Gene detail

Detailed information of BRAKERRLHP00000029079.1 in Dendrophyllia cribrosa

Genomic Location: JAJLRJ010000007.1:43085047...43104900
NR annotation: CAH3160457.1, unnamed protein product [Porites evermanni]
Species Dendrophyllia cribrosa · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

BRAKERRLHT00000029079

ATGAAGGTTACGGTATGTTTTGATACAGTGTGCGTCATCGTTCCTTGTGGCAATGGCGACTTGACATCCGCGGACGAGTTTATCCAAGTGCATTTTCTGGAAACAAATGAAGACCACGGCATACTTGACCCAGATGATGTCCTATCTGATGTAGTCGACGACAAAGACAAGTTACTTGCCGTGTTTCAAGAAGGTTCTACTTTTCACCGGCCATCACAAAATGGAGGATATGGGACAGGAGCATCTTCAGCAGGAACAGCAAGTCCTGATCTATCTCCTCACGAAGATGAAACATCGAAATTTATAGAGGAACAACAACCTATAAAAACATATGTTCCAgtcaagaataaaattgaaaacaccAATGGTGAAATCAAGCCTTTATTCAGAGTGTCAAAAAGTCCTCCACCTCCAATTGCACCAAAACCTGTAAGACCTGTTAGACAGGTTAACAATCACATCAACGGTACTAGGACTAATTCATATGTTGAATCTATACCTTCAGAAGATTCTGGAATATCTACGCATGATGACCGTGACAGATATCGAATTGGTTCAGATTCATCAAAGTCAGAAATAAATGACAATGTATCGGTGAAACCTGCAATTTATAAGAGTAGGACTGGAGAGACCACGTTTGTTGCTATAGGGAGGCCTATCAAATCACCAGTATATAATGGCCATTCCAATGGAGAACGGAGACGATTTTCGTCAACAAGTTCTGATCATGCAGATAATGAACACAGTGAAGTTGAAGAAGAGACCTTTTCATTAGGAAGAAACTCAGCGCGGAAATCAATGTTTGTAGACAGCCCTATGTTGGACAGATGGGCGGAGCTACAGGAGGAAAGAATGTTTGCGGTAAATAATCACAGAGGGGAACCAGTGAGTGTGGTTACATCACCATCAGAGCCAAGCTCAAACGAACCAGACTTTAGTAATCAATATTGCGATGATCAGCACTCAGAAGATTCAGAAAGCAGTGGTGAACCTGACATGGTTATGATAGAGTTAAAGCGGGATGATCCTGATGAGGGATTAGGTTTCACAGTTGCAGGATATCGGACAGCTGATGGCAGGGAACTTGGTCTTATTGTTCGAAACATCTCACCAGATGGCTGTGCTGCAAATGATGGCAGGCTACaaATTGCTGACAGGATTGTTGAAGTGAACGGTTGGAGTCTTATGGATATGCCAAATGAAAGagcCGAGGAGCTGTTTGCTACAGCCATCAAAGCACCTGTAGTCAACATCGGTGTATCTCGCTCTCACTCATTCGTACCTGGACAAAAGACTAACGAACCACTTGAAATAATCCACGCTACACCTCAACTTGAAATTACTGAATCAGAGCAACAAGAACAATCACAGCGAGAAATATTACCTTTGACACCTCAGTCTCTTATTGGGTCACCGTCTATTCCCGATTcaagtttcaagaaaataagCAAAAGAATTCTCATTGAATTAATGAAAGGTAATGACGGTCTTGGGTTTAGCATCACAACGCGAGATAATCCCGCAGGAGGGAACACGCCTATATTTGTTAAAAGTATCCTGCCAAAAGGTGCGGCCATTGAAGGAGGACAATTAAGAAGTGGAGATCAAGTTGTAGAGGTAAACGGAGAGAAGATGAACGGCAAAAGCCAAGCTGAAGCTGTTAATGTTCTGCGAAGCACTCGGGGTCTGGTAAAGCTTTTAGTGCAAAGGGAAGAGATATTACAATCACCCCAAACGCCGGCGATTGAGGTGAATGAAGACAGCTTGCGTCACTTCAGAGAAGAAGGCCTTCAAGTACTTACGTTTAAAATTCCTTTGGACATGTCAGGCGCCGCGGGCTTGGGAGTCAGCGTAAAAGGAAAATGCCGCGCACCTCGTGACCAGGGTAGGGACAGTCCGATAGACAAGGGCATCTTTTGTAAGTCTATCATTCCTGGGGGCGCGGCGGCTAAAGATGGCCGCCTTCGCCCTGAAGACCAGCTTCTCCGTGTAAACGGCAAATCATTGGTTGGTTTAACCAACCAATCAGCGATGGAAACGCTCAGACATGCGATGCAATCCACGCGACCTAATCAAGCGTTCATTGACGTCACTATAGCGCGGGAACAGGATGAAACAGTCCCTCCTCCTGGGGCGTTACTCCATAGTACCTCCCTTGAGAAGCTTAATGCCCCTGATCAAGAGAGGCCCATTGAAGCGGGATCCGAGAAAAAACCTGTCGAGGAGCcaccgcagaatttctccgaGACCGACGGTGGTTTGCCTAACAAAGGAAGACTTTCCAGCAGTGGATCCACTGGAGAGGACCAATTTGATGAACCCATTGTTAAAAGGAACTTAACACCCCTTCGAGCTCGAAACGCTGTTCAACGTAACGATTCCTACTGCGTAGCAGTCAATAAAAGTCAAAGTGCTGGCGGACAGTTATACAGTCCTTTTAGGCAACGTCCAAACCATCGACCCAGTCCCCTGGCTGTTGGAAATGACCGACCGCAAGCTTTCGGTCCCAGTGTTCCGGCAATGACATCAACACCAGTGGAAAATCGAACAAGTGTCGCTCCGTTGAACGTTCCTACAGAAAGGCCAACTAGTACTGTTGCTATACCAACACCACCATTAGGAAGCACTGATGAGAGACCTTTGGGTCCAGCTGCTCCTTCACAGGTTTCTTCAAAACCACAGCCACCTCCAAGATGGGACTCTGAAGCGGATACTGCGAAGGTTAATTACGGTTTGCCACCAGGGCTCCAATTACGGCTCAAAATGCCGGACAGACAAAAATCACCTGAGAGAGGAACCACCCCCACTACTCCGCCACCCCCTCCCGCTCAGTTTTCGAACCCGTCACCCACAAGGGATTTTCCTCCTTCGTACGATCAGGCGGTCGCCCGGCTAGGGAGGACTCCTCACCCGTCCGTCAGCTCAGAACCGACCACCCCGGTCAGAGAGCAGCGGAAGTCGTGGCACGAGGACATGAACGGGGAAACTCCCATCATCCGGCCACCTAGCCCGTTTTCCTCCGAAGAAATGAATCCATTCCAAAGAGATGGGTTCGGCAGGTTGTCCATGTCGGAGAAAAGGGGACGAGCTGCACTGGACGCTAGGCAGTCGGAGTACTTCATTAAACGAGATCAAGTGGAAGATGAAGaTTATAGCTCTGATGACGGCAAGGTCGAAGAGACAAaacccgatataacgaataaacaCCCTCCTCTTAGAAAGGCCGATTCAGAAGAGCTTCTGCGAGAACAGTTCGAAAAAGGTCCCCAAGACGAAAGACGATCGCTTCCTTTCGGTCGGATGCAAAAGAGCAAATCTACTGGTCAGCTTAAACATGTCGGCGTGaaagacaaaaataaaaagTCAAAGAGCAACGATAATCTGAGTTTCACCAATGCTGTGGAAAGTGCCAACCACTCTTATCCAGGTGGTGACGTACCTAATGGTCACGCACGCTTAAGTCCAGAAGAAGAGGTACCTATAACAATGAGGAGTAACGCTGATTTCACTGCAGTACAACAGAAGCTTGCTGTCAAGAAGCCTTTCTACAAAGGCATCGGAAATGTGTTCAAGATCGGCAAAGGGAAGCGCGGGGATTACAGTTTGTCAGACAATGACGGACCCGCTTTCAAGCACACATACAACAGGGAAGCGCTAATCGATTTTCCCGCCGAACAGCGGTACCGACAGCTTGTCAATCATTACGGGCAGGAACAACCCTCCGATCGCGCCAGAACGCTTCCGTCTCGCAGCAAAAAGAAACACGACGTTAGAGACAAAGGACACGAAGAAAAACGAGCGCCTCCGATGATCGGAAGAGTGACAATTACTGCGCCTACTAGGGTTTAA

