Gene detail

Detailed information of ENSLDHP00000041457.1 in Eunicella cavolini

Genomic Location: chr5:3468828...3489899
NR annotation: XP_028414491.1, DNA mismatch repair protein Msh2-like [Dendronephthya gigantea]
Species Eunicella cavolini · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

ENSLDHT00000045426

AGCAGACTTGTGCAGCCCAAACATGACTATTCATTCCAAATGCGGGTGGGGGTGGGTAGATGGTCAATGCTGGCGATCAGGTGTAATCTATTGTGTCCAAAAGGAGAATACTACACCGTCCATGGAAACGATGCAATATTTATTgctaaagaaattttcaaaaccaTGAACATTGTCAGACATATCGGATCAGGTGTGTACACAATATTGCCATCAGTTGCACTGAGCAAAGCAAAGTTTGAATCAACAATAAGAGAactgttgttggtacggcagtACAGAGTGGAGTTGTATAGGAACAAGGGAGGGAAGGGAACTCAACAAAACTGGTTCCTTGCAGGGAAGGCTTCGCCTGGAAACTTACAACAGTTTGAAGAAATTTTATTCGGAAATAACGAGATGTCTGCTTCTGTTGCTGTGATGGCTTTCAAGCTTTCTGGCGATGCTTCTCAAAAGATTGTTGGCGCCGCGTATGTTGATGTTTCCGAAAGAAAAATCGCTGTCTGTGAAATCGCCGACAATGATCAATTTTCAAATGTCGAGGCATTGTTAGTCCAACTGGGTCCAAAGGAATGCATCGTGCAGGCAAACGATCAAAGTGCTGATGCAGGAAGACTGAAGGAAGTCATTCAACGAAGTGGTGTCCTTGTTACAGAAAAGAAGAAAGGTGATTTCTCTACAGTTGATATCGCACAAGATCTGAACAGACTTTTGAAAATCAACTCTGGAAACAGTTCAACCCTACCTGAGGTTGACTTAAACCATGCAATGGGATGCGTTGCTGTTATCATCAAATATCTGGAGATGTTATCAGACGACTCCAACTTTGGTCGATTCCGCATTTCTACCATCGATTTAAACCAGTACATGAAACTTGACGCCGCTGCTGTTCGTGCTCTGAATCTTTTGCCTTCGTCCTTGGATGGCTCTAATAAATCAGTGAGTCTCCTCAGTTTGTTAAACAAGTGTAGAACCCCACAAGGCAAGAGACTTCTTGGACAGTGGATTAAGCAGCCTCTTCTAGACGAGAAAAAAATTGAGGAAAGACTCAACATTGTCGAAGCTTTCTTCAGTAATGTTGTTCTTCGACAAACAGTTCAGGTAAAATTTTTCAAGAATCATAAATTAtgtttttacacattttttatgTCTATGTTCTTCCTAATGCAGGAATTAGTGATTAGTCTAGATGGTTGCCAAGACGACCACAGATCACTGATCAATGAACTGTTCATTGCACCATTACAGgaaTTGACAGAAGATTTTTCGAAGTATGTGGAATTAATTGAAACAACAATTGACCTGGATCAAGTAGAAAATCACGAATTTCTTATCAAACCTTCATTTGATGAAGGACTACAAGGTCAGAAGCACCCTTCCCAACTATATATATCGTACGATTCCGCGAGAGTTGGACAAAAGGCCGGGAAAACTGTTAAACTGGAAACGAACAACCAGTTTGGATATTATCTTCGCATCACTAGGAAGGAAGAGAAAAAACTGCGAGGAAATAAGAAATTCACAACTTTGGACACAAGAAAAGATGGTGTACGTTTTACAAGCTCTGTGTTGAGACAACTGAACGATCAGTTCCAAGCCCTGAAGGAAACCTATGATGACGTTCAAAGTAAACTGGCGGAGGAAGTTATTAAAATTGCAAGTGGCTACGGTGAACCGATGCAATTACTGAGTGATACTCTGGCAAAACTCGATGTCCTAATAAGGTACAGTAAATTGAAACTTACTGCAGCTAGACATCCATGTCTTGAGGTCCAAGATGAAATCGCATTTATTCCAAACGATGTTATTCTGAACAGAGACGAACAATCCTTTTTGATAATCACCGGTCCCAACATGGGTGGAAAATCGACATATATTCGATCAGTAAGCGTCGCCGTTCTGATGGCTCAAATTGGATGTTTTGTTCCTTGTGAAGAAGCTGAGATCTCGATCAAGGACGCCATATTGGCTCGAGTGGGCTCTGCTGATAGTCAGCAGAAAGGTGTTTCAACTTTCATGTCAGAAATGTTGGAAACAGCCTCTATACTTCGGAGTGCAACAGAAAATTCGTTGATTATTATTGACGAACTCGGACGGGGAACGTCGACATACGACGGATTTGGTTTAGCTTGGGCTATCTCAGAGTTTATATCAACACGTATTAAAGCGTTGTGTCTATTTGCAACACATTTCCACGAACTGACTGCTTTGGCAGATGTTGTCCCAAGTGTGAGGAATTTTCACGTCACGGCCATGACCACCGGAGATACTCTTACATTGCTGTACAGAATCAAACCAGGTGTATGTGATCAGAGTTTTGGAATCCACGTTGCGGAATTGACTAATTTCCCACGTAAAGTTATTGAGGTTGGCATGATGTCATGTAGCGTCTTGTACCATCTTCATTTAAACGAAGATCAGTGTTTCTTAAATAACCAAATAACTGACCTATCTAGTTATATTTCTGTATTACAGGAAGGGGATAAACTGATACAAGAGTATCTACAAAACGTGGCTGCACTACCTGTCGATAATCTAACAGAATCTGAAGTTTACTCAAAGGTTTCGGGTTTAAAAAATGCACTGCTTGCGAAAAATAATAGTTATATTAACGAAATGCTGACAAGAAATACTCAAGTCGGTGTGGTGTGA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P43246	DNA mismatch repair protein Msh2 OS=Homo sapiens OX=9606 GN=MSH2 PE=1 SV=1
