Gene detail

Detailed information of ENSTHXP00000035767.1 in Siderastrea radians

Genomic Location: chr8:49027785...49040082
NR annotation: no NCBI-NR hit recorded
Species Siderastrea radians · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

ENSTHXT00000053340

ATGCAGCCTGGCCTTCTGTGCAATCTTTTGAAAATGGCGGCCAGAGACGGTGATATTTCTGATGAAGAGTTACGTCGCCAACTTAAGGCTTTAGGTGAGGACGTCGGACCCGTTACTGACAACACGAGGTCTTTTCTATTCCGTAAGCTTAAGCGCTTGCGGAACCAGCAAGGGAGCAGTAGGCTTAGGAAGGAAAAGACTCCCCCGAGGCGAAGACCTTCACCCGCTCGCAAGTCTTTACCCGCAACAACCAGAAGTCAGAGTCCGTCTCGAAAACGTTTCGGGTTCTCTAGCGATGAAGAAGACGCAGGGCCGAGTTTGTCGAGTACTTTAAGAGACTCAGATAGATTAAGGGGAAGACGTACAGAAGCAGCGTCCAGTGATGGTGAATCTTTGGGAAGGTCTGAAAAGACAAAACCTACGCCAACTGGGAGAGGTGAGTTAAGGCAGCGGGTGCCAAGTTTTATCGAGCACAGCGTTCCTGAGAGGACTTTTGATTCTACAGACGATAATAATGGAGAATTTTCAGATCAAGATGGACCAGTTTTCCTTAAACCAAAAACTCATTCAAGTGGCGTATCAAGATATACACGAACAACAAGACGCGAAATAGATGAAAGTGAAAGATCTGAGACTATGCGTTCGTCCACAACGTATGGCAAATACGAAAGCGTGAATGCTGGTTCGCAATTAAACACTACTCTTCGAGAGAGACAAACTGGAGCCAAAGACGTAAAAACTAGCCTCTTCTGGTCCTTGACAGGAAAGATCGTACTGGTGATAAGCGTGATTTGCATTGGTATCTTGTTGTATGTGGCACTCAAAAAGCACTCGAGCGAGAAAGGACTCCTTGAGCAGTTTGTGAAACTTCCAGTTTGCAAAGGGGATAATCAGGTTCAGCAATACAATGATACGCCTCCTGGCTGTGTGCCATTACTCAACATCAGTGAGCACTATGCAGACTCTTTGTATAAAAAGCTCATCGTAAAAGCAGGTAAGATTGCATGTATCCCCACAATACTGAGTTGTTTCATGCCATGTGGTCACCCTGTGGCGTGTATGCAACTGTACCttaccttttttccattgcaGTATACAAGACCTGGGGATGAGCAGAAGTTGATTCTCAAAAAAACACTGGAACTGATACTTAAACACCCTGAATGGAAATTAAGATTGTTTAAGAAAAACAACGAGGAAGTCACTTCTATAGAAAATGTGACATGGACCGAAAATGTGACATGGATCGATACTTCAGTTTCTGCCAAACCCCTGTTGTGTCGCATTAATGAAGCAGTGTCCCGCTTGGCTTACCTCTCTTTTGTGATCGCTTTTGTTATTGGAGGACTAGTAATTGCATATTTCATTGTACGGCAAAGATGGAGGAGAGAGGAGGAAGAAACACGGTTGATGTATCAGTTTGTGGAAAATATTATTGACATCTTACGAGAGCATCATGAAGCCAGTAAAACTGAGAAGAATTTGTTGCCTTATCTTCCAATTCCCCATGTTAGAGATATGCTGATTCCTCCAACAGACAGGCAAAGACTGTCAAAAGCCTGGAACAGAGCAGTGCGATTTTTGAGTGCAAATGAATCTCGCATACGAGTTGAAAGCCAGAGGATAGCTGGGGAGGATTTTGAAGTTTGGAGGTGGATTCAGATTGTTACACCTAAACCTCATAATCCCAAATTGTCACTTTCAGGCAACAAACATGGAAAGTACTGGCAGGGACAAGcatttGAAAACTTTCAGTCAGCTGTGAATCCGCCTGTTATTAGCCCTACGCCATGTTTGAAGATAAGAAACATGTTTGATCCTGATGTTGAAACTGAGGATAGTTGGCATGTGATGATACAAGATGCCATTTTGGAGAAATGTATTGAGAACGGGGCAGGTGTTGTTCACATAGCAGTTGACAAGAGTTCTAGTGAGGGATGTGTTTATGTTAAGTGCGACACACACCATTCAGCAGGATTGGCCTTTAGAAGTCTTCATGGATGCTGGTTTGATGGTCGTCTTGTCGCTGTGAAGTATCTAACCTTGAAGCGGTACCACCAGCGGTTTCCAGTAGCCTTGGAAGCCACTGAACGCCTGAGTCCATCAGGATCTTCACCATCCTCTCTTGTTACATTTGATCCTGATGAGGCGGGAGATGGGGATGTCAATGATTCTGACATTGAATTTTAG

Transcript

ENSTHXT00000053340

Protein

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004347 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03020 all species →	LEM	LEM domain	Domain	Interproscan
PF15519 all species →	RBM39linker	linker between RRM2 and RRM3 domains in RBM39 protein	Domain	Interproscan
PF09402 all species →	MSC	Man1-Src1p-C-terminal domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR003887 all species →	Domain	LEM domain	Interproscan
IPR041885 all species →	Homologous_superfamily	MAN1, winged-helix domain	Interproscan
IPR011015 all species →	Homologous_superfamily	LEM/LEM-like domain superfamily	Interproscan
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan
IPR029123 all species →	Domain	Splicing factor RBM39, linker	Interproscan
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan
IPR018996 all species →	Domain	Man1/Src1-like, C-terminal	Interproscan
IPR034394 all species →	Domain	MAN1, RNA recognition motif	Interproscan
IPR052277 all species →	Family	Inner Nuclear Membrane ESCRT-Associated Protein	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13428 all species →	INNER NUCLEAR MEMBRANE PROTEIN MAN1 LEM DOMAIN CONTAINING PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0006998 all species →	Biological Process	nuclear envelope organization	Interproscan
GO:0030514 all species →	Biological Process	negative regulation of BMP signaling pathway	Interproscan
GO:0031490 all species →	Molecular Function	chromatin DNA binding	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
K19410	LEMD3; inner nuclear membrane protein Man1	-	Cytoskeleton proteins	ko04812	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 Siderastrea radians 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 Siderastrea radians, 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 →