Gene detail

Detailed information of BRAKERLUSP00000013127.1 in Blastomussa wellsi

Genomic Location: chr2:17791034...17843076
NR annotation: XP_020607071.1, protein RRP5 homolog [Orbicella faveolata]
Species Blastomussa wellsi · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

BRAKERLUST00000013127

ATGGCGACCAAGACGGTTCGCAGCAAAAGCAGCACCAAATATGGAACACCGAGCATTTTTCAGTCGAGACAAATTGAGGAGGAAGATTTTCCAAGAGGTGGTGCTTCTGCTCTGAGTCCACTTGAAGTGAGGAAAATCAAGAATGAGGCAGAGAAAGACATACTCTTTGGGAAGTCACCATCAGATTTGGAATCGAGCTCAAAAAgcgaaaagaaaaagaagaaacacaAGAAGACTACTACAGTGAACGAGTTGGATAGAAAAGTTGAATTAGAAGGGAAATCAAAACTTAAATATGTGGAGCCCCTCACATTCAAGAAACTCTATGTGGGGATGAAAGTGTTTGGAGCAATACGGGAAGTGAATGAATATGACATGGCCATCAGTCTGCCAAATGGACTGAGTGGATTTGTTCACATTACCCATATAAATGAGAAGATCTCTGAAAGATTAAAGGAAATGTTACAGGCTGATGACGGTAAAGATATTGCAGAGACAACAAGTTTTCCAGAGCTTGCCAAATTCTTCGATGTTGGATCACTGGTGCAGTGTTCTGTCTTAGAGCTGGAAAGCTCAAAACCcagacaaaagaaaatcaagCTATCTTTGGATCCTAAAGAGGTTAACAGTGGCCTGAGCAAGACATCTCTGAAGCAAGGGATGgtccTTCCAGGTTTTGTGAATAGTGTTGAAGACCATGGGTACCTCATATCATTTGGCATTGACAACACAAGGGCCTTTCTGCCAAAGAGCAAACTTAATAGAGAGTTTGAAGAAGGACATCCATTGTGCTTGTTGGTGGAGTCTGTGTCTGAGGAACAAAGGATTATAACAGTTAGTGCAGACAAAGATTTGATTCAACATTCACTGATCAAAGAAGATATGAAGTTAAAATTCTCTGCACTTCTTCCTGGCTTGCTGGTGAAGGCATCTGTAACTCAGGTAACCCAAAGTGGTCTAATCCTGAATTTCCTTGGAGGTTTTGAAGGATCTGCAGACACTTTTCATCTACCAAATTGTGGTGTAGATGCAAAAGACTTGGAAGAAACCTATCCAAAGAAAGCGAAGGTTAAATGCCGACTGTTGTATGTGAATGTGAATACGAAGACAGTCGGGCTAAGCCTTCAAGAGAATGTTGTTCTCAATAAAGCTGCCACCTTTGGTCAGTTGTCTGTTGGAGATGTCATTGATGATGCTACTGTTGTTAGAATGGATCAGGGACTGGGTCTATTGTTGAGATTGTCTGATGACATTCTTGGATTTACTCATATTTCGAGGGTGTCAGATGAACATGTGGAGAAACTGGGGAAGAAATACAAAGTTGGAAGCACTCATAGGTGCCGTATTCTAGGCTTCAGTTCGTTAGATGGCTTGGTTAACTTGACTATGGAAAAGTCTGTCATTGAGCAGCCATTCTTACGCTATCATGACATCAAGCCTGGAACTGTGATCAAGGGCAAGATAATAACTTTGGAGAAGTTTGGAATGCTCGTTTCTGTATCAGACCACATCAGAGGCCTGTGTACTACACTCCACTTAGCAGATATCAACCTGCAACACCCAGAGAAGAAGCTAAAAGAAGGAAAAGTTGTCAAATGTAGGGTTCTTTCAGTTGAGCCAGATCGTCGCCGAATGTTGCTCACTCACAAGAAGACATTGGTAGAGTCCTCACTTCCGCTTATTACAGATTTCAGTGATGCTAAGCCAGGGGTCAGCTCTCATGGTTTTATTACTGCCATCAAAGACTTTGGCTGCTTTGTGGCATTCTACAATAACGTCAAGGGACTAGTGCCTCGATGCGAACTTGGGATTCCAGCTGATACTGATCCTCGCAGTGCATTCTACATTGGACAAGTGATGGCGTGCCATGTGCTGAGTTGTCAGCCTGATCAGGCCAGGTTGAGGCTCTCATTTAAGTTACTAGAAGCCGATGTGGTGAACAGTACAGCTGAAGGCCTGGATGTTTTACTTCATCCCGGTGGCACGCCAGCATTTCTTCCGGTTTCCCATTTGTCCGACCATCTGAGTAACTGTGAGGCTCTTCTTTCTGTGTACAAACCCCCAATGAGACTGGCAAATGTTGTTTATTATGGCAAGAACAAAGACAAGTCCATTATGGTTTCATTGAAACCTTCTCTTCTTAAAGCAGCATCAGATAAGAGGATTTTAATCAACTTTAAAGACCTGGAGGTGGGGATGGTCTTACCAGGCTTTGTCAAAAAAGTGATGAGCTATGGGATATTCATTGAATTTTCTATGGGAATTTTTGGCCTTGCTCCAAACTCTtttctAGCTGATCAGTTTGTGTCAGAACCTGCATCACACTTTCAGACAGGGCGAACAGTCATGGCAAAGGTGACTGAAATTGACGCGGAGAGACAGCGATTTCTTGTTAGCCTTAAAATGTCCAACTGTTGCCCTGATCAGAGTGTAGAAGGGATCTCTGTACCTGGTGTGGAGCTGCTGGAAAATTTTGTCTCAGAGAGATGGAAGATTATCCAGCATCTAGCATCTAGTTCAGaaGAGATGAAGGCGCTGGCCTCCTTGAATCGAGGAACTTGTGTCAATGCAAAGGTTCTTAACGTCAAATTTCAAGGCATTGTATTAAAGCTTGCGGAGGGTTTGCAGGGTTTTGCTCCTCACCAGCTTGCGAAAGGAGTAAGCTGTGTACCAGGGGAGGTGGTGTTTGGCTGTGTGTTAGACTTGGATGTTGACAAGAAGCTGGTGTTAGTGTCACTGAATCCTGAGCTAGTAGCAGAGAGGAAGGCTGTGGAGATGCAGAAAGAGATACAAAAGAAGGTGAAAAGTGGGCGCATCCTCAACGCATGTGTTCAGTTGATCACAGATAACTACATGGTGGTCACACTCCCTCAACATAACTACAGGCTGGCTTATGCTCCCACTAAACTGCATTTGAATGACATCAGAGATGCGTCCAAGCGGTTTGCTGTGGGGCAACAGTATTCTTCAGTTGTACGAAGGCCAGGCAAGTTGGAAGATGGTCTGTTGCCAGTAGTGACGCTTCAAGAAAAGCAcattgaaaaggaaaatatcGTGCCTGGAGCTATCACCACAGCTCAGGTGAAGTCAATCAAGGATGTTCAGATGAACATGAACCTGTGTGGAGGAAAATTTCACGGAAGAGTTCATGTCACACACATTTGTGATGATATCACAGAGGGAGAGTCGCCACTGAAAGCCTTCCACAATGGAGACAGAGTTCAAGTCAAAATTCTTGGATTTCGCGACATGAAAACACACAAGTTTTTACCAATAACGCACAGAAATTTCACCAAGGCGGTGGCTGAACTTACAATGAAACCAAGTGAGTTGTCAGCAAGTGGCACCGAACAACAGAATGCCTCAAATGAAAGCAGAGATGGAAGCGAGACTGACAAGCAACTCACACAGTACAAAGTTGGCGAGGAAGTTAATTGTTTCGTGAAGTCGGCTACTGACCATTGTGTGTGGGTGATGGCGTCTCCGTCTGTTAATGGCAGAGTGGTACTGCTACACGCCTCATCCGATTTAGAGGTGTTGAAGTCGCTGAAGACCCACTTCAAACCAGGTGATGCTTATAAATGTGTTGTGTTGAGCATCGACGAAGAAAGAAGTTTGCTGGATCTTTCCCTGACTGTCAAAGCGGAATCTACCATCAAGGCGGACCAGGTTTTGACAGGCCAGATTACCAAGATTCTTCCCGACCAAGGACTCCTCGTCCGGCTACCCATGTACAAGTGTGGCCTGGTCACTCTGACAGACCTCAGGGACAGCTATGTGGAAAATCCTTTGGAAGGCTTTGAAGTCATGCAGCTAGTTAGGTGTTTCGTTTTGTCGACAACGGGAAAAGACCACTTTGATCTGTCACTGAGACCCTCAAGGACCGAAGCTGTGTCCACGGTGAACGAGGAAGTTTCAGGGACTGGTGAGCTGGACCGCGAGATTAAAAGCTTGAGTGACTTGAAAGAAGGAGATATCGTTCGGGGCTACGTAAAGAGCTGCTCTGACTGCGGTGTGTTTGTCAGGCTCGCACATCACATTGTCGCTCGGGTACAGATAAAGAACCTTTCGCAGTACTACGTGAAGCTTTGGAAACCTCTGTTTCCACAGGGAAAACTGGTGAAAGGCAAAGTATTAAGTGTTGACTCAACCAAAGGTCACGTGGAATTGTCCCTAAAGGGAACAGATGTTGGGGGACCCGACCCAGCTCCTAAACCAAAGCGGTTTGAAGAAGAGAAGCGAGACAAGGAAAGGAAGGAGCAGAAAAGGAAGAGAAAGAAGGCGAACGATAGCGAAACAAAGGATGAGTCAGACGAGGAGGCCGAAGAAATATTGAAGAGGCTCAAGACAGACTCCGATCATGAGGACAGTCCAGGAGGGGTAAGCGAGGAAGAGGACGATGGATCTGAAAGCAGTTCGGATGAAGAGGACCAAGACGCTGAGAAGCACAAGACAAACGGTGTCCCAAGATTACAGGTTTCCAGTGGATTTGACTGGAGTGAGGAGGGCAATTTCGGAGAGAAGCCGCAAAACAACAAAAGAGAAcatgaagatgacgatgaaaGCAGCGAGAGTGAAACCGAAGCCAGCTCTCAGGTTGCTCGCAAGAAGAGCAAACGGCAGAAGAGAGCAGCAAAGAAAGCCGAAGAGGATTTCTTGTATAAGACGGAACAATCGCTTCTAGACCAGGATCGCGTACCCGAGACTGCCGAGGACTTTGATCGCGTCGTGTTATCATCTCCCAACAACTCGGTAGTGTGGTTACAGTACATGGCGTACCATCTTCATACCACAGACATCGACAAGGCACGGGCTGTGGCAGAGAGAGCGCTGAAGACTATCTCATTTAGGGAAGAGCAGGAAAAACTGAACGTGTGGGTAGCCCTAATGAACCTGGAAAACTTGTACGGCACCCAAGAGTCCCTTGTTAAAGTGTTTGAGCGAGCCCTCCAGGAGAATGAGCCCAAGAAGGTGTTCTTTCAACTTATAGGTATCTACACAAGAACAGATAAATTGGAGTTGGCCGAACAACTGTACCAGACAATGTGTAAGCGATTTAGCCAAAGCAAAAAGGTGTGGGTCGGTTTCGGAACGTTCTACATGAAGCAGGGAAAGCTGGACTTGGGCAGGAAACTGCTGCAAAGGAGTCTGAAGAGTCTACCGAAGAGAAAGCatgTCGAAACTATAGTCCAGTTTTCTCTGCTCGAGTTCAGATATGGCGAGCCGCAGCGAGGGCAGACGATGTTTGAGAGCATTCTAACCAACTATCCCAAGAGAAGCGATCTGTGGTCCGTTTATCTGGATATGATGATCAAACAAGGAGATGTCGAGCCTGTCAGACAAATATTCGAGAGAGTGATCCACATCAATCTGTCCTCCAAAAAGATGAAGCTCTTCTTCAAACGGTACTTGGACTTTGAACGAAAGTATGGCGACGCTTTCAGTGTTGAAAATGTTAAGACCAAGGCTATGGAATACGTTGAATCCAAGGCGGCGCTAAGTTAA