Q5XXB5	DNA mismatch repair protein Msh2 OS=Chlorocebus aethiops OX=9534 GN=MSH2 PE=2 SV=1
Q3MHE4	DNA mismatch repair protein Msh2 OS=Bos taurus OX=9913 GN=MSH2 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003076 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF05192 all species →	MutS_III	MutS domain III	Domain	Interproscan
PF01624 all species →	MutS_I	MutS domain I	Domain	Interproscan
PF05188 all species →	MutS_II	MutS domain II	Domain	Interproscan
PF00488 all species →	MutS_V	MutS domain V	Domain	Interproscan
PF05190 all species →	MutS_IV	MutS family domain IV	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR007696 all species →	Domain	DNA mismatch repair protein MutS, core	Interproscan
IPR011184 all species →	Family	DNA mismatch repair Msh2-type	Interproscan
IPR036678 all species →	Homologous_superfamily	MutS, connector domain superfamily	Interproscan
IPR032642 all species →	Domain	DNA mismatch repair protein Msh2, ATP-binding cassette domain	Interproscan
IPR007695 all species →	Domain	DNA mismatch repair protein MutS-like, N-terminal	Interproscan
IPR036187 all species →	Homologous_superfamily	DNA mismatch repair protein MutS, core domain superfamily	Interproscan
IPR045076 all species →	Family	DNA mismatch repair MutS family	Interproscan
IPR000432 all species →	Domain	DNA mismatch repair protein MutS, C-terminal	Interproscan
IPR007860 all species →	Domain	DNA mismatch repair protein MutS, connector domain	Interproscan
IPR016151 all species →	Homologous_superfamily	DNA mismatch repair protein MutS, N-terminal	Interproscan
IPR007861 all species →	Domain	DNA mismatch repair protein MutS, clamp	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11361 all species →	DNA MISMATCH REPAIR PROTEIN MUTS FAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0006298 all species →	Biological Process	mismatch repair	Interproscan
GO:0030983 all species →	Molecular Function	mismatched DNA binding	Interproscan
GO:0003690 all species →	Molecular Function	double-stranded DNA binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006312 all species →	Biological Process	mitotic recombination	Interproscan
GO:0032301 all species →	Cellular Component	MutSalpha complex	Interproscan
GO:0140664 all species →	Molecular Function	ATP-dependent DNA damage sensor 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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K08735	MSH2; DNA mismatch repair protein MSH2	-	DNA repair and recombination proteins	ko03400	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 Eunicella cavolini 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 Eunicella cavolini, 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 →