Gene detail

Detailed information of g1517.t1 in Calvadosia cruxmelitensis

Genomic Location: not available for this species
NR annotation: XP_052703739.1, centrosomal protein of 63 kDa-like isoform X6 [Crassostrea angulata]
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
C6DAW6	Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase OS=Pectobacterium carotovorum subsp. carotovorum (strain PC1) OX=561230 GN=arnC PE=3 SV=1
Q6D2F0	Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase OS=Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672) OX=218491 GN=arnC PE=3 SV=1
Q7N3Q6	Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase OS=Photorhabdus laumondii subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01) OX=243265 GN=arnC PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000030 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000189 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000808 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0001718 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0002156 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0003437 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0003485 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0003605 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0005895 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0010949 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0061667 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00149 all species →	Metallophos	Calcineurin-like phosphoesterase	Domain	Interproscan
PF00271 all species →	Helicase_C	Helicase conserved C-terminal domain	Domain	Interproscan
PF00652 all species →	Ricin_B_lectin	Ricin-type beta-trefoil lectin domain	Domain	Interproscan
PF17045 all species →	CEP63	Centrosomal protein of 63 kDa	Coiled-coil	Interproscan
PF00535 all species →	Glycos_transf_2	Glycosyl transferase family 2	Family	Interproscan
PF19725 all species →	RPC5_C	DNA-directed RNA polymerase III subunit RPC5 C-terminal	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR051918 all species →	Family	Serine/threonine-protein phosphatase CPPED1	Interproscan
IPR029052 all species →	Homologous_superfamily	Metallo-dependent phosphatase-like	Interproscan
IPR041867 all species →	Domain	CPPED1, metallophosphatase domain	Interproscan
IPR004843 all species →	Domain	Calcineurin-like phosphoesterase domain, ApaH type	Interproscan
IPR001650 all species →	Domain	Helicase, C-terminal domain-like	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR049730 all species →	Domain	SNF2/RAD5-like, C-terminal helicase domain	Interproscan
IPR000772 all species →	Domain	Ricin B, lectin domain	Interproscan
IPR035992 all species →	Homologous_superfamily	Ricin B-like lectins	Interproscan
IPR031470 all species →	Domain	Centrosomal protein Cep63/Deup1, N-terminal	Interproscan
IPR001173 all species →	Domain	Glycosyltransferase 2-like	Interproscan
IPR050256 all species →	Family	Glycosyltransferase 2	Interproscan
IPR029044 all species →	Homologous_superfamily	Nucleotide-diphospho-sugar transferases	Interproscan
IPR045576 all species →	Domain	DNA-directed RNA polymerase III subunit RPC5, C-terminal	Interproscan
IPR029055 all species →	Homologous_superfamily	Nucleophile aminohydrolases, N-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR43143 all species →	METALLOPHOSPHOESTERASE, CALCINEURIN SUPERFAMILY	Interproscan
PTHR45623 all species →	CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 3-RELATED-RELATED	Interproscan
PTHR18875 all species →	SARCOMA ANTIGEN NY-SAR-24/CYTOSKELETAL PROTEIN SOJO	Interproscan
PTHR48090 all species →	UNDECAPRENYL-PHOSPHATE 4-DEOXY-4-FORMAMIDO-L-ARABINOSE TRANSFERASE-RELATED	Interproscan
PTHR46601 all species →	ULP_PROTEASE DOMAIN-CONTAINING PROTEIN	Interproscan
PTHR10937 all species →	GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE, ISOMERIZING	Interproscan
PTHR34615 all species →	PX DOMAIN-CONTAINING PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0016787 all species →	Molecular Function	hydrolase activity	Interproscan
GO:0000785 all species →	Cellular Component	chromatin	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0003682 all species →	Molecular Function	chromatin binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006338 all species →	Biological Process	chromatin remodeling	Interproscan
GO:0016887 all species →	Molecular Function	ATP hydrolysis activity	Interproscan
GO:0042393 all species →	Molecular Function	histone binding	Interproscan
GO:0140658 all species →	Molecular Function	ATP-dependent chromatin remodeler activity	Interproscan
GO:0005814 all species →	Cellular Component	centriole	Interproscan
GO:0007099 all species →	Biological Process	centriole replication	Interproscan
GO:0098535 all species →	Biological Process	de novo centriole assembly involved in multi-ciliated epithelial cell differentiation	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0099621 all species →	Molecular Function	undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase activity	Interproscan
GO:0004360 all species →	Molecular Function	glutamine-fructose-6-phosphate transaminase (isomerizing) activity	Interproscan
GO:0006002 all species →	Biological Process	fructose 6-phosphate metabolic process	Interproscan
GO:0006047 all species →	Biological Process	UDP-N-acetylglucosamine metabolic process	Interproscan
GO:0006487 all species →	Biological Process	protein N-linked glycosylation	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
K10012	arnC, pmrF; undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase	EC:2.4.2.53	Cationic antimicrobial peptide (CAMP) resistance	ko01503	deepkoala
K16763	CEP63; centrosomal protein CEP63	-	Chromosome and associated proteins	ko03036	deepkoala
K21814	CPPED1; serine/threonine-protein phosphatase CPPED1	EC:3.1.3.16	Protein phosphatases and associated proteins	ko01009	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 →