Gene detail

Detailed information of ENSOJPP00000017180.1 in Anthopleura xanthogrammica

Genomic Location: SCAFFOLD_41:242470...257349
NR annotation: XP_031570980.1, protein Smaug homolog 1-like [Actinia tenebrosa]
Species Anthopleura xanthogrammica · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

ENSOJPT00000019839

AGAGGCTTTTATGGGGACGAATGTGAGCAAACTAGAAGGCAGATTCGCGAGGAACATAAGTATTATAGACTTTATCCTCAAGAGATATGAAGCCTGCACACACACAATTTAGGGATCAAGTGGGAGCTTTGGTGAATTGGTTTTCCAACTGGAACGAGTGTGAACAAACTATTGCTTTATACACTCTGTTGAAAAGGATTTCAAATACACAAGCCAGGTTTTTGTCTCTAATCTTGGAGCACACATTTCGGGACGACCCTGCTGATATCCAACTTCTCCAAAAAGAAGCTAACGACAAAGAATTTCTAAAGAACTTGTGCAAAGAGAGTAAAGTTGTTGCTGTGCAGCAGCTTCTGGCACATCTACCCCTGCTGGCGCCAGGGAACGACAAAGCACGCTACGAATACCTCCAATTATTACCAAAAATCTTGACGCATTCAGTCCAGAACTCTGTCCACCAAGATGAGTGTATGCAACTATTATCTTTAGCTCTCGTCCATCCTGCTTTCCCTCCTGAGGAGAGGAACTCGTTACTGTGTTGGCTCAGTCACTTGGAAAAGGCACTAGGAATCAAAGAGAGACAAAACTCTGGGCCACCCAGGCTACAGACAACTGACAGTacagaacatgaaaaaaacctTGTGCGACATAATTATATGCAAGGGAGAATGAATGGGTGGAGAAATCAGCAGCTCGTTCACAGAGATTCTGGAATTGGAACCTCATTCGATATGTCGACATATGGCAGTTACGGCAGTATGGGGTCATCTATTTCTTCTATGATGAAGAAAAGTAGATCAAACTCCCTCACTCCTCCCCCGCCAGTCGAGGAACAAGATTCAGTGCTGTTGGATGACTTTCCTGAGTGTCTTCAAGTTGAGATCCGTCCGGGCAGGTCCCAGTCATTTCCAGTGGATCCTCAATATCTAAATCACCAGCTTTCACCACAATCGTCAACTGAAAGTGAAATAGATGATCCTGCTATGAGAATGAGGGGAAGTAGTTTGAATGAAGATGCTAAACCAGGAATGAGAGATGTCCCAGGATGGTTAAAGGGCTTAAGACTTCACAAGTATGGTAGTCTGTTCTCTCAGCTGTCTTACGAGGAAATGCTGGATTTAGACGAGAATTATTTAGAAACTAAAGGAGTAACTAAAGGAGCAAGAAATAAGATACTGCTGAGTATTAAAAAGCTAAGAGAAAGATGTGAAGCACTGCAAAAACTAGAAAAGGAAGTTCTTCAAACTGGCAAACTACAGAATGTGTTGACAGAGTTACGGCAGATTGTTAATACTCCAATAAAACCCTTCAACCCACCTCCTGGAATACCAACAACCATGGCTGGCACCTCTGATGTGACAGGAGCAGTGATAGACCAACAAGGTGCTGCTGTTAATGTTCCACCCCACCCAGAGGATCTGCCGGCATGGATTACTAGAGTAATGGGAAAAGCATGCACACAGATCATAGTGTCGAGAGCTGATGAAGAGTATTGTACACTTTACCTTCAGCTTCTGGATAGAACACTTAATTGTGAGGCATTTACTCCTTTGCAAAAGCGACGTCTTCAGACCTGGAAACAACAATGTCAGAGACTTGCAAGACAACAGCAATTTGCACGAAGACCAAGTTCACAAGAAAAATCAAAGGGGTGGTATTACCCATGTCTCTCGAATCCACCTATTGATCACAACAGTCTTTGCCCTCCTGCTGGTCCAGGGGGTATACCTAAGCGTCAGCGAGGTTCTCCACGTAATATAAATAAAGGTACTCCTGCTGGACAGTTGAGAAGTAACAGTACAGAGACACAGCCAAGCAGTGGAAAGGCAAGACTGGTGAGGTCGCATGCCATTATCGGCAGAACCAAGTCATTACCAGTCAGACCTACCATCTCTCAAAGTTCACTGCAACAGCAAAATTCAGCAGATATTGAAGGTATTGACAACAGTCTGGAGTCACTGGCTATAAGAGTGACAGAGCAAGCCCTTTCAGATAATCCCAGTGATCAAACCTGATCAAGATCTTCCAAGATATATACGTGTGTTTAAGGTGCAACCAAGTTGCTGTTCTAGTAAATAATGTAGCAATGTATAAAGGCACTTTTACAGAAGTCTTTCAAATCCAAAGATGTTTCCAGCAGTAGAACCATCAACACCTTGTCATCTGTATCGCTGCACTCACCAACTACTCCTCTGGCTGGACTATCGAGTTCGAAAATCTACATTTTTGACCATGTTGGATGCAAGGATAACATAGCATAACTGGTAAAGCCTGTTTATTGGTAATATAAGTTCCCACCACTGTCCATCTATAGAGGGTGATTACTCAACCCccctcacccccccccccccaatcacCATGACATCCCGTCATTCTTATGGGTACTTgtcatagaccccttgcatgtgatgtcaaagcagctcaatttggaggaaaacaaaaacaaaaaaaattcaatctcctgagaactggaaacctattgctttgtcctccaaattgagctgcattctgaaggGTCTATAATATTGCAACCATGTTTAGTGACTTGCTTTCATGGCAGGGGGTGTGAGAGGTATCGCCTTCATAACATACTTCAAGATTATCTTACCTGTTTGTACCCACTGGGTCTTGTCATTCATGAAACACCATAATTGATCCTCAACTGGTGTTATTGAATTTTTAACTTAGTTAATGGTTCTTATTTGAGTATAATATCATCCAAGTTgtgatattttattgatattgcTAGTATAGAGTGATCAGATTGAAccagtaaaataaaatctagGGTAATAGTTACTATCAGCGCCCAAAACCATCAGTCAACCAATTGTTGACTGTTAGTCGACCGATTGATCTGTGGTATGTAGAGATGACCTGTCAAACAATTGTCAACATTCTGCCGACAGATGGTTTAGGGCACTAATGGTTACTAATACCTATAATCTAATAGACATTATCTCAgagtcaaaagaaaacaaaagaattagtt

