Detailed information of amic_s0068.g9.t1 in Acropora microphthalma

Genomic Location: sc0000068_pilon:103946...113550
NR annotation: XP_015757767.1, PREDICTED: non-structural maintenance of chromosomes element 1 homolog [Acropora digitifera]
Species Acropora microphthalma · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q8WV22Non-structural maintenance of chromosomes element 1 homolog OS=Homo sapiens OX=9606 GN=NSMCE1 PE=1 SV=5
Q5RAZ5Non-structural maintenance of chromosomes element 1 homolog OS=Pongo abelii OX=9601 GN=NSMCE1 PE=2 SV=1
Q3T0X7Non-structural maintenance of chromosomes element 1 homolog OS=Bos taurus OX=9913 GN=NSMCE1 PE=2 SV=2
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0005900 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF07574
all species →
SMC_Nse1Nse1 non-SMC component of SMC5-6 complexFamilyInterproscan
PF08746
all species →
zf-RING-likeRING-like domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR013083
all species →
Homologous_superfamilyZinc finger, RING/FYVE/PHD-typeInterproscan
IPR011513
all species →
FamilyNon-structural maintenance of chromosomes element 1Interproscan
IPR002219
all species →
DomainProtein kinase C-like, phorbol ester/diacylglycerol-binding domainInterproscan
IPR014857
all species →
DomainNon-structural maintenance of chromosomes element 1, RING C4HC3-typeInterproscan
IPR036388
all species →
Homologous_superfamilyWinged helix-like DNA-binding domain superfamilyInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR20973
all species →
NON-SMC ELEMENT 1-RELATEDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0000724
all species →
Biological Processdouble-strand break repair via homologous recombinationInterproscan
GO:0004842
all species →
Molecular Functionubiquitin-protein transferase activityInterproscan
GO:0005634
all species →
Cellular ComponentnucleusInterproscan
GO:0006281
all species →
Biological ProcessDNA repairInterproscan
GO:0030915
all species →
Cellular ComponentSmc5-Smc6 complexInterproscan

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
KOEnzymeEnzyme IDPathwayMap IDSource
K22817NSMCE1, NSE1; non-structural maintenance of chromosomes element 1EC:2.3.2.27
DNA repair and recombination proteinsko03400deepkoala

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 Acropora microphthalma 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 Acropora microphthalma, 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.

AnalysisWhat it doesStatus
Primer designDesign PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.template foundopen →
BLASTSearch 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 foundopen →
Expression heatmapDraw 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 / orthogroupLook 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 analysisStart a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.open →
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