Detailed information of amic_s0094.g21.t1 in Acropora microphthalma

Genomic Location: sc0000094_pilon:419324...427225
NR annotation: XP_029194859.1, LIM and senescent cell antigen-like-containing domain protein 1 [Acropora millepora]
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
Q99JW4LIM and senescent cell antigen-like-containing domain protein 1 OS=Mus musculus OX=10090 GN=Lims1 PE=1 SV=3
P48059LIM and senescent cell antigen-like-containing domain protein 1 OS=Homo sapiens OX=9606 GN=LIMS1 PE=1 SV=4
Q7Z4I7LIM and senescent cell antigen-like-containing domain protein 2 OS=Homo sapiens OX=9606 GN=LIMS2 PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0006532 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00412
all species →
LIMLIM domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR001781
all species →
DomainZinc finger, LIM-typeInterproscan
IPR047946
all species →
FamilyLIM and senescent cell antigen-like-containing domain protein 1/2-likeInterproscan
IPR047944
all species →
DomainLIMS1/2-like, LIM domain 1Interproscan

 PANTHER
PANTHER termDescriptionSource
PTHR24210
all species →
LIM DOMAIN-CONTAINING PROTEINInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005737
all species →
Cellular ComponentcytoplasmInterproscan
GO:0005911
all species →
Cellular Componentcell-cell junctionInterproscan
GO:0005925
all species →
Cellular Componentfocal adhesionInterproscan
GO:0045216
all species →
Biological Processcell-cell junction organizationInterproscan
GO:0098609
all species →
Biological Processcell-cell adhesionInterproscan
GO:1900026
all species →
Biological Processpositive regulation of substrate adhesion-dependent cell spreadingInterproscan
GO:2001046
all species →
Biological Processpositive regulation of integrin-mediated signaling pathwayInterproscan

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
K23354LIMS1_2, PINCH1_2; LIM and senescent cell antigen-like-containing domain protein 1/2-Domain-containing proteins not elsewhere classifiedko04990deepkoala

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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