Transcript

BRAKERLUST00000013127

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
A7MB10	Protein RRP5 homolog OS=Bos taurus OX=9913 GN=PDCD11 PE=2 SV=1
Q14690	Protein RRP5 homolog OS=Homo sapiens OX=9606 GN=PDCD11 PE=1 SV=3
Q6NS46	Protein RRP5 homolog OS=Mus musculus OX=10090 GN=Pdcd11 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003130 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF05843 all species →	Suf	Suppressor of forked protein (Suf)	Repeat	Interproscan
PF00575 all species →	S1	S1 RNA binding domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR003029 all species →	Domain	S1 domain	Interproscan
IPR012340 all species →	Homologous_superfamily	Nucleic acid-binding, OB-fold	Interproscan
IPR048058 all species →	Domain	rRNA biogenesis protein RRP5, S1 domain, eleventh repeat	Interproscan
IPR008847 all species →	Domain	Suppressor of forked	Interproscan
IPR048059 all species →	Domain	rRNA biogenesis protein RRP5, S1 domain, first repeat	Interproscan
IPR045209 all species →	Family	rRNA biogenesis protein Rrp5	Interproscan
IPR019734 all species →	Repeat	Tetratricopeptide repeat	Interproscan
IPR011990 all species →	Homologous_superfamily	Tetratricopeptide-like helical domain superfamily	Interproscan
IPR003107 all species →	Repeat	HAT (Half-A-TPR) repeat	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23270 all species →	PROGRAMMED CELL DEATH PROTEIN 11 PRE-RRNA PROCESSING PROTEIN RRP5	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006396 all species →	Biological Process	RNA processing	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0005730 all species →	Cellular Component	nucleolus	Interproscan
GO:0006364 all species →	Biological Process	rRNA processing	Interproscan
GO:0032040 all species →	Cellular Component	small-subunit processome	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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K14792	RRP5, PDCD11; rRNA biogenesis protein RRP5	-	Ribosome biogenesis	ko03009	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 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 →