Gene detail

Detailed information of g294.t1 in Calvadosia cruxmelitensis

Genomic Location: not available for this species
NR annotation: WP_259782298.1, 16S rRNA (guanine(966)-N(2))-methyltransferase RsmD [Aestuariispira ectoiniformans]
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
O34331	Putative rRNA methyltransferase YlbH OS=Bacillus subtilis (strain 168) OX=224308 GN=ylbH PE=3 SV=2
I6XFS7	RNA/DNA methyltransferase Rv2966c OS=Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) OX=83332 GN=Rv2966c PE=1 SV=1
Q61824	Disintegrin and metalloproteinase domain-containing protein 12 OS=Mus musculus OX=10090 GN=Adam12 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000042 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000460 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000715 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0001010 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0001384 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0003649 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0004083 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0008521 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0019864 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0021523 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0061614 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0061685 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03602 all species →	Cons_hypoth95	Conserved hypothetical protein 95	Family	Interproscan
PF07727 all species →	RVT_2	Reverse transcriptase (RNA-dependent DNA polymerase)	Family	Interproscan
PF13733 all species →	Glyco_transf_7N	N-terminal region of glycosyl transferase group 7	Domain	Interproscan
PF00528 all species →	BPD_transp_1	Binding-protein-dependent transport system inner membrane component	Family	Interproscan
PF01424 all species →	R3H	R3H domain	Domain	Interproscan
PF00177 all species →	Ribosomal_S7	Ribosomal protein S7p/S5e	Domain	Interproscan
PF13912 all species →	zf-C2H2_6	C2H2-type zinc finger	Domain	Interproscan
PF00096 all species →	zf-C2H2	Zinc finger, C2H2 type	Domain	Interproscan
PF03351 all species →	DOMON	DOMON domain	Domain	Interproscan
PF01421 all species →	Reprolysin	Reprolysin (M12B) family zinc metalloprotease	Domain	Interproscan
PF00652 all species →	Ricin_B_lectin	Ricin-type beta-trefoil lectin domain	Domain	Interproscan
PF00431 all species →	CUB	CUB domain	Domain	Interproscan
PF00433 all species →	Pkinase_C	Protein kinase C terminal domain	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR004398 all species →	Family	RNA methyltransferase, RsmD	Interproscan
IPR029063 all species →	Homologous_superfamily	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Interproscan
IPR013103 all species →	Domain	Reverse transcriptase, RNA-dependent DNA polymerase	Interproscan
IPR052510 all species →	Family	Oomycete RxLR Effector	Interproscan
IPR043502 all species →	Homologous_superfamily	DNA/RNA polymerase superfamily	Interproscan
IPR027995 all species →	Domain	Galactosyltransferase, N-terminal	Interproscan
IPR029044 all species →	Homologous_superfamily	Nucleotide-diphospho-sugar transferases	Interproscan
IPR003859 all species →	Family	Beta-1,4-galactosyltransferase	Interproscan
IPR035906 all species →	Homologous_superfamily	MetI-like superfamily	Interproscan
IPR000515 all species →	Domain	ABC transporter type 1, transmembrane domain MetI-like	Interproscan
IPR036867 all species →	Homologous_superfamily	R3H domain superfamily	Interproscan
IPR001374 all species →	Domain	R3H domain	Interproscan
IPR036823 all species →	Homologous_superfamily	Small ribosomal subunit protein uS7 domain superfamily	Interproscan
IPR005717 all species →	Family	Small ribosomal subunit protein uS7, bacterial/organellar-type	Interproscan
IPR023798 all species →	Domain	Small ribosomal subunit protein uS7 domain	Interproscan
IPR000235 all species →	Family	Small ribosomal subunit protein uS7	Interproscan
IPR020606 all species →	Conserved_site	Small ribosomal subunit protein uS7, conserved site	Interproscan
IPR013087 all species →	Domain	Zinc finger C2H2-type	Interproscan
