Gene detail

Detailed information of g335.t1 in Calvadosia cruxmelitensis

Genomic Location: not available for this species
NR annotation: WP_103727615.1, DNA cytosine methyltransferase [Novosphingobium sp. HII-3]
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
Q71TL0	DNA N-6-adenine-methyltransferase OS=Escherichia phage P1 OX=2886926 GN=dmt PE=1 SV=1
P34882	Type II methyltransferase M.AquIA OS=Picosynechococcus sp. (strain ATCC 27264 / PCC 7002 / PR-6) OX=32049 GN=aquIMA PE=1 SV=1
P00476	Orphan methyltransferase M.SPRI OS=Bacillus phage SPR OX=10725 PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000001 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000015 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000022 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000033 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000132 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000330 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000989 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0001201 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0001570 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0001968 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0012673 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0021536 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0033286 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03109 all species →	ABC1	ABC1 atypical kinase-like domain	Domain	Interproscan
PF00520 all species →	Ion_trans	Ion transport protein	Family	Interproscan
PF02214 all species →	BTB_2	BTB/POZ domain	Domain	Interproscan
PF00621 all species →	RhoGEF	RhoGEF domain	Domain	Interproscan
PF16614 all species →	RhoGEF67_u2	Unstructured region two on RhoGEF 6 and 7	Disordered	Interproscan
PF00145 all species →	DNA_methylase	C-5 cytosine-specific DNA methylase	Domain	Interproscan
PF00858 all species →	ASC	Amiloride-sensitive sodium channel	Family	Interproscan
PF01414 all species →	DSL	Delta serrate ligand	Domain	Interproscan
PF07657 all species →	MNNL	N terminus of Notch ligand C2-like domain	Domain	Interproscan
PF05970 all species →	PIF1	PIF1-like helicase	Family	Interproscan
PF18701 all species →	DUF5641	Family of unknown function (DUF5641)	Domain	Interproscan
PF17917 all species →	RT_RNaseH	RNase H-like domain found in reverse transcriptase	Domain	Interproscan
PF17921 all species →	Integrase_H2C2	Integrase zinc binding domain	Domain	Interproscan
PF13650 all species →	Asp_protease_2	Aspartyl protease	Domain	Interproscan
PF00078 all species →	RVT_1	Reverse transcriptase (RNA-dependent DNA polymerase)	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR045307 all species →	Domain	ADCK1-like domain	Interproscan
IPR051130 all species →	Family	Mitochondrial structure and function regulator	Interproscan
IPR004147 all species →	Domain	ABC1 atypical kinase-like domain	Interproscan
IPR011009 all species →	Homologous_superfamily	Protein kinase-like domain superfamily	Interproscan
IPR011333 all species →	Homologous_superfamily	SKP1/BTB/POZ domain superfamily	Interproscan
IPR005821 all species →	Domain	Ion transport domain	Interproscan
IPR027359 all species →	Homologous_superfamily	Voltage-dependent channel domain superfamily	Interproscan
IPR003131 all species →	Domain	Potassium channel tetramerisation-type BTB domain	Interproscan
IPR000219 all species →	Domain	Dbl homology (DH) domain	Interproscan
IPR001849 all species →	Domain	Pleckstrin homology domain	Interproscan
IPR011993 all species →	Homologous_superfamily	PH-like domain superfamily	Interproscan
IPR035899 all species →	Homologous_superfamily	Dbl homology (DH) domain superfamily	Interproscan
IPR050750 all species →	Family	Cytosine-specific C5-methyltransferase	Interproscan
IPR018117 all species →	Active_site	DNA methylase, C-5 cytosine-specific, active site	Interproscan
IPR001525 all species →	Family	C-5 cytosine methyltransferase	Interproscan
IPR029063 all species →	Homologous_superfamily	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Interproscan
IPR001584 all species →	Domain	Integrase, catalytic core	Interproscan
IPR036397 all species →	Homologous_superfamily	Ribonuclease H superfamily	Interproscan
IPR050951 all species →	Family	Retrovirus-related Pol polyprotein	Interproscan
