Gene detail

Detailed information of acyt_s0146.g53.t1 in Acropora cytherea

Genomic Location: sc0000146_pilon:791450...806569
NR annotation: XP_015778161.1, PREDICTED: PDZ and LIM domain protein 7-like isoform X2 [Acropora digitifera]
Species Acropora cytherea · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

acyt_s0146.g53.t1

CAGGTCCATTAACCTCGGTTTGTGTTGGAGCTTGAAACCTCTTGACTGAGAGAATGAAAATCTGTAGTTAAGTGTGTGCGGATATATTATTCAAGCCTGTTGCTGAATTTTGACAAATGGCTGATACAAAATACACGGTTGTGATGAAAGGAGGGGGACCATGGGGTTTTCGTCTTCAAGGAGGGAAAGATTTCGGCTCTCCGCTTGCTATATCAAAGATTACACCGGGCTCCAAAGCTGATCTCGCAAACGTCAGCCCAGGCGATTACATCCTTGAAATTAATGGTTATTCAGCGGCAAACATGACCCATTTCGATGCCCAAGATGTCGTGAAAAACGCAAACGAACTCGACATCCTTCTAGAAAGGAGAGAGGGCACAAAGACAATTGCTTTCACTGAAACAATTCATTCTGCCAAATCTGATCAAAAATTCAACGCTAAGGCAAAACCATTTGGGGCGCCAGCAATACTGTCACAGCCATCACAGCCACATACAGCAGGGACAGGTCATACATCACCAGCTGGAGCAAGCACATGGCAGCCACCAACTGTCCAAGCTAAGCACGCCCCAGTTGCAGCTTCTGCCCCTTCTGTCTCCTCTGTCCCCCCTGCCTCCTCTGTCCCCCCTGCCTCCTCTGCTCCCCCTGCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAtttttcttttttttttttttttgtctgctgtttttttttttgtctgcattattGGCAGCAGTTGATCTCTCCGATGCAGACCTTGCACAGCATTTTAAACTGAATATAACTGACAATGGAGATGTGGGCTTTGCTGAGGAGTCGTCAGCGTGGGGTCATCCACCAGATCCTAAGGTCCAGTCGAAATCATTCAAGCGGCTTCAAAAGCATCTTCAAGAACATGAAGACGATGATCTGCCCCCACCACCTCCTGAGGCATATGATGACCAtgatggtgaccataatggtgaccgtgatggtgatAGCAAACAAATTCAATCCCGAACTTTCAGAATGTTGCAGGATGCTGTTGACCATGGAGAAACTGCTTCAAGTGTGTTTGACAGGCAGAAAGCTGACCGCAGTAAGCCTTCTGATCAGTCATTGCCAAAGATGTACCGCCCAGCTCCACCAATAATCAAGCCCGCTTCGAGTATGCCAGTGGCACCACCTGCGCCAGTCATGTCCCGGCCAGGCCAGCCACAGCCTGTTGCCCTCCCAGGAATGGTTCCAATGAGTCAACCAGTTGGCTCACCACCTAAGCGCAGTCCTCCCCATAAAATGCCATCAGCTGCTTCTCCAGCAGCAGTGTCACCCACCTCGAGAACCCCTCCTGGCCAACTTGAAGTGAAGAGGGCCCCTGCTAAACCTCCATCTGCTCAGCCTCTTGAAGAGACCAGGACTCCATTTTGTGATGCCTGTGGAGAGGAAGTCTTTGGCCCTTTTGTCAGTGCAATTGGCAAAGCATGGCATCCGGATCATTTTGTTTGTGATGGCTGTGGTGAATCACTGCAAAATCAAGGTTTTATTGAGGAAGGGGGCAAGTTGTATTGTGAAAAGGATTATAACAAGTATTTTGCCCCCCACTGTGACACATGTAAGCAGCCAATCCAAGGGCCTTGTGTTCAAGCCGTGGGCAAGACGTATCACCCGGAACATTTTGTGTGCTCATACTGTGGCCGTCAAATTGGTTCCGAAGGTTTCAAGGTTGATCGCGGAAAACCTTACTGTCAAGACTGCTATAACAAACTCTTTAGCGTAAAATGTACCTTATGCAAGCATCCGATTGGTGGAGGGGAGAGATGGGTTGAGGCTATGGGAGAACCTTGGCATGCCACGTGTTTCAAATGTCAGCGTCCAGGATGTATCACTCACCTCGAAGGAAAACAATTTTATCAATATGGCGGCAAACCATACTGTGTCCTGCATGGTGCGCCGTGACAGAAGTAGCGAATTTCAAATTTTTTTCTACGGCATGGATGGCAGCTGCTTCTTCCCTAATGTGAATGTAAAATACTGTGGGGTGTTTCGTGGGGTAATGGATTGCAGTGTTAGTAAACAAATAGTTATATCTTTTGGATAATGATCTTTAAAATCCTGGCTTCTAAATTTGTACTTAAAAGATCCGACCTCGTGAAATTGATACGCCTTGGTGCCTTCCTGGCTTCTTAGATCATCTGTGGAAAAAGGCGGTTAGCTCATCGTTGTTGAAGCGTTTCATCGTTGCTGTTAACTCGCCTGTGTTCTTTGAAAACAAATATGAACGTGAGAAGCGAAATAGCCTGAAAGAGATTGAGTAAAATGAAATAATAAATCGAAAAGAAAATATGTTACAGCAAAGCTTCCAAATTTTTTTGACATAATTATGCTGTACTTATTTTGTTTTGTGGAGTGTATTTTTTTATTCGCATGAAGCTTCGGCAAGCAGCGGAAGTCAGTGGAATCTTTCTACTTGAGAATAAGTAGTTTATTTTTGCATTGGAACTTCTTTTCATAAAATTAGCCTAGAGATCGTGGTAAGAGTTAGTGGCCTAAAAGTTATGAGAGAAAAGAGAGGAAAATTAACCATTGTTTCCTCCAATTTCTTGTCGGGCTTTCCCATAGGTTAACGCCGGATGCTTGTGAACATCTTTTGTAATATTTCTGCTTTTCTTTCTTCGTCTTTACTGTAAGTTTTGTTTCTCTTTTGGTCGCGATAAATAGCTTAGAATTGAGGTTTGTTGAATTGAAGGTTTTTTGGCTCGAAGTGCTTGTTTGCGCAAGATTGGAGTAATTTGACTAAATAATTAGTTCGCTGCAAGATTTGGCTCAATGCAGAGAGCTGAGGCTCGAAATAGTAGtttgtttgttttattttttttttctttCAAGATAAATTCTATTTCAATCAATAAATTTATGGATTTTAT

