Gene detail

Detailed information of BRAKERYMEP00000036573.1 in Astreopora myriophthalma

Genomic Location: BLFK01001079.1:419010...437937
NR annotation: XP_029179281.2, AT-rich interactive domain-containing protein 4A-like [Acropora millepora]
Species Astreopora myriophthalma · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

BRAKERYMET00000036573

ATGGATGAATCCACCAAAGACTGGGACACAGTGAAAGacgtttttaaaataacttcaaagaaaaagagtGATGTTTTGgatttaaagaagaaaaacattgaACGTATTCCAAGTGGACTGCTTCAactaaatttttcaagtttgagaTATCTTTATCTTGAGGAAAATGCCATTTCATCTTTGCCAGaagatttctttgtttcttttgcaaGTTTAGTATGGCTTGATCTCAGAAACAATGAACTTAGTGAAATTCCCAGAAATGTTGGAAGGCATAAGAGTCTGAAGACACTATTGCTAGGAGGAAATCAACTCAGGTTTTTGCCTCTGGAAATGGGATTTGTGAAGACATTAAATGGACTGAACTTATTTGATAATCCCCTAGAGGATCCACCACAGTCAGTGATTTCCAAAGGTATTTATGCTATCAAAGCATACCTGCTTGGAAAGCTTGGCATTAGTGCTGGACAGCTGGAGACCGAAGACAGAGAAACAGGCTACCTCAGAAGCACTGAAAGTGAAGACGATTTAACAGGAGATGAGGAAGAAATGAGTAAAGAAACTAACAGCATCAGGGACAAAACTTCAGAATACAATAAGAGATGCATGCCTTCTAACACTAACCACAAGGAAGTTGATCATCTTACTACGGTGTCAGTGGACCCGAGAGTTGCCATGTCTCATTATGGAGCACTGCTTGGTGATATCCCAAATTCGTATATTTTTAAACCTTGGAAAACTGGACTGTTCTTTAAAAAGGAAgccCTTGCACAACCTCATTTTTCAAGGAAAGTGGCAATGAAAAAGAGGGAGTTTCACGCTGACAGACACAATATCAATGGATATGTTGTCTTCAAAGAGAAGGAATGTGCTTCCAAATCATTAAGGAGCAATGGTATGGAAGTTGATGGTTTTCACATCAGAGTTGATTTAACTGGGCAAAATAATAAGCATGATCATGCatgttcaatatttgttggAAATTTGCCGTTTGATACAGAGGAAGAACCATTGCGGCAAGTATTTGTAGACTGTGGCACCATTGAGGCTGTGCGTATTGTTAGGGACAGCAAAACCAGCATTGGCAAAGGATTTGGGTTTATTCTTTTTAAGGAAAAGGAGGCTGTaatgtttgctttaaaaaagaacagaacagaTTTCCATGGGAGACCATTACGAATCTATCCTTCTTCAGAAAACCCACAACAAGGCCAATCAAAACAAGGCCAGAGGAAAGGACCCAAGGCTTATTCATTCAGTGGAATTACTGCAAAACGAGGGAAAACCAAGCAAGGACTAGGAAAAGGACAGAAAGCGAGACAAGGCCTCAGCACAAAACCTCTCAAAAATCAGAGATTTCAAAAAGAAGCAGCAATTAAACGTGACAATACCAAGAATTTGAGTAGGGCTAGTAAGATTTCAAAGACGAACTCCAAGCAAAATTTCAGAGGCACTGATGTAAGTGCCAAGTATCGTGGAGCTTTCTGCGAAGCCAACGTGAAAGTCGTGAAGAAGCTTGTCAAATGCAAGATTACAATATCTAAAACAAACACTTCGCTCACAGTCCATGATGATTGTGTCAAAGGCGCTCTGAAGGTGGGAGCTACCGTTGAAGCCAAAACTCCCGATGGACAATTTATGGAAGGAGTCATTACAAAACTTACAGATGCTAGTGTTTATACCGTCGTTTTCGATGATGGCGATGAAAGAACATTAAGGAGAACGTCTTTGTGTTTGAAGGGGGAAAGACATTTTAACGAAAGTGAGACTTTAGACCATCTTCCTCTTACTGATCCAGAGAATTTTGGTACCCCAGTTGTGCAGGatggaaagaaaaggaaaaagagaagacTGAGCCAGGCAGCCAGcATGGATGACTCAGAGACTGAGCGAGATGAACAAACACCTGCTGTGGTGTCATCGAAAAAGAAGTGTCTGTTTGATGACAGTATTGTTGGGAAGGTTGTCATTGTGGAAAGTGGTTCAAAGAGAAGGAACATGTGGTTTCCTGCATTGGGTGTTAATCCAAGCAAGAATGAGGTTGACTTAATAAAATCAAAAGAGAAATGCCTTGTGCGTTCGTTCAAAGATGGAAAATATCATGTGATAAATGTCAAGGATACGAAGGATTTTACAAAGGATCAGGATCCAGTGCATAGTGTGAAAGGCGAGAACAGAAAGCTGAAATCAGCTGTAGACAGAGCACTGGCTTACGTAGAAACAGGAAGAGTACCCAGCATCTGGGAAGAAAATGCTTCTGATGTGATAGTTCACGAGGACAGCGAAGAGGATTCCAAAAAGGCCCATTCTTCTGAAGATGAGAGCAGCATTGATGAGGATGGAGAGAAAAAAGCCTTTAAGGAGAAGCTGTTAGCTTTCATGAAGGAGAAGGGAACACCAATTACAAGACCTCCAGTTCTGGGAAATCAAGATTTAGATCTTCACAGGCTTTACAAGATGGTGCAAGAACATGGTGGAATGGAAAAGGTGTCAAACGAGCCATCCCTGTGGAGAAAGATTTATCAACAAATGGACATCGCTGTTGTGCCACCCAGTGCATCACACCACATTAAAATGGCTTACAAAAAGTACCTTTATACTTTTGAACTTCATGAGAAGGAAGCACTTAAGTCACCTGATAAAGATTTTGCTGATCACAACTCCAGCGACAAGAATATCAAAGCTGAAAGTCCTGAGAGTCCTGCAGACAGCAGTGACGAGAAACATTTGGAATGCTTAGAACCTTTACCAGACCTTGATGATGATCAGGATGAAGTCATAGTGAAGAAAACAGAGTGCAAACAAAGCACACGGATCAAGGAAATGAAACGACAGCAAAGCCGTGAGTTTGACAGTGGTGTGCTCAGTGACGCTCAAGCTAAAAGTCTTGAGGAGGATGTGTCAGTTGATGTTGTCAATAGTCCAGAGTCATCGTCTGATTTGAGTGAGCCACCTTCTGACAGCAAATCTGATATTCCAGTGGATGAATGTGCATTTGAGGTTGGGGACAAAATACAAGTCAAGTATGGTCGCGGACGGAATCACCGGCTCTATGACGCTAAGattATTCATATCGACCCAGAAGCCAGTGAAGGTACCATGTACTGTATTCATTATGCCGGCTGGAATAATAGGTATGATGAATGGATAAAACCCGAAAAGATTGCTGGCTGGGGAACCAGACAGACGCGAAATAGGACAGGAGGTGCTGGCAAAGCACAGGAGTCTATTGCAAAAGCAACTCCAAAGCCAGTTGTACGACCAACAGCTAAGCCTGCAGGCAGGAGGACACCTAAGACAGTAGGAGGGTCTGTCAAGGAAGCCAGCTCCAAACAGTTGCCTGCACAAAATGGTGCAAAGAATTCTTTAAAGAGACCCTGCTCTCCATCAACAAGGTCAGGGTCATTGTCACCATCGCTTGGAAAGTCACCAAAAACAAGTTCAGGAAGAGGGACAAGTCGCACCAGGTCGGAAAGGAACTCACTTTCTGAGATGTCAAATGGAATTGATGAAGTGAAAAGTCCTACATCAAGAAGAAGGCAAAAGTCAGCAACCCCAGAACCTTCATTAGATCAACAAAACAAATCTGTGGACATAGTGAATCATGTCCAGTCAATTCCTGACACCATTCCGGAAGAACCTGACACACAAGCAGTGGAAGAAAAGAGTAATTCTGCATCAAATAGTGAGTCGGAGGAAAACAGTAAGAAAGCAACTCCTTGTGAAAATGGAATAGCACATGAAAATCCTGAGGCAGAGCAAAAATCTGACCACAGCTGTAGTACATCAAATGGTAAAAGGAAGGACAAGCATAAAAGAACTATAAATGGCTTAATAAAAAGTGCCAGATCCCCTGAAACAATAAGTAAAGATTTAGAAGACATGAAAGATACCTGCTCTGAGCCCAAGAAAATTAAAGTAGAACATGAGGTTACCATGCAAGATGCGGAAGTAGAGAAATTTCTTAAAGACGGCACAATAGCTACAACTCCAATCCAGCCTGCACAAACACAGGGTACACCAACTGCTATGGAAACGGTCTCTTCAAGTCCATCGTCTTCGGAAGACACCAAGTCTGAACTTACCACTGACACTGTAGCATCAAGCTCTGCACAATGTAGCAATGGAAGTGAAAAGGCTAATGGCCCTGTGGAGAACACTTGTGGGAGAAATTCAAATCAAAAGATTATAGAACATGATAAAAAGGATAAAGATACCAAACCAGAGAAGAAAAGCTCTGAGCAACATCACAGGAAACATAAGAAACGGAAGGAGAAAAGGAAGCATCGTCATGCATCTGGTAATGACAGTACAGGCAGTGATGCCCCAGGGAGTCCATTGTATAGTCAGCCTGCAGGAGTGTTTCCATCGCCACGTCGGCCAAGAATGTCTTTTGATATGGATTTAGAGGAAATTAAAGCAAAAGAGGATGGTGGTGAACGCATCAGATTACTCCAggataaaataaatgaaatgaggAAGATCTATAGCTCTCTAAAAGCTGAAGTAGCCAGCATtgacagaaagagaaaaagactCAAGAAGAAAAGAGAGGCTGTTGAGGCACAAGAGTTACAAAAGTCCATCccgtcatcatcctcatcatcgcATACCATTCCTTCGTCAAGTATCCCTCCTGTGGAATGCAGATAG

