Gene detail

Detailed information of g495.t1 in Calvadosia cruxmelitensis

Genomic Location: not available for this species
NR annotation: XP_001626535.2, translation machinery-associated protein 16 [Nematostella vectensis]
Species Calvadosia cruxmelitensis · all data for this species · gene families

Sequence

Sequence data are not available for Calvadosia cruxmelitensis.
Nucleotide and protein sequences are provided for the species whose genome annotation is complete (see annotated genomes); for this species only the assembly is archived. The functional annotation below is likewise unavailable.

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q5RC80	RNA-binding protein 39 OS=Pongo abelii OX=9601 GN=RBM39 PE=2 SV=1
Q14498	RNA-binding protein 39 OS=Homo sapiens OX=9606 GN=RBM39 PE=1 SV=2
Q8VH51	RNA-binding protein 39 OS=Mus musculus OX=10090 GN=Rbm39 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000014 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000034 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0001676 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0002780 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0002897 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0003764 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0008967 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0015209 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0024780 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0061936 (this species only) · gene tree & orthology
Transcription factor family	Homeobox · all TF in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00665 all species →	rve	Integrase core domain	Domain	Interproscan
PF00076 all species →	RRM_1	RNA recognition motif	Domain	Interproscan
PF15519 all species →	RBM39linker	linker between RRM2 and RRM3 domains in RBM39 protein	Domain	Interproscan
PF00046 all species →	Homeodomain	Homeodomain	Domain	Interproscan
PF00763 all species →	THF_DHG_CYH	Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain	Domain	Interproscan
PF04268 all species →	SoxG	Sarcosine oxidase, gamma subunit family	Family	Interproscan
PF02882 all species →	THF_DHG_CYH_C	Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain	Domain	Interproscan
PF11176 all species →	Tma16	Translation machinery-associated protein 16	Family	Interproscan
PF00261 all species →	Tropomyosin	Tropomyosin	Coiled-coil	Interproscan
PF10223 all species →	Menorin	Menorin	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR003609 all species →	Domain	PAN/Apple domain	Interproscan
IPR036397 all species →	Homologous_superfamily	Ribonuclease H superfamily	Interproscan
IPR012337 all species →	Homologous_superfamily	Ribonuclease H-like superfamily	Interproscan
IPR001584 all species →	Domain	Integrase, catalytic core	Interproscan
IPR050951 all species →	Family	Retrovirus-related Pol polyprotein	Interproscan
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan
IPR003954 all species →	Domain	RNA recognition motif domain, eukaryote	Interproscan
IPR006509 all species →	Family	Splicing factor, RBM39-like	Interproscan
IPR000504 all species →	Domain	RNA recognition motif domain	Interproscan
IPR029123 all species →	Domain	Splicing factor RBM39, linker	Interproscan
IPR050649 all species →	Family	Paired Homeobox Transcription Factors	Interproscan
IPR009057 all species →	Homologous_superfamily	Homeobox-like domain superfamily	Interproscan
IPR001356 all species →	Domain	Homeobox domain	Interproscan
IPR017970 all species →	Conserved_site	Homeobox, conserved site	Interproscan
IPR020630 all species →	Domain	Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain	Interproscan
IPR036291 all species →	Homologous_superfamily	NAD(P)-binding domain superfamily	Interproscan
IPR046346 all species →	Homologous_superfamily	Aminoacid dehydrogenase-like, N-terminal domain superfamily	Interproscan
IPR007375 all species →	Family	Sarcosine oxidase, gamma subunit	Interproscan
IPR000672 all species →	Family	Tetrahydrofolate dehydrogenase/cyclohydrolase	Interproscan
IPR020631 all species →	Domain	Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain	Interproscan
IPR038356 all species →	Homologous_superfamily	Tma16 superfamily	Interproscan
IPR021346 all species →	Family	Translation machinery-associated protein 16	Interproscan
IPR000533 all species →	Family	Tropomyosin	Interproscan
IPR019356 all species →	Family	Menorin	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR37984 all species →	PROTEIN CBG26694	Interproscan
PTHR48036 all species →	SPLICING FACTOR (PAD-1), PUTATIVE (AFU_ORTHOLOGUE AFUA_1G15810)-RELATED	Interproscan
PTHR24329 all species →	HOMEOBOX PROTEIN ARISTALESS	Interproscan
PTHR48099 all species →	C-1-TETRAHYDROFOLATE SYNTHASE, CYTOPLASMIC-RELATED	Interproscan
PTHR46704 all species →	CXC DOMAIN-CONTAINING PROTEIN-RELATED	Interproscan
PTHR13349 all species →	UNCHARACTERIZED	Interproscan
PTHR19269 all species →	TROPOMYOSIN	Interproscan
PTHR21184 all species →	MENORIN (DENDRITIC BRANCHING PROTEIN)	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0015074 all species →	Biological Process	DNA integration	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006397 all species →	Biological Process	mRNA processing	Interproscan
GO:1990446 all species →	Molecular Function	U1 snRNP binding	Interproscan
GO:0000977 all species →	Molecular Function	RNA polymerase II transcription regulatory region sequence-specific DNA binding	Interproscan
GO:0000981 all species →	Molecular Function	DNA-binding transcription factor activity, RNA polymerase II-specific	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0004488 all species →	Molecular Function	methylenetetrahydrofolate dehydrogenase (NADP+) activity	Interproscan
GO:0004477 all species →	Molecular Function	methenyltetrahydrofolate cyclohydrolase activity	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0035999 all species →	Biological Process	tetrahydrofolate interconversion	Interproscan
GO:0005884 all species →	Cellular Component	actin filament	Interproscan
GO:0006936 all species →	Biological Process	muscle contraction	Interproscan
GO:0007015 all species →	Biological Process	actin filament organization	Interproscan
GO:0051015 all species →	Molecular Function	actin filament binding	Interproscan
GO:0005615 all species →	Cellular Component	extracellular space	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
K13091	RBM23_39; RNA-binding protein 23/39	-	Spliceosome	ko03041	deepkoala
K14860	TMA16; translation machinery-associated protein 16	-	Ribosome biogenesis	ko03009	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 Calvadosia cruxmelitensis 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 Calvadosia cruxmelitensis, 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.	sequence table not available	–
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.	sequence table not available	–
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 →