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q62920	PDZ and LIM domain protein 5 OS=Rattus norvegicus OX=10116 GN=Pdlim5 PE=1 SV=2
Q8CI51	PDZ and LIM domain protein 5 OS=Mus musculus OX=10090 GN=Pdlim5 PE=1 SV=4
A1ZA47	PDZ and LIM domain protein Zasp OS=Drosophila melanogaster OX=7227 GN=Zasp52 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002843 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00595 all species →	PDZ	PDZ domain	Domain	Interproscan
PF00412 all species →	LIM	LIM domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001478 all species →	Domain	PDZ domain	Interproscan
IPR050604 all species →	Family	PDZ and LIM domain-containing	Interproscan
IPR001781 all species →	Domain	Zinc finger, LIM-type	Interproscan
IPR036034 all species →	Homologous_superfamily	PDZ superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR24214 all species →	PDZ AND LIM DOMAIN PROTEIN ZASP	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0001725 all species →	Cellular Component	stress fiber	Interproscan
GO:0003779 all species →	Molecular Function	actin binding	Interproscan
GO:0005912 all species →	Cellular Component	adherens junction	Interproscan
GO:0030018 all species →	Cellular Component	Z disc	Interproscan
GO:0030036 all species →	Biological Process	actin cytoskeleton organization	Interproscan
GO:0031941 all species →	Cellular Component	filamentous actin	Interproscan
GO:0051371 all species →	Molecular Function	muscle alpha-actinin binding	Interproscan
GO:0061061 all species →	Biological Process	muscle structure 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
K19867	PDLIM5_6_7; PDZ and LIM domain protein 5/6/7	-	Domain-containing proteins not elsewhere classified	ko04990	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 Acropora cytherea 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 Acropora cytherea, 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 →