagaaaaatggacACGAGCTTGCCACAGTGGACTGGTTAGCATACCAGGGAGCCCCTGACGGGGGAGTGTCCGGAAGCTTGGACATGCCAACATGGTGGACTGGAACGAACTGTCGTGCGGTGTCACTACCTTCGAGAGAGTTTAAATCGGTGCCCACTGTGCTTGTGTCATCGGAACATGAAAGACGTGGTGTAAAGCATGATGCTTCCTCTGTGTGGGTAGAGGATTTGACGACAACGTCCTTCAAGATCTGCATCAGAGAATTACAGAATTTTGATGGAGCTCACCAAAGCATCTATGTTGACTGGATGGCATTCGAAGAGCTTCATCGACCTCTGTTTAGGGAACATGGATCTATCTACTTTGCTAACGGGAACAAGCCCTCCAAAGACTTTAACTATGCTTTCTGTGAGGATGTTGCCTTTAAGAAGCATTATAACGACTCTCCAGCACTTTTGATTTCTGCAAACCACTCAACAAACGGAGGAAACCTTAATCCAGCGTACAACGCCATATCAGCCTGGGCTGAGtatatAAACAAGACAGGATTTAGAGCATGCGTGAAGGAGTTGTTTGTGAACCAGCATGATCCTCTGTCAATTTCATATGCAGTCATGCCAGATGTCTGTGAACCAGGCTGGAGTTTCTACAATGGTTCCTGTTACTTTACCAGTGAAACTTGTGAACCATGGTCCAACGCCAGTACAATCTGCAGAAGCATGGGGGCAAATCTACCCGCCATTGAAACTCAAGAGGAAAATGTGTATATTCAGCACAGACACAATGGTGCAAAGGCGTGGATTGGTTTGAATGACATTGCTACTGAAGGATTGTTCTCCTGGGTGGATGGGTGTCCTGATAAATTCCGCTACTGGGCCGTGAAACAGCCAAACGACTTTAGGGGGGAGGACTGCGTACACACTCTTGGTGCTAGACATGGATACACGTGGAATGACGTCGATTGTGCTGCATGTCATCAGTACACTTGTAAAAAAGATTATGATGAATGTACCAGTTCTCCTTGTTTTAACGGAGGTACTTGCAAAAATGGTAAAAGGACGTTTAGCTGCACATGTCCTCCAACTCACAAAGGAATTTCATGTGAAAAATTTGACGAATGTTCCAGCAACCCTTGTCTAAATGGCGGTACTTGCACTGATGGAGTGAATAACTTCACGTGTTCTTGTCCCTCGCCTTTTTTTGGAAAAAGGTGTCAAGAAACGGACGAATGCCAGTCCAATCCTTGTCAAAATGGTGGGACATGCGTAGATGGCGTGTACAGTTTTACCTGTTCGTGCCCTAGCTTCTTTGCTGGACCACGATGTGAAGTTTCTCCTGCCGTATCCTGTAAGAATCACTACTCGGCGGGGTTGACCTCGAGTGGAAACTATTACTTGAAAGTATCGGGACAGTCTTTCCAGGTGTACTGTGACATGTCCTCTAACGGAGGTGGTTGgactctcatctcacgtttctCAAATGCTGACAGTACAAACTGGATGCAGTCCAGCGGCAACTGGTGGTATGACCTCACATCTTCTTATGGAAGCGTTACCAGTCCATCAAATAACTACGACATGATATCACCGGCATTCTGGCTTGTCACTGGCAACTACATCAAAATAACCCGGAGTGACGACAGCTCTAACACAGCCTTGTTATACACCAGCAGCTGCACTGGCGGGAGAACCTTCAGAAGCTTTATAACAAGATATGGCAACTTTAGACATGGCAATATCTGGAACAGTGACGCATGTCGTGCAAGCTGCTACATCCCTAGCTATGGTGGAAGCTACTCATCCACAGTGGGTTTCAGTCAGGCCCACTGCAGCAGCAACCTTCAAAGTAGTCGTTACCTGTCATTCTGGTGTGACTGGAGCAATGGTGACGGAGCCGTGATGATGATTGGTGGAGGAGGTAGTTCATGCAGTAGAGCAGACCATGGAATCGGTATCACAGAAGCTAACGAAGCCAAGTTCGGCTCAAGAATCGGAGAAGGAGACTTCGGTGATAATGGCAACTGTCCTACCAGTTACTCTCTCAACCTGTGGATTAAATAG

Transcript

FUN_003818-T1

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q8MIS5	CD209 antigen-like protein 2 OS=Macaca mulatta OX=9544 GN=CD209L2 PE=1 SV=1
Q8HY12	C-type lectin domain family 4 member M OS=Hylobates lar OX=9580 GN=CLEC4M PE=3 SV=1
Q28670	Aggrecan core protein OS=Oryctolagus cuniculus OX=9986 GN=ACAN PE=2 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000086 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00059 all species →	Lectin_C	Lectin C-type domain	Domain	Interproscan
PF00147 all species →	Fibrinogen_C	Fibrinogen beta and gamma chains, C-terminal globular domain	Domain	Interproscan
PF09458 all species →	H_lectin	H-type lectin domain	Domain	Interproscan
PF12661 all species →	hEGF	Human growth factor-like EGF	Domain	Interproscan
PF07648 all species →	Kazal_2	Kazal-type serine protease inhibitor domain	Domain	Interproscan
PF00008 all species →	EGF	EGF-like domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001304 all species →	Domain	C-type lectin-like	Interproscan
IPR002181 all species →	Domain	Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain	Interproscan
IPR019019 all species →	Domain	H-type lectin domain	Interproscan
IPR000742 all species →	Domain	EGF-like domain	Interproscan
IPR002350 all species →	Domain	Kazal domain	Interproscan
IPR001881 all species →	Domain	EGF-like calcium-binding domain	Interproscan
IPR037221 all species →	Homologous_superfamily	H-type lectin domain superfamily	Interproscan
IPR000152 all species →	PTM	EGF-type aspartate/asparagine hydroxylation site	Interproscan
IPR016187 all species →	Homologous_superfamily	C-type lectin fold	Interproscan
IPR050906 all species →	Family	Notch signaling pathway	Interproscan
IPR018097 all species →	Conserved_site	EGF-like calcium-binding, conserved site	Interproscan
IPR018378 all species →	Conserved_site	C-type lectin, conserved site	Interproscan
IPR036056 all species →	Homologous_superfamily	Fibrinogen-like, C-terminal	Interproscan
IPR016186 all species →	Homologous_superfamily	C-type lectin-like/link domain superfamily	Interproscan
IPR013032 all species →	Conserved_site	EGF-like, conserved site	Interproscan
IPR014716 all species →	Homologous_superfamily	Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1	Interproscan
IPR036058 all species →	Homologous_superfamily	Kazal domain superfamily	Interproscan

PANTHER

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

Gene Ontology

GO term	Category	Description	Source
GO:0007155 all species →	Biological Process	cell adhesion	Interproscan
GO:0030246 all species →	Molecular Function	carbohydrate binding	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005509 all species →	Molecular Function	calcium ion binding	Interproscan
GO:0005112 all species →	Molecular Function	Notch binding	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 FUN_003818-T1.

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 Colpophyllia natans 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 Colpophyllia natans, 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 →