Gene detail

Detailed information of scaffold13.g71.t1 in Morbakka virulenta

Genomic Location: scaffold13:2958945...3072809
NR annotation: XP_047130653.1, rho guanine nucleotide exchange factor 11 isoform X3 [Hydra vulgaris]
Species Morbakka virulenta · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

scaffold13.g71.t1

GTTGATTATTTTTCTTTGGACATAAATTGGAGTTAACACTATTGAAATTGTTTTTCGTGCTTGTTAAACTTGGCGAAGCAGGGAAAGGAGTATCAGTTATCTACCGTAGTGAACTGTACAGTAGATTTAAAACTAAGCATTGACAGGTTGAAATGTAGTTAATGAAGGCAAACTCTTAAAGATCAATGCGACTTGCCTTCCATCGATTAAGCTTGATCTGTTTGGTTTTCTGCGATGGAAATTCAAGCCTTACAAGTACTGACCATTGGCACATAAAATTTGGATGTTACAGGACATAGATACTGTGTGGTTTATTGTACCGAAACTAAGAAGATATGAGTGTAAGGAGGCTACCAAAGGAACAGGAGGGTAGCTTAATCCAGAGATGCGTCATTGTGCAGAAAGATGAAAATGGATATGGTCTTACAGTCAGTGGGGATAATCCGGTCTATGTGCAGTCCGTCAGAGAGAATGGAAGTGCTGCAAAAGCGGGTGTTCAAGTAGGAGACAGGATAATCAAGGTCAATGGGATGCCCGTAACCAAAGCAAACCACATAGAAGTTGTGAAGCTCATTAAAAGTGGTTCATATGTTGCATTAACCTTGCTTGGAAAGGCTCCCGTTGAAAGGCCAAGTAGTGGAACACCGTCCCCTTTAGTGGAAAGATCATTTACTTTCAGCAGAAATTCAAGCACATCACCCACACAGAAGGATGCACAAGAGCAACAGCAACAACAGAATGATCGGGTGGTTTCTTTACAGCGGATGCTGGACCAGGAGTATCTGTATTACAACAAAACATTAGAATCTTATAAAATCGCCCCGTCATCAAAGCTGCAAAAGGATCTTGCGGAAACCCAGACAAGGATCAAAGCAATCGAAAGCCAGATACGAGTTATATCATCAAATCATAATACTCTCAAGCAACAGCTCACCTCACAATCAGCTCGTTCAGTATTTAAACCATTAAACGAAAACAAGCAGGCATCTCCGAAAGCTGTCAATCATAGCCGCTCAAAATCAGCTTACGCAATAAGATCCCACTCCGCTTCGGCCATTCCATATTCGTCACCATTTGCCTCTGATTACCCGAGGTCAGAGTATGACTTTTACCCAAGAGCAACAAGTTTAGACCATCCGGACGATAACGAGCCGGAAAGTAAATCGGATAGTCCACTTCCAGATTCTAGACCACCTTCTGAAGAAGGTGAACAGCAACCAGCGATGGCAGCGGCAACAAAAACAGCTGGACTTCAGTTAATTACATCGATAAACGAGGGATTAGAATCATCTCCAGTGGTAGAGACAACTGAACAACAAATGGAAAGTGAAAATACAGTGAAGAAAGGAGACTACGATGAGCAAGATTTTAGTGTTGTGGTGCCACCACCGGTAATTTTACCACAGCTTAGTGTCACGCAAAGCGATGAATTTGTTGAAAACCAGGATAGTGTCTTTCAAGGTGGCAAGATAGAACACCTAAACCCTTTGAACCCCGCTATGTCCGTGATATCGATGGAGGATGAAGAATTTGAGCCAGATAATGAGAAGATTGATGACCATGGACCTTTTGTTGACTTAAATTGCTTAAAGAATAAACCAGCACACCTGGCAATATTTCTCCATTTTCTGATGTCCAACAGTGATCCCAGTGCCTTATTTTTCTGGCTGGTTACAGAAATATATGCTATTGAGCAGGGGTCAGTGAAGGAGTACAAGAAGTGGGCATACGAAATCTATTCAGTCTTTTTGTCACCAAATGCGCCATTGAAAGTCACTGTAAGCGAGAGCACTGATCTTGCAATCGACGAAAGCCTGAACAACAAGAACTGCACGGAAGAAGGGGTTAGGAATATTTTCAAAATGGCAAGGCTATTCGCTTTCAATGAAGTGAGTGAGCAGCTGGCAGATTTCAGAACCAAGAGAGCACTTGGACTTGGAAGTCTATTTGGCGATCATCAGCTCGAAGatcccagagctccaatagcaatagggacaacttctactttcttcagtttccacagtgtttttatttctcttttcaaatcttgatacttttctacttatttttcttcttctctgccacgttcgcatccgccggtactgttatgtcaatgattattgccgtatgttccttcttttctaccaagactaaatctggccttcttgcttcaatcacattatcacactggatatttacatcccacaacaactttacatcatcactctccaaaactccttcaggggtatgctcgtaccatttcttactgcattccagtcctcttttcttgcatatatcccaatggatctttctcgctacgttatcatgacgcctcttgtactccttctgagctaatttctggcatgcacttacaatgtgttggatactttcacctgtttgaccacacaatcgacacagggggcttccagccgttctatcaatgtgatacttcacataatttgtcctgatggattgctcttgtgctgcacaaatcaaggcttctgtaccaaccttcaaatcacattttgacaaccattcccaagtcttcaccttatctacatcatctgtcaggtctctgacaaactgtccatgcattctcttttcattccatgtatcttttgctttgttttcattccttgccttaatatctctagcctcctccagttcagttgcatttaatttctcgaattcggctacacccttcaaaagtttctctttagatttggccacgtacactttcagactactctcctcttctttgacacatcgttctatacttataagacctcttcccccatcttttcttttcacatacagcctgtcagtatcactcttgggatgaaaagcaccatgcattgtcattgttttccttgtttgtctgtctaaatctttaagctccttttctctccattgtataattcccgctacataccggaatatagccactgcccatgtgttgatcgccgaaaccttatttttcccattcaaccttgatctaagtaccagccttacccttcttttgtattcctttctaattgcatctttcatttcagcttctttgattttatctaattccacaatacctagataagcgtacccttcctccccaacctctttcattgtctgtccatcagctaacttaattccttcacttctaataatcattcctcgtttcaatgtcaaaatgccacactttttcatcccaaattccataccaatgtcgttgctgaacatgtgaacggttctaacaagcatactcatctgatcttcagttttcgcgtatagcttcaggtcgtccataaacaataaatggttgaccttgtattccgtctttccccattcataagccgcattcactttccgcaatatcagtgacaatggtatcatactaaggacaaataatagtggtgatagactatctccctggaaaattcccctcttcacaaaaacctgtccaagatcttccccgttggatgtcagtgataccttccactgtttcatgcttcttccaagaaagttccttacattctcagctattccaaacatcgtcaaacattcgcttatccaactatgcgggaccagatcataggcttttcggtaatctatccaagacatggacagattcgtacgccttttcttgcaatctctgagtacggttctgtctatgagcaggtgatctttggtgcccctgcttcttcgcctacatcctttctgttcatctggtaatatattgctctcttctagatactggtacatttcatctgctacaatacccgtcaaaagtttccacattagtggaaggcaggtaatgggtcgataattatcaatcgctgtgcctttctgtggatctttttgacaaagcactgttcgaccatgtgttgtccattgaaagacctcctcttctcttaacataccatcaagttgggatgcgattctttcgtgaagagcggcgaagtgttttagccaatatccctgcactc

