Gene detail

Detailed information of evm.model.HiC_scaffold_141.6 in Chrysaora quinquecirrha

Genomic Location: HiC_scaffold_141:55054...104178
NR annotation: XP_020620866.1, lisH domain and HEAT repeat-containing protein KIAA1468 homolog [Orbicella faveolata]
Species Chrysaora quinquecirrha · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

evm.model.HiC_scaffold_141.6

atgatttgctctaaatctcggcttgattcggaattggataaaatacggtctattctcattgaaaacggttaccctggggacgtcatttcggattgttttcgcaagaagatcgcaagtttttcggctgataaaaagtatggtccgcaaaagtgccctgtttacctaaaaatgcgttggataggaaacgtctcattgcgattcgaaagtcaaattaaaaggccattactaagtgcttcgctgctgccaaccctgggaAGGTCAGCTAGCAATTTGACTCTGGATTCAATTGATGACTTTTCCAGATATTCAGATGATGCAGGGAGAGAAACTGATGAAAAGGTTGCAGTTTTAGAATTTGAGCTGAGAAGagcaaaagaaacaataaaagaGCTCAGAGAAAACCTCACTGAATATGCTAAAGGTACCAAGTCCAACTGTGTATTGTATGATAcaagtttttttctttttcaggagCCAGTTAAACCATTTGAATTACGTGCATTGAACTTCGTGACAAGTGaatatttattgaaaaatgagTATAAGTTGACTGCTGTTACTTTTGGAGAGGAAGTTGGGGATCAGGACCTTGATGACTGGGATGATGTTGGTGTAAACACTCCAAGGCCCCCAaatcttttgcatttatttcgAGATTATGGCAAACATGTTATAAAGCCTATAGAAGAGGACAAAGAAGAGATTGAATGCCTTAAAGAGGAACTCCACAAACTGGATGCCGAGTGTAAACATTTGGCGGAGGAATGTGGTAAATTAAGAGAAGAAAACAAGATGTACCAAGACGAAATTGCCAAGAAAGAAAGTTTTCAATTCGACCAAGCTGTGCAGGAATCATCAGAACCTTCGCCAAAATCTTCCTTGGTCAGTACAGATGAAACTATTGCACAAGCCGAAACCGAACCGCATCCTAGAGCTCAAGAAAGCAAGCAGTCAGAAGCAATTGTTATTCCGGATATAGTCGTGAATGAAGATGCAACGATGCCTAAATCTGAAGTTTATGCTGACGAAGATTCCATTAAGAATCTCGATGTTGAGTTAGAAACTCACGATATGCAAAGCAATGATGATAGTGTGTCAGTAGAAGAACTGCTTGCTGTCAGTGAGGCCGACGGCGACAACCATTCAGAAGATAGTTTCCGTGATATCGCTGAAAGtaaagaaacaaatgaaagtCAAATGGAAGCCGAGgagCCAGTTAAACCATTTGAATTACGTGCATTGAACTTCGTGACAAGTGaatatttattgaaaaatgagTATAAGTTGACTGCTGTTACTTTTGGAGAGGAAGTTGGGGATCAGGACCTTGATGACTGGGATGATGTTGGTGTAAACACTCCAAGGCCCCCAaatcttttgcatttatttcgAGATTATGGCAAACATGTTATAAAGCCTATAGAAGAGGACAAAGAAGAGATTGAATGCCTTAAAGAGGAACTCCACAAACTGGATGCCGAGTGTAAACATTTGGCGGAGGAATGTGGTAAATTAAGAGAAGAAAACAAGATGTACCAAGACGAAATTGCCAAGAAAGAAAGAAggccaaagaaaaacaaaccagCACTTGAAAAGAAAGCAGGGCATGCTAATGTGTCATCAAGTGTAAGTGTAGAAAGTGATGAAGATAATCATCTTTTTGAAAATGCCGTGCAAGTTGTTGCAAGATGTCTACCAAATGTCATTCCTAATGTTTTGCTCAACAAACGAGAGGAGCTAATCCCAATTATTCTATGTGTCGTTCGACTTCACCCGGATGTTAAAGTCAGGGATGGCCTGCTGCATATGCTCTTCAACTTGATCAAACGACCTGACGATGAACAGAGGAGGATGATTATCGATGGCTTCGTCGCCTTTGCCAAAAAAGTTGGGCCAACCAGAATTGAAGCTGAATTGCTTCCTCAGTGTTGGGAACAGATCGCACACAAATACCCCGAACGAAGATTACTCGTTGCAGAAACATGTGGGTGTTTGGCACCTTATATACCTGCTGAACTTCTGAGTTCTTTAATGCTCTCCATGCTGAAGCAGATGATTCAAGATGATCGCAGTGAAAAAGTCAGAGAAGCTGCAACAAAAAGTTTAGCCTTGACGTTGGCttttgttgatgatgaagacaaGTACTCACAGgCAATCAGCCTTCTTATGAAAACATTACTGGACAACTGTGAGCCAGTCTCAGAAGCATCAAGAAAATTGCTTTTGCCAGTCATTGCTGTTTGGACCATAGAGCTTGGAAATCTACATTCACATATGCTGAGCCCTCTTTTAGATACTGCAAAGTCGTTATTAGAGGATGCTTCCAGAGAAACTCCTAAACTTGATGATGAAAATTACAGCCATTCATCACAATCTCTGGATTTACATTTTAAAATTATCTTTGGGTGTTTCACAGATTTGGTTCCATTGCTGTTTGCGTTTGTGTTATTGACAGCTCCATTTCACGTAGACGAAACTGAAAgtgaaataaatataaaagAATTCCGTCTTCCATCTGCACAGAATATTCTAGAAAGAACTGAAATCATATTTGGTGATGATCACAAATTAGGAATTTTTGTAGATAAATTTGATAGACATTTTGAAAATAATAGTGCTGAATCGTGGACTGCCATTGATTGGGTTTGTGAAAATGctggaaaccttcctcacttaacaattaaaaataggcgtgttttgagtgttgcaaaatattttctattgttctactggACCTTCCTTCGGTCAATGACCGGTCAacgaccgtgtgaccgtaactttttcctgactgaTCGTACTAGAATTACTAATCTACACGGTCTCAGTCACGCTCATAAAATCTGGACCAACAACGACAGCAGCTTTCAACAACAACCAGTTTGTGCAGCTTtccagcaacaacagcaactaaagatggtagctgcgataactgggactcgtgtaataagtctaggatcGTACCTTTTTGGATACGCTACTGAAgtggatccatttggatccgttcccgatccgTCCCCGTGTAAATCCGATGAAACTAGCAATTTTTATCCAAACAGGTTTGAGCAGATGTTGTCAGCTCGAGGTGATGGAGCAGCTGATTATACCTCATTTCGAGAAATTAATGAGAGCAACAGATTTTGCGCGACGCGCACGATCCGCGATGCTATCGCGGACCCCTCGATAGAGCTTTCGGATCGCGAGGTCCGCGATAGACCCCTCGATCCACGCGATCCTCTTGCTCTATCGAGGGGTCCACAATGTCGATCGAGAGGCCCGCGATCTCGATCGAGGATACGCGATCTCAATCGAGGAGTCCGCGATTGCTCTATTGTTATATACCGGCGGATGAGAAAGTTAGGTACAAACTCAGAACTCCAAAAAGACCTTGTTCAAGTATTACGAGAAGCTCTTGTGCACCCTTCGACTGTGGTCAGGATAGCAACAGCTCCTCTACTAGAGATTCTTGTTCCACTCGTTGGTAATGATTCGCTTTTTTCTCAAGTTGCATCCGCTCTAATAACACTTTCCAATGATCGAGAATTCGCTGTCAAAGTTGCTACTGTATCAGCCCTTGGAACTGTAGTCGAAACAAGAACGGATAAAAGTCTTTTAGAGAAGATTTGTCTTCAACTTCAGTCTCTGATGGACGATCCTGGCTTGAAGGATAATATAGAACTGCAGAAAACTTTGCTGCGAACATTTTCACGGATCATTCCGAATTCAGAACCCAAATTCAGAGAGGACTTTCTAATACATAGACTACGTAAAATGGTTGAGCTGAATAGCTTCATTGAAGATTTGAAGATCCAGGTTGATATGGCACGTGAACTCACTCAGTCTTTAAGTGCACTGTTATGCTGCTATATTCCTGTAGATTTAATTTCGTCACAAATCATTCCAACTCTTCGATATCTAGAACGTGACATGAGAGAGCTCGCGCCAGATGTTTTCGACACAGTTTCAACACTTATACTTGACGCTGAACATAGAGTGAAAGCTGACAGTGATAGCTCTGGCTCTTCTGCAAGTGCAAAGGATGAAATGAAGAACAAACTGCTTAGTGGATTTAATAGACTGAAAGATGTGTCACATAAAAAGCGagacattttcaagaaaaaagatagATTTCGCTGGCAGCGAAAAACGATGTCCATCTTCACTGAAGACATGAAGTACTTTGTAGTTTCGCTCtcttgtttttctctttttgtaATGGCCGCTTGTGAGAGGACAAAGCCGCGAGAGAAATTCTTCAAGATTTGCCTTACTGGACAGAAAAATGTCGGGAAAACGTCCATATTTAATGCAATAAGAGGCAAGCCGTTTACTAGAAATCCAAAAGCAGAGATAAATTATTATTCGCATGTGGTGAACGTCGATGGTGAAAATGTTAAGctcaAAATCTGGGACACTGCTGGGATGGAAGAGTACAATTCATTGACAGAAAACTATTACAGAAGTGCCAAAGGCATTATTGCTGTGTATTCAGTAGTATGTAGTGAAAGCTTCACACATGTTTTAGAAGATGTTAAAGATGTAAAGAACTGTGACTATGCTCCAGATGCACTGTTCTTTCTTGTTGgtaataaaattgacagaaattCAGATATTCAAGTGCCAAAGGAAAGAGTCAATCATCTACTTTTAGAGGAACCTGGGAAATTTCAGAGACATTTTGAAACATCTGCAAAGTCACATCAAGGAATAGATGAGTTGTTTGGTGGTATAGCTCACTCTCTTGTAGCTGCTCATTCAAGACCAGTTGCAGAGGGGGAAAATGATCTCAGGGAACGCTATGAAAATAGAGGGTCTCGTTGTTGTCCAAATTAG

