Gene detail

Detailed information of evm.model.HiC_scaffold_14.486 in Chrysaora quinquecirrha

Genomic Location: HiC_scaffold_14:5985611...6014307
NR annotation: XP_047122749.1, protein phosphatase 1 regulatory subunit 21 isoform X2 [Hydra vulgaris]
Species Chrysaora quinquecirrha · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

evm.model.HiC_scaffold_14.486

ATGACAGAAAAGAAATTTCCACTTTCATCAACATCTCCTCCACTATCGTTTGAATTGAAGAATGTTGCCAAAGAGCTTGAGGACAGTGATGTGGATTCGCATTGTGTATCAtcttattttgatgatgatgaaaatgAATATGGAGAGCATGAATTCAATGGACTTCCACAACACTTGTATTTAAAATGGAGAAAGGCAGCTTTAATTGTGTGTGGTGTGTCAGTATTCTTTGAGTTTGCTCTTGGATTCTCATCTCTTGttttctcGATTATATACAGAAGTCCTGGAACCTTTGGAGTTGCAaTTGACTCAGTGGTTGATATAGCAACTACCTTTGTTGTGATCTGGAGATTTTGTGGTCTTGCAGGCTCACATTTTTCCCTTGAAAGAGAACAGAAAGCTACTTATGGGATTTCAGTGCTGTTTATCTTGTCTAGTTTCGCTGTGTTTgcaaaagcaatttttgaccTGATCAGATCAAACAAGCCTTACCATCCGTATATCTTGTGTGTAATTGCATCGATCAGCATGTTCATATACACTGCAGTTGGTTGGGCAAAATACTCGATTTCAAGAAGACTTAAAAGTCAAGTTTTATTCTATGACGcCGTAAACACTTTCTGCGTTGATCTCATGGCATGTATGCTGTTACTAAGCCTTCTTGTGTATAAATATACCTCAACATGGTTTATAGGATCCATCGTCGCCATGCTAATCTCAACTTTCCTTTTTGTCTATGGTGCAAGTTTGTGCGCCCACTCAGTTAACGATCAACAATCATGGCCGCCGCAAAAGTCGATGCTCGAAAGCCCTCGGAATAAATGTAACTTCAGCATGGATAGTGAGCTCCATATCAAATATCAAAAGCTTGGACAAGAGTACCAAAAGTTGCGTGCCCAAGTCAGTGTGCTAAAGAAAGGTGTGATAGATGAACAAAGTAACAGCAAAGTTTTGCAGGAaactttgaaacaaaaggatcaGTCACTCAGAAAATATGAACAAGAACTGGACAGCTTGCAATTTAGAAATGATCAGCTGTCTAAGAGAGTGGAAATTTTGCAGACTGACTTAGATGTTTGGGAAAGAGGTGGAAGCAAGCCAAAGAGTCATGCTGATTACAAGCCAAATGAGATAAATGAAAGTGTCAGAGAACAGGAACTTCAGAGTAAAATTAGAGAAAATGAAATGTTACATGAACAGTTGCACGAAGCAAGTGAACAACATGAAATTGTAACGAAGAAGCTAAAAGAAAGACTTGAAATCCTCGAAAGAGAATCTGGTAGTCATAATAAAGTGTTAGAAGAAACAAATGCAAGATATGATCGAATTGTTGAAAGATTGCAAGAAGACAGAGCGATGATGGAAGGTAAAATAAAGAAGCAAGAAGAAGAGTTGAAAATTGCAAACATAATGATAGAGAAATAccaaaaacagcTGAAAGGAACACACAGTGAATTGAAATCAAAACTCGAAAAGACAACGAAGATTCTCAAAGAGAAAGTCCCATTTGATGACACAGCTGAAAGCAATTTAAACTTGCTTAACGTTCCTGTCTGTGACAGAGCTCATCAGatACAAGCTATAGATCTTGTTGATAAATTCACGAATCATTTTGTTGACTTCATGGCGGGCTTATCAGATTTTCATACTTATCAAGAACAGCGTTTGGGGATATTCTCCGCAGATGTAAAGCAAGAAGTCCTCAGTCCCATCAATGAGAAAGTAAGTCGTTTTATTTTAACTAGCCTGGCTACAAATCGACAAGCACAGCAAGCAATGAAAGATTTCAATGATTGTCTTAAATCAGAATACTTTATCTCTTTAGAAACGTGTTCTGGATTGCCAAATGTCTCTCAAAGCTTCAATAAATGCACAAAATATCTTGAGAAGTTATTGCCATACCAGATATTAAGTATTGAAGAGGAATGTCGACTGGGAACTTGTAATGAGAAtatggaaaaagaaaacaggaattttctaaaacttttgaaacaattttcatcGACATTTTCAAGATTGAATAGATACCTGTCACTTCTTGCATCTTTCAGTCAAAATTCAGACATAAAAGCAAAAAGTAGCGATTGTTTTAGACTGCTTTACAGACAAGTGGAGCTGCTTAACAACACTTCACAAGAGATGTGTAAAACGTACTACACAAGGACAGATGCTTACAATCGTTTACCATTGATTACCGAGAGATTGAAAAACACTGATGAGTGCATCATATCATCTCTTGCATCTAtggcaacagcaacagcaaagTTTGTCAGTTTCTTTGAAGAAAATCTTGATTTTATTGGTCGACCTTGTGGATTCAGGCGGAAAGGTTGCATAAGCGACAGTGATCAGGCGATCATTCCATCAGTCAAAACATTTCAATTAAAAGCTGCAAATTATATGCAAAGACTGCAAAAGGATACTGCACCGATAACTGTTCCTTATGAAATCGCAGTTAAAAATAATCGAACGTTGGTTACGTCGACTGAAAGTAGAGATACTCTGGCTGAAGAGGTTGCAAGTGCCAGAGAAGCTATCGCTAAACTTGAACAAGTAAGAAGAAATTCTGTTAGATTAAAGAAGGTTTATTATgcaattgattcagtgtTTTCTGCTCTTGGAGAGGAACTTGGCAAAATGAAAACTGAAGCCATTCACAGTCGATCTTCAAGTGATACAATTGATGATATTGTACAAAGAGAGAAAATTGTCAGCATTCCAAATCAATCGCCATCCTTGACGAGACAaatatcatcatcttcttcatcatcaactaAAACTACAACTGATCAGTCTTCATTTTCACAGCCAATTGGCACGATAGAGATGTGGAACAAAGAGAGGgaTGTTGGTGATTCTGAtcgtgattatgatcatgaagaACTTGTTAAAAGTCATCTTACATCAAGAATTACAGATCTTACAAAACAGCTACAATTTGCAGATAGCAAAGCAGTTACGCATTACGCAGAGTGTCGTGCACTATACAAACAACTGGTCCTGGCTGATAAGAGTAAGAAAAAGATATCAAATGAACTGAGTCAAGCAAATCGAAAAGTAGTTACTCTTGAGgATGATCTCGAGACGACAAAAAGAAGTTATGAAGATCAAATCAAAATGTTGAGTGACCATCTTTGTGGCATGAATGACAAATTAACATCACAAAAAGATCAGATTGACCAGCTtaaaactacaacaacaaatcCTTCGAAATCATCGATGAAACGTCCATTTGCTGAGTTACTTGAAGTAACGTGGCTGAGTTACTTGCAGACAAGAAAAGACATGATAAAATCTCTTCCTGTGGCACTTCTATTCTTCCTCCCATTCATTGGTTACTTTGCACCAATCATTGGGTTTCTGTTTCCAAAGAAATTGCTGTCACATCAGTTCTGGGATGTTGAACAAAGAAAGAAGTTTGCATTTGAGGATCACGTGAGGAGAAGTCAATATTATTTGCCATTGATACAAGAAGTTGGATGGTCAAGCCGAGAGTTGAAGAACCAAGATCTCTTTGAATTGTGCATTAAGGCAATTGATGGAAATCACTTAGAAAACGATGATCTCCTTGTATTACAAGAcatattcaatgatattttgATGAAAGTCGATAAAATGCCTAGGTTTCATTTGGAAAAACTCTGCAAAACATGGCTTCTTCCTGTCAAATGGTACATTCCCAGCAAAGTATTAAGAGAATTATTGACATACAGAATTAAGCAAataattgaagatgatgatgcaaTAAGGAGAGAAGGCATGGATTCCTTATCTGATTTGTGTATTCGACAGGCCTGTCACGCACGTGGTCTGGACAAATCATCATTCGATGTTCCAGTCATGAAAGATTGGTTACAAGATTGGATGCATTTGACCAAAAAAGTCACAGaTGGAAACTTATCCTTCGTTGCCCATTGTGCAGTATTCAAAACTATAAACTTTGGAAAAGATATGGAGAACGATAAAGAAGAAAATCGACTGGAGATGAGTATTTTGATGGAAGATTTATTGAAGGAGATAACAACACTCTCATCTAGGCTTGACGAGAGTCAATCTGACTCAAATTCGACTTCTGAAGTTGGTCAACAAAACATGATGGCTGCCCATGGGATTGACTCGTTGCAAATGAGAAATAAAGCTCGTTCAAAGAAGAGAAGAGGGAAGAAAAGACGGATTGATTGTCATCCAGAATTATACACGGAATCTGAGAGTTCATGTTCTGATACAAGCGAGGATGAAGCGATTCGTGATTATATTGAGAACGTAACAGGGGGAGCTGCCAATTCATCTAGGCCCACAGTGAGTGACTCTGATGAAGACTTTGTGCCAAGAAGAAGGGCTGTTAATTTATTAAGTGGTGTCCCTTGGAGTCCGATTGATGTAGGGGAGAGTGATTCATTTAGTGAAAACATAATGAGCTTGAGctcaagaaagaaaagaaaatcaagaaaatga