Transcript

BRAKERRLHT00000029079

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q99NH2	Partitioning defective 3 homolog OS=Mus musculus OX=10090 GN=Pard3 PE=1 SV=2
Q9Z340	Partitioning defective 3 homolog OS=Rattus norvegicus OX=10116 GN=Pard3 PE=1 SV=1
Q8TEW0	Partitioning defective 3 homolog OS=Homo sapiens OX=9606 GN=PARD3 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002869 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00595 all species →	PDZ	PDZ domain	Domain	Interproscan
PF12053 all species →	Par3_HAL_N_term	N-terminal of Par3 and HAL proteins	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001478 all species →	Domain	PDZ domain	Interproscan
IPR036034 all species →	Homologous_superfamily	PDZ superfamily	Interproscan
IPR021922 all species →	Domain	Par3/HAL, N-terminal	Interproscan
IPR052213 all species →	Family	Partitioning defective 3 homolog	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR16484 all species →	PARTITIONING DEFECTIVE 3 RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0000226 all species →	Biological Process	microtubule cytoskeleton organization	Interproscan
GO:0005912 all species →	Cellular Component	adherens junction	Interproscan
GO:0005938 all species →	Cellular Component	cell cortex	Interproscan
GO:0007155 all species →	Biological Process	cell adhesion	Interproscan
GO:0008104 all species →	Biological Process	protein localization	Interproscan
GO:0016324 all species →	Cellular Component	apical plasma membrane	Interproscan
GO:0030010 all species →	Biological Process	establishment of cell polarity	Interproscan
GO:0035091 all species →	Molecular Function	phosphatidylinositol binding	Interproscan
GO:0043296 all species →	Cellular Component	apical junction complex	Interproscan
GO:0045197 all species →	Biological Process	establishment or maintenance of epithelial cell apical/basal polarity	Interproscan
GO:0051660 all species →	Biological Process	establishment of centrosome localization	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
K04237	PARD3; partitioning defective protein 3	-	Protein phosphatases and associated proteins	ko01009	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 Dendrophyllia cribrosa 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 Dendrophyllia cribrosa, 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 →