Transcript

evm.model.HiC_scaffold_141.6

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q148V7	RAB11-binding protein RELCH OS=Mus musculus OX=10090 GN=Relch PE=1 SV=1
Q9P260	RAB11-binding protein RELCH OS=Homo sapiens OX=9606 GN=RELCH PE=1 SV=2
Q6P6Y1	RAB11-binding protein RELCH homolog OS=Danio rerio OX=7955 GN=relch PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004191 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00071 all species →	Ras	Ras family	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR006594 all species →	Conserved_site	LIS1 homology motif	Interproscan
IPR040362 all species →	Family	RAB11-binding protein RELCH	Interproscan
IPR016024 all species →	Homologous_superfamily	Armadillo-type fold	Interproscan
IPR011989 all species →	Homologous_superfamily	Armadillo-like helical	Interproscan
IPR005225 all species →	Domain	Small GTP-binding protein domain	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR021133 all species →	Repeat	HEAT, type 2	Interproscan
IPR001806 all species →	Family	Small GTPase	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR32059 all species →	RAB11-BINDING PROTEIN RELCH	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005802 all species →	Cellular Component	trans-Golgi network	Interproscan
GO:0032367 all species →	Biological Process	intracellular cholesterol transport	Interproscan
GO:0055037 all species →	Cellular Component	recycling endosome	Interproscan
GO:0005525 all species →	Molecular Function	GTP binding	Interproscan
GO:0003924 all species →	Molecular Function	GTPase activity	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_141.6.

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 →