IPR036236 all species →	Homologous_superfamily	Zinc finger C2H2 superfamily	Interproscan
IPR000945 all species →	Family	Dopamine beta-hydroxylase-like	Interproscan
IPR045266 all species →	Domain	Copper-dependent monooxygenases, DOMON domain	Interproscan
IPR005018 all species →	Domain	DOMON domain	Interproscan
IPR000859 all species →	Domain	CUB domain	Interproscan
IPR000772 all species →	Domain	Ricin B, lectin domain	Interproscan
IPR035992 all species →	Homologous_superfamily	Ricin B-like lectins	Interproscan
IPR001590 all species →	Domain	Peptidase M12B, ADAM/reprolysin	Interproscan
IPR035914 all species →	Homologous_superfamily	Spermadhesin, CUB domain superfamily	Interproscan
IPR024079 all species →	Homologous_superfamily	Metallopeptidase, catalytic domain superfamily	Interproscan
IPR036436 all species →	Homologous_superfamily	Disintegrin domain superfamily	Interproscan
IPR001762 all species →	Domain	Disintegrin domain	Interproscan
IPR000961 all species →	Domain	AGC-kinase, C-terminal	Interproscan
IPR011009 all species →	Homologous_superfamily	Protein kinase-like domain superfamily	Interproscan
IPR017892 all species →	Domain	Protein kinase, C-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR43542 all species →	METHYLTRANSFERASE	Interproscan
PTHR45895 all species →	INTEGRASE CATALYTIC DOMAIN-CONTAINING PROTEIN-RELATED	Interproscan
PTHR19300 all species →	BETA-1,4-GALACTOSYLTRANSFERASE	Interproscan
PTHR42929 all species →	INNER MEMBRANE ABC TRANSPORTER PERMEASE PROTEIN YDCU-RELATED-RELATED	Interproscan
PTHR11205 all species →	RIBOSOMAL PROTEIN S7	Interproscan
PTHR24393 all species →	ZINC FINGER PROTEIN	Interproscan
PTHR10157 all species →	DOPAMINE BETA HYDROXYLASE RELATED	Interproscan
PTHR11905 all species →	ADAM A DISINTEGRIN AND METALLOPROTEASE DOMAIN	Interproscan
PTHR24351 all species →	RIBOSOMAL PROTEIN S6 KINASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0008168 all species →	Molecular Function	methyltransferase activity	Interproscan
GO:0031167 all species →	Biological Process	rRNA methylation	Interproscan
GO:0005794 all species →	Cellular Component	Golgi apparatus	Interproscan
GO:0005975 all species →	Biological Process	carbohydrate metabolic process	Interproscan
GO:0008378 all species →	Molecular Function	galactosyltransferase activity	Interproscan
GO:0016757 all species →	Molecular Function	glycosyltransferase activity	Interproscan
GO:0070085 all species →	Biological Process	glycosylation	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0055085 all species →	Biological Process	transmembrane transport	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0003735 all species →	Molecular Function	structural constituent of ribosome	Interproscan
GO:0006412 all species →	Biological Process	translation	Interproscan
GO:0015935 all species →	Cellular Component	small ribosomal subunit	Interproscan
GO:0000028 all species →	Biological Process	ribosomal small subunit assembly	Interproscan
GO:0003729 all species →	Molecular Function	mRNA binding	Interproscan
GO:0005840 all species →	Cellular Component	ribosome	Interproscan
GO:0019843 all species →	Molecular Function	rRNA binding	Interproscan
GO:0022627 all species →	Cellular Component	cytosolic small ribosomal subunit	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0004500 all species →	Molecular Function	dopamine beta-monooxygenase activity	Interproscan
GO:0004222 all species →	Molecular Function	metalloendopeptidase activity	Interproscan
GO:0006508 all species →	Biological Process	proteolysis	Interproscan
GO:0008237 all species →	Molecular Function	metallopeptidase activity	Interproscan
GO:0004674 all species →	Molecular Function	protein serine/threonine kinase activity	Interproscan
GO:0018105 all species →	Biological Process	peptidyl-serine phosphorylation	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0006468 all species →	Biological Process	protein phosphorylation	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
K02992	RP-S7, MRPS7, rpsG; small subunit ribosomal protein S7	-	Ribosome	ko03011	deepkoala
K11071	potB; spermidine/putrescine transport system permease protein	-	Transporters	ko02000	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 →