Transcript

BRAKERYMET00000036573

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P29374	AT-rich interactive domain-containing protein 4A OS=Homo sapiens OX=9606 GN=ARID4A PE=1 SV=3
F8VPQ2	AT-rich interactive domain-containing protein 4A OS=Mus musculus OX=10090 GN=Arid4a PE=1 SV=1
A2CG63	AT-rich interactive domain-containing protein 4B OS=Mus musculus OX=10090 GN=Arid4b PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005753 (this species only) · gene tree & orthology
Transcription factor family	ARID · all TF in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF08169 all species →	RBB1NT	RBB1NT (NUC162) domain	Domain	Interproscan
PF01388 all species →	ARID	ARID/BRIGHT DNA binding domain	Domain	Interproscan
PF11717 all species →	Tudor-knot	RNA binding activity-knot of a chromodomain	Family	Interproscan
PF00076 all species →	RRM_1	RNA recognition motif	Domain	Interproscan
PF13855 all species →	LRR_8	Leucine rich repeat	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan
IPR036431 all species →	Homologous_superfamily	ARID DNA-binding domain superfamily	Interproscan
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan
IPR003591 all species →	Repeat	Leucine-rich repeat, typical subtype	Interproscan
IPR012603 all species →	Domain	ARID4A/B, PWWP domain	Interproscan
IPR002999 all species →	Domain	Tudor domain	Interproscan
IPR001606 all species →	Domain	ARID DNA-binding domain	Interproscan
IPR025995 all species →	Domain	RNA binding activity-knot of a chromodomain	Interproscan
IPR000504 all species →	Domain	RNA recognition motif domain	Interproscan
IPR034221 all species →	Domain	RBM34, RNA recognition motif 2	Interproscan
IPR032675 all species →	Homologous_superfamily	Leucine-rich repeat domain superfamily	Interproscan
IPR016197 all species →	Homologous_superfamily	Chromo-like domain superfamily	Interproscan
IPR051232 all species →	Family	AT-rich Interactive Domain/SWI1 Chromatin Remodeling	Interproscan
IPR001611 all species →	Repeat	Leucine-rich repeat	Interproscan
IPR000953 all species →	Domain	Chromo/chromo shadow domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13964 all species →	RBP-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0000976 all species →	Molecular Function	transcription cis-regulatory region binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:0005515 all species →	Molecular Function	protein 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 BRAKERYMEP00000036573.1.

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 Astreopora myriophthalma 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 Astreopora myriophthalma, 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 →