IPR012337 all species →	Homologous_superfamily	Ribonuclease H-like superfamily	Interproscan
IPR001873 all species →	Family	Epithelial sodium channel	Interproscan
IPR001774 all species →	Domain	Delta/Serrate/lag-2 (DSL) protein	Interproscan
IPR011651 all species →	Domain	Notch ligand, N-terminal domain	Interproscan
IPR036691 all species →	Homologous_superfamily	Endonuclease/exonuclease/phosphatase superfamily	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR051055 all species →	Family	PIF1 DNA helicase	Interproscan
IPR010285 all species →	Family	DNA helicase Pif1-like	Interproscan
IPR040676 all species →	Domain	Domain of unknown function DUF5641	Interproscan
IPR041373 all species →	Domain	Reverse transcriptase, RNase H-like domain	Interproscan
IPR041588 all species →	Domain	Integrase zinc-binding domain	Interproscan
IPR043502 all species →	Homologous_superfamily	DNA/RNA polymerase superfamily	Interproscan
IPR021109 all species →	Homologous_superfamily	Aspartic peptidase domain superfamily	Interproscan
IPR000477 all species →	Domain	Reverse transcriptase domain	Interproscan
IPR001995 all species →	Domain	Peptidase A2A, retrovirus, catalytic	Interproscan
IPR043128 all species →	Homologous_superfamily	Reverse transcriptase/Diguanylate cyclase domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR43173 all species →	ABC1 FAMILY PROTEIN	Interproscan
PTHR11537 all species →	VOLTAGE-GATED POTASSIUM CHANNEL	Interproscan
PTHR46026 all species →	RHO-TYPE GUANINE NUCLEOTIDE EXCHANGE FACTOR, ISOFORM F	Interproscan
PTHR46098 all species →	TRNA (CYTOSINE(38)-C(5))-METHYLTRANSFERASE	Interproscan
PTHR37984 all species →	PROTEIN CBG26694	Interproscan
PTHR46670 all species →	ENDO/EXONUCLEASE/PHOSPHATASE DOMAIN-CONTAINING PROTEIN	Interproscan
PTHR47642 all species →	ATP-DEPENDENT DNA HELICASE	Interproscan
PTHR22955 all species →	RETROTRANSPOSON	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005216 all species →	Molecular Function	monoatomic ion channel activity	Interproscan
GO:0006811 all species →	Biological Process	monoatomic ion transport	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0055085 all species →	Biological Process	transmembrane transport	Interproscan
GO:0005249 all species →	Molecular Function	voltage-gated potassium channel activity	Interproscan
GO:0005251 all species →	Molecular Function	delayed rectifier potassium channel activity	Interproscan
GO:0008076 all species →	Cellular Component	voltage-gated potassium channel complex	Interproscan
GO:0016021 all species →	Cellular Component	membrane	Interproscan
GO:0071805 all species →	Biological Process	potassium ion transmembrane transport	Interproscan
GO:0051260 all species →	Biological Process	protein homooligomerization	Interproscan
GO:0005085 all species →	Molecular Function	guanyl-nucleotide exchange factor activity	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0008168 all species →	Molecular Function	methyltransferase activity	Interproscan
GO:0015074 all species →	Biological Process	DNA integration	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0005272 all species →	Molecular Function	sodium channel activity	Interproscan
GO:0006814 all species →	Biological Process	sodium ion transport	Interproscan
GO:0007154 all species →	Biological Process	cell communication	Interproscan
GO:0007219 all species →	Biological Process	Notch signaling pathway	Interproscan
GO:0007275 all species →	Biological Process	multicellular organism development	Interproscan
GO:0000723 all species →	Biological Process	telomere maintenance	Interproscan
GO:0003678 all species →	Molecular Function	DNA helicase activity	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0004190 all species →	Molecular Function	aspartic-type endopeptidase activity	Interproscan
GO:0006508 all species →	Biological Process	proteolysis	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
K00558	DNMT1, dcm; DNA (cytosine-5)-methyltransferase 1	EC:2.1.1.37	Prokaryotic defense system	ko02048	deepkoala
K05857	PLCD; phosphatidylinositol phospholipase C, delta	EC:3.1.4.11	Membrane trafficking	ko04131	deepkoala
K08869	ADCK, ABC1; aarF domain-containing kinase	-	Protein kinases	ko01001	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 →