Transcript

evm.model.HiC_scaffold_14.486

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q6IR70	Protein phosphatase 1 regulatory subunit 21 OS=Xenopus laevis OX=8355 GN=ppp1r21 PE=2 SV=1
Q6ZMI0	Protein phosphatase 1 regulatory subunit 21 OS=Homo sapiens OX=9606 GN=PPP1R21 PE=1 SV=1
Q5ZL12	Protein phosphatase 1 regulatory subunit 21 OS=Gallus gallus OX=9031 GN=PPP1R21 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005487 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF10205 all species →	KLRAQ	Predicted coiled-coil domain-containing protein	Coiled-coil	Interproscan
PF21636 all species →	PPP1R21_C	Protein phosphatase 1 regulatory subunit 21, C-terminal	Coiled-coil	Interproscan
PF10212 all species →	PPP1R21_helical	Protein phosphatase 1 regulatory subunit 21, six-helix bundle	Domain	Interproscan
PF07766 all species →	LETM1_RBD	LETM1-like, RBD	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR019343 all species →	Domain	Protein phosphatase 1 regulatory subunit 21, N-terminal	Interproscan
IPR049372 all species →	Domain	Protein phosphatase 1 regulatory subunit 21, C-terminal	Interproscan
IPR019348 all species →	Domain	Protein phosphatase 1 regulatory subunit 21, six-helix bundle	Interproscan
IPR040024 all species →	Family	Protein phosphatase 1 regulatory subunit 21	Interproscan
IPR027469 all species →	Homologous_superfamily	Cation efflux transmembrane domain superfamily	Interproscan
IPR033122 all species →	Domain	LETM1-like, ribosome-binding domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR21448 all species →	SMOOTH MUSCLE MYOSIN HEAVY CHAIN-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005769 all species →	Cellular Component	early endosome	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0043022 all species →	Molecular Function	ribosome 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 evm.model.HiC_scaffold_14.486.

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 Chrysaora quinquecirrha 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 Chrysaora quinquecirrha, 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 →