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9NZN5	Rho guanine nucleotide exchange factor 12 OS=Homo sapiens OX=9606 GN=ARHGEF12 PE=1 SV=1
Q8R4H2	Rho guanine nucleotide exchange factor 12 OS=Mus musculus OX=10090 GN=Arhgef12 PE=1 SV=2
O15085	Rho guanine nucleotide exchange factor 11 OS=Homo sapiens OX=9606 GN=ARHGEF11 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001592 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00595 all species →	PDZ	PDZ domain	Domain	Interproscan
PF09128 all species →	RGS-like	Regulator of G protein signalling-like domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036034 all species →	Homologous_superfamily	PDZ superfamily	Interproscan
IPR001478 all species →	Domain	PDZ domain	Interproscan
IPR016137 all species →	Domain	RGS domain	Interproscan
IPR036305 all species →	Homologous_superfamily	RGS domain superfamily	Interproscan
IPR015212 all species →	Domain	Regulator of G protein signalling-like domain	Interproscan
IPR044926 all species →	Homologous_superfamily	RGS, subdomain 2	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45872 all species →	RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 2, ISOFORM D	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0001664 all species →	Molecular Function	G protein-coupled receptor binding	Interproscan
GO:0005085 all species →	Molecular Function	guanyl-nucleotide exchange factor activity	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0007186 all species →	Biological Process	G protein-coupled receptor signaling pathway	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 scaffold13.g71.t1.

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 Morbakka virulenta 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 Morbakka virulenta, 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 →