Gene detail

Detailed information of ENSAVKP00000032040.1 in Catalaphyllia jardinei

Genomic Location: chr5:8527819...8536471
NR annotation: XP_020604381.1, LOW QUALITY PROTEIN: S1 RNA-binding domain-containing protein 1-like [Orbicella faveolata]
Species Catalaphyllia jardinei · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

ENSAVKT00000034653

gaGTTCATTAACCAAACAGGCTGAAAGAGAGAGTGTCGATCTATTCATGATGAACTTGTACCGCCTTCTCCTTACCCCTCCCATCAGGGGAAAGAATGTCCTTGGTCTAGACCCAGGCTTCTCTCATGGGTGCAAGTTAGCGGTCTTGGGTTCCACAGGCGAGGTTCTAGAGACAAGAGTGATATTTCCatttggaaaaaaatcaaatgcTGCACAAGCCAAAAACACAGTAGTAGAACTTGTTTTAAAGCACAGCTGTGACTATGTCGCTATTGGGAATGGAGTTGGATGCCGAGATGCTGAAACATTTATTAGCCAGCTCATCAAGCAACGAGTGTTTGCGCCTCTGGAAATCGCATACTGtATCGTCAGCGAAGATGGAGCCTCTATTTACAGTGCGTCACCAGAAGCAGCAGCTGAACTTCCCGGCCTTGACACAAGCCTTAAGGGAGCTGtATCGATAGGGAGGAGACTACAGGATCCTCTGGCTGAATTAGTGAAAATTGAGCCCAAGCATTTGGGTATTGGAATGTACCAGCATGATATTCCTGAGTCCCTGCTTCGAGGAGCTTTGGACGGTGTGGTGGAGGACTGTGTCAGTTTTGTAGGAGTCAATTTAAATGTCGCTGGAGTCAGTATGTTAAGGCGCATAGCTGGCTTAAATGATAAGAAAGCGAAAGCGATTCTAGCGTGGCGAGAGGAAAATGGCGCCTTCACCAACCGTGAGCAGCTGAAAGCAGTCAAGGGGATTGGGCTCAAAACCTACGAACAGTGTGTCGGGTTCGTCCGAATAATGAACAATTTACGTCGCCATGGCAACGATGATGAGCCTTCCGCCAGCGGACAGCAAAGGACTGCGGATAATAGCATCTTTGAAACGATTGTTGTGTTGGATTCCGACGAAGAAGCACAGACAACGGCGCGTGGGAAGAAAAGAAAGGGCGGCAGCACTGAGgacaaagtaaagaagaaaaagaaaaaaattgtgagGGAACAAGAGTTTTGTCCGGAGCCACTGGACATAACTTGGATTCACCCAGAATCCTATCCAGTTGCTAAAAGTGTTATTGAGATGCTGGGTATGCTACCAGAACAGATTGGTCAACCAATGATGAAAACTGCCATCGACAAGTTGTTACAGACTCGCAGCATTGCAGAATTAGCGAGGAGGTTTGGTGTAGGTACACCCACATTACAACATATTATTGATGGTCTCAAACAACCAACGGATCACGACATACGAGTCAATTTCCAGAAACCCTTGTTCAAACGAGATGTGACCTCGCTAGAAGACCTTCATCCGGGAACTCGGTTAAGCGGCCGCGTCAcgaatatgacgtcattcggGGCCTTTGTAGACTGCGGTGTCGGCCGTGATGGCCTGGTACACAACAGTAGCATGGGAAGATTTAAAGGCAAGGTCGGCTTGGGAGATCTTGTGGAAGTCACTGTTAAAAGTGTGAATATCCAGAAACAACACATCGGTCTGATTTTAACGGACATATCATCAAGGTTTGATCCACAGCTGTTAGTGTCCATCGGAAATTTATCTCAATCTTGCGCgcgataaaaaaaagaaatatactttTGTTTACGAATCTAAACAAGAAAAGACTTGATCGCGTCAAGGTCAAATTgttaacaataacaaaagagaaaatagttgatataaattatatttattaGAGCAAAGCGAAGTTCGAAATTAACTTTTCGTTATATTGCTGTTGCATCTGTTGTTTGAAAtaacaatttgaatttttgataTTCTGAACTGAGAAAACTCTTCAGTAGGTTTCTGCGTAAATGTTTTGTTACTCTATAAGCAAGAGAAATACAGGTTGTCATTTAATAGGATAAACTGTCCCCTCAGTTGTTGCTCTTTTATCCATCTTGTCGTCAAATCCTGCAAGTTATATTCGTTCAGAACATTAGTCTAAATTCCAGTGGGCCGTTTCTCGAAAggcccggaaacttttcgggtcCGTAAAGCCATTT

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q8N5C6	S1 RNA-binding domain-containing protein 1 OS=Homo sapiens OX=9606 GN=SRBD1 PE=1 SV=2
Q497V5	S1 RNA-binding domain-containing protein 1 OS=Mus musculus OX=10090 GN=Srbd1 PE=2 SV=3
Q5RDI0	S1 RNA-binding domain-containing protein 1 OS=Pongo abelii OX=9601 GN=SRBD1 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003732 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF17674 all species →	HHH_9	HHH domain	Domain	Interproscan
PF00575 all species →	S1	S1 RNA binding domain	Domain	Interproscan
PF12836 all species →	HHH_3	Helix-hairpin-helix motif	Domain	Interproscan
PF16921 all species →	Tex_YqgF	Tex protein YqgF-like domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR010994 all species →	Homologous_superfamily	RuvA domain 2-like	Interproscan
IPR012340 all species →	Homologous_superfamily	Nucleic acid-binding, OB-fold	Interproscan
IPR041692 all species →	Domain	HHH domain 9	Interproscan
IPR003029 all species →	Domain	S1 domain	Interproscan
IPR050437 all species →	Family	Bacterial ribosomal protein bS1	Interproscan
IPR037027 all species →	Homologous_superfamily	YqgF/RNase H-like domain superfamily	Interproscan
IPR032639 all species →	Domain	Tex protein, YqgF-like domain	Interproscan
IPR006641 all species →	Domain	YqgF/RNase H-like domain	Interproscan
IPR012337 all species →	Homologous_superfamily	Ribonuclease H-like superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10724 all species →	30S RIBOSOMAL PROTEIN S1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0003729 all species →	Molecular Function	mRNA binding	Interproscan
GO:0003735 all species →	Molecular Function	structural constituent of ribosome	Interproscan
GO:0006412 all species →	Biological Process	translation	Interproscan
GO:0006139 all species →	Biological Process	nucleobase-containing compound metabolic process	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

No KEGG orthology assignment for ENSAVKP00000032040.1.

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 Catalaphyllia jardinei 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 Catalaphyllia jardinei, 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 →