Gene detail

Detailed information of BRAKERLUSP00000025434.1 in Blastomussa wellsi

Genomic Location: chr6:23250263...23270411
NR annotation: XP_020627563.1, integrin beta-1-like, partial [Orbicella faveolata]
Species Blastomussa wellsi · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

BRAKERLUST00000025434

ATGCAAATTTATACAGGTGTTCCTGATTGTACAACAATAGAATCATCTTGTGGAGCCTGTATACAAAATGTCGACCCACCATGTTCTTGGTGTGAAGATGCGGAATATATTTGGTTGGAGCAGCCAAGAGCACGATGCGATGACATTAAGAACCATACCAGAAATGGGTGCAAGAAAATAGCAAATCCGAAATCTGCTTATGTTACACATGAAAGTAAGCCACTTGATGCAGATGTGAAAGTTACACCACAGAATTTAACATTGTCTCTTAGACCAGgTCAACCAGCGACCATTAAGGTGGATGTTAAGATGCCAGAAAATTACCCTGTAGACTTGTATTATCTGATGGATTTATCTGGCTCCATGGTAGAAGATCTTAAAAAATTTCCATCCCTTGGTCAACAAATAGCTGAAGAAATGAATAATATCACAACTAGATTCCGTCTTGGATTTGGTGGATTTGTGGACAAGCCTATTGCTCCTTACATTGCCACTGAACCTACAAGCTTGGCACACCCTCATGATCCAACATCTCCAAATCCTGTTTCTGTTCCAGCATTTGGTTTTATTAATCAGTTGAAATTGACCCCAAACTACACTGAGTTTGAGAATACAATACGGCATGTGAACATTTCAGGGAATGTTGACAATCCTGAAGGAACACTAGATGCCCTGATGCAGATCGCAGTCTGTGGTTCGGAAATTGGCTGGGTGGACAAGCAGTCTGCCAGAAGATTGGTTATCGTCATTACTGACGCCAATTACCATTTTGCTGGCGATGGCTTGcTTGGTGGAGTTGTCAAGCCGAATGATGGTCATTGTCACACAAGCAGCGGCAAATACATGGCATCAACAACAATGGACTATCCATCTCCAGGTTTTCTTAAACAGAAGCTAATTGATGAGCAATTGTCACCAATCTTCGCTATCAATAAGACAAAGGTTCATGAGTACAGTCAGTACAAGGAATTAGTTAATTTCTTTGGCAAGGAATCTGGAGCTGTAGTTGATTTATTGAGTGAAGATTCTTCTAACATTGTCCAGCTCATTAGAGATGCTTATGAGACAATTGCTCAAACGCAGACAATTCGTGACACAGCACCTGAAGGTGTGAAGGTGAACTATACAGCTTACTGTCCTGATGGAAAACAAGTTGGATCAAAGACTTGCGCCAATGTTCAGATTGGCCAGAAGGTGTCTTTTGAGGTCTCTGTCACAGTGGATGACTGTGACCTGAAAGAAAAGAGCTTTTCCCTGGTGACACCATTTGGGAATGTGGACATAAACCTGGATTTCATCTGCAGCTGTCAATGCGAGAATGAAGAGAATAAAGAAAAATCCAGCTCGCACTGTTCTGGAAATGGTACGTTAGCCTGTGGACTGTGCAAATGTGACAAAGATTGGGCTGGTCGGAAATGTCAGTGCCTAGAGGAAACCAAACTTGCACCAAGCAAATGCGTAAGGGACAATGCGACGGATACACAAGCGTGTAGTGGGGCAGGAACCTGCCTCTGCGGAGACTGTGAGTGCAAGAAAACAGGGCTTCGTCCTGGTGAAATCATCAATGGTAAATATTGTGAATGCAGCAACTTGAATTGCCCATCAGACCCGGACACTGATCTAATATGTGGCGGGCCTGATCATGGTCGGTGTGTGTGCGGGAATTGTAGCTGCTCAGGCAACTGGACGGGCCCCTCGTGCAGCTGCACAAAGCGCACTGAAGGCTGTATGAAAGATGGGGTGCTGTGTAACGGGTATGGTACGTGCGAATGTGGCAACTGTGTTTGTAACGCGTCCACCGTTTACAGAGGAAAGTACTGCGATGAATGCCCGAGCTGCGCTGGAAAATGTTCTCTCAACAAGGACTGTGTGCAATGCTTGGTGTTTAAGAGTGGTATAATAAGTGCCGAGGACTGCACGACTCGCTGCAAAGATTTCAAAATCACTGAAGTCGACGAACTCTCTCCTGAAATGGGAGAAAGGTGCACATTTAAGGACGACGATGACTGCTCGTTCAGCTTCAGTTACAAAGAAAATCCTGGCAAGGATGTTGTGATATCGGTACAACGGCAGAAAGTGTGCCCCAAAGAAGCGGAAGCACTCGCCGTCATTCTTGGAGTAGTCGGAGGAGTACTGGGCGTGGGTCTAGCCCTGCTCCTTATTTGGAAACTCCTCGCTACTATCCAGGACCGGCGAGAATTTGCCAAGTTCGAGAAGGAGAGACAAAATGCTCAGTGGGACACGGGTGAGAATCCCATCTTTAAACAGGCGACAACTACCTTCCAGAATCCCACTTATGGTGGAAAATAA

Transcript

BRAKERLUST00000025434

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P07228	Integrin beta-1 OS=Gallus gallus OX=9031 GN=ITGB1 PE=1 SV=1
P11584	Integrin beta-PS OS=Drosophila melanogaster OX=7227 GN=mys PE=1 SV=3
Q9GLP0	Integrin beta-1 OS=Sus scrofa OX=9823 GN=ITGB1 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000791 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF18372 all species →	I-EGF_1	Integrin beta epidermal growth factor like domain 1	Domain	Interproscan
PF07965 all species →	Integrin_B_tail	Integrin beta tail domain	Domain	Interproscan
PF08725 all species →	Integrin_b_cyt	Integrin beta cytoplasmic domain	Domain	Interproscan
PF00362 all species →	Integrin_beta	Integrin beta chain VWA domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036465 all species →	Homologous_superfamily	von Willebrand factor A-like domain superfamily	Interproscan
IPR015812 all species →	Family	Integrin beta subunit	Interproscan
IPR040622 all species →	Domain	Integrin beta, epidermal growth factor-like domain 1	Interproscan
IPR002369 all species →	Domain	Integrin beta subunit, VWA domain	Interproscan
IPR036349 all species →	Homologous_superfamily	Integrin beta tail domain superfamily	Interproscan
IPR012896 all species →	Domain	Integrin beta subunit, tail	Interproscan
IPR014836 all species →	Domain	Integrin beta subunit, cytoplasmic domain	Interproscan
IPR032695 all species →	Homologous_superfamily	Integrin domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10082 all species →	INTEGRIN BETA SUBUNIT	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005178 all species →	Molecular Function	integrin binding	Interproscan
GO:0005925 all species →	Cellular Component	focal adhesion	Interproscan
GO:0007160 all species →	Biological Process	cell-matrix adhesion	Interproscan
GO:0007229 all species →	Biological Process	integrin-mediated signaling pathway	Interproscan
GO:0008305 all species →	Cellular Component	integrin complex	Interproscan
GO:0009986 all species →	Cellular Component	cell surface	Interproscan
GO:0016477 all species →	Biological Process	cell migration	Interproscan
GO:0033627 all species →	Biological Process	cell adhesion mediated by integrin	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 BRAKERLUSP00000025434.1.

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 Blastomussa wellsi 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 Blastomussa wellsi, 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 →