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q80XS6	Protein Smaug homolog 2 OS=Mus musculus OX=10090 GN=Samd4b PE=1 SV=1
Q5PRF9	Protein Smaug homolog 2 OS=Homo sapiens OX=9606 GN=SAMD4B PE=1 SV=1
Q9UPU9	Protein Smaug homolog 1 OS=Homo sapiens OX=9606 GN=SAMD4A PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003139 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00536 all species →	SAM_1	SAM domain (Sterile alpha motif)	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR037634 all species →	Domain	Protein Smaug, SAM domain	Interproscan
IPR001660 all species →	Domain	Sterile alpha motif domain	Interproscan
IPR037093 all species →	Homologous_superfamily	Smaug, PHAT domain superfamily	Interproscan
IPR013761 all species →	Homologous_superfamily	Sterile alpha motif/pointed domain superfamily	Interproscan
IPR050897 all species →	Family	SMAUG/VTS1 RNA-binding	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12515 all species →	STERILE ALPHA MOTIF DOMAIN CONTAINING PROTEIN 4-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0017148 all species →	Biological Process	negative regulation of translation	Interproscan
GO:0030371 all species →	Molecular Function	translation repressor activity	Interproscan
GO:0043488 all species →	Biological Process	regulation of mRNA stability	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0000289 all species →	Biological Process	nuclear-transcribed mRNA poly(A) tail shortening	Interproscan
GO:0000932 all species →	Cellular Component	P-body	Interproscan
GO:0003729 all species →	Molecular Function	mRNA 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
K27396	SMG; protein Smaug	-	Messenger RNA biogenesis	ko03019	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 Anthopleura xanthogrammica 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 Anthopleura xanthogrammica, 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 →