Gene detail

Detailed information of g253.t1 in Calvadosia cruxmelitensis

Genomic Location: not available for this species
NR annotation: MCG8336451.1, TraR/DksA family transcriptional regulator [Pseudomonadota bacterium]
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
Q71X99	ATP-dependent helicase/nuclease subunit A OS=Listeria monocytogenes serotype 4b (strain F2365) OX=265669 GN=addA PE=3 SV=1
Q8Y511	ATP-dependent helicase/nuclease subunit A OS=Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) OX=169963 GN=addA PE=3 SV=1
Q929A9	ATP-dependent helicase/nuclease subunit A OS=Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262) OX=272626 GN=addA PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000050 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000732 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0001727 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0001935 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0002505 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0004228 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0006366 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0006410 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0008139 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0014655 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0016584 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0017799 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0018186 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0030294 (this species only) · gene tree & orthology
Transcription factor family	RHD · all TF in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF15508 all species →	NAAA-beta	beta subunit of N-acylethanolamine-hydrolyzing acid amidase	Family	Interproscan
PF02275 all species →	CBAH	Linear amide C-N hydrolases, choloylglycine hydrolase family	Domain	Interproscan
PF19745 all species →	FUT8_N_cat	Alpha-(1,6)-fucosyltransferase N- and catalytic domains	Domain	Interproscan
PF00554 all species →	RHD_DNA_bind	Rel homology DNA-binding domain	Domain	Interproscan
PF06159 all species →	DUF974	Protein of unknown function (DUF974)	Family	Interproscan
PF20519 all species →	Polycystin_dom	Polycystin domain	Domain	Interproscan
PF08016 all species →	PKD_channel	Polycystin cation channel	Family	Interproscan
PF01477 all species →	PLAT	PLAT/LH2 domain	Domain	Interproscan
PF00580 all species →	UvrD-helicase	UvrD/REP helicase N-terminal domain	Domain	Interproscan
PF12705 all species →	PDDEXK_1	PD-(D/E)XK nuclease superfamily	Domain	Interproscan
PF13361 all species →	UvrD_C	UvrD-like helicase C-terminal domain	Domain	Interproscan
PF14580 all species →	LRR_9	Leucine-rich repeat	Repeat	Interproscan
PF00612 all species →	IQ	IQ calmodulin-binding motif	Motif	Interproscan
PF00293 all species →	NUDIX	NUDIX domain	Domain	Interproscan
PF00615 all species →	RGS	Regulator of G protein signaling domain	Domain	Interproscan
PF00665 all species →	rve	Integrase core domain	Domain	Interproscan
PF01258 all species →	zf-dskA_traR	Prokaryotic dksA/traR C4-type zinc finger	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR029130 all species →	Domain	Acid ceramidase, N-terminal	Interproscan
IPR029132 all species →	Domain	Choloylglycine hydrolase/NAAA C-terminal	Interproscan
IPR016699 all species →	Family	Acid ceramidase-like	Interproscan
IPR045573 all species →	Domain	Alpha-(1,6)-fucosyltransferase, N- and catalytic domain	Interproscan
IPR027350 all species →	Domain	Glycosyltransferase family 23 (GT23) domain	Interproscan
IPR008366 all species →	Family	Nuclear factor of activated T cells (NFAT)	Interproscan
IPR014756 all species →	Homologous_superfamily	Immunoglobulin E-set	Interproscan
IPR008967 all species →	Homologous_superfamily	p53-like transcription factor, DNA-binding domain superfamily	Interproscan
IPR011539 all species →	Domain	Rel homology domain, DNA-binding domain	Interproscan
IPR037059 all species →	Homologous_superfamily	Rel homology domain (RHD), DNA-binding domain superfamily	Interproscan
IPR013783 all species →	Homologous_superfamily	Immunoglobulin-like fold	Interproscan
IPR010378 all species →	Family	Trafficking protein particle complex subunit 13	Interproscan
IPR046791 all species →	Domain	Polycystin domain	Interproscan
IPR013122 all species →	Domain	Polycystin cation channel, PKD1/PKD2	Interproscan
IPR000434 all species →	Family	Polycystic kidney disease type 1 protein	Interproscan
IPR001024 all species →	Domain	PLAT/LH2 domain	Interproscan
IPR036392 all species →	Homologous_superfamily	PLAT/LH2 domain superfamily	Interproscan
IPR051223 all species →	Family	Polycystin	Interproscan
IPR014016 all species →	Domain	UvrD-like helicase, ATP-binding domain	Interproscan
IPR011335 all species →	Homologous_superfamily	Restriction endonuclease type II-like	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR014017 all species →	Domain	UvrD-like DNA helicase, C-terminal	Interproscan
IPR000212 all species →	Family	DNA helicase, UvrD/REP type	Interproscan
IPR011604 all species →	Homologous_superfamily	PD-(D/E)XK endonuclease-like domain superfamily	Interproscan
IPR038726 all species →	Domain	PD-(D/E)XK endonuclease-like domain, AddAB-type	Interproscan
IPR000048 all species →	Binding_site	IQ motif, EF-hand binding site	Interproscan
IPR001611 all species →	Repeat	Leucine-rich repeat	Interproscan
IPR032675 all species →	Homologous_superfamily	Leucine-rich repeat domain superfamily	Interproscan
IPR015797 all species →	Homologous_superfamily	NUDIX hydrolase-like domain superfamily	Interproscan
IPR000086 all species →	Domain	NUDIX hydrolase domain	Interproscan
IPR047016 all species →	Family	Regulator of G protein signaling 6/7/9/11	Interproscan
IPR016137 all species →	Domain	RGS domain	Interproscan
IPR024066 all species →	Homologous_superfamily	RGS, subdomain 1/3	Interproscan
IPR044926 all species →	Homologous_superfamily	RGS, subdomain 2	Interproscan
IPR036305 all species →	Homologous_superfamily	RGS domain superfamily	Interproscan
IPR001584 all species →	Domain	Integrase, catalytic core	Interproscan
IPR012337 all species →	Homologous_superfamily	Ribonuclease H-like superfamily	Interproscan
IPR036397 all species →	Homologous_superfamily	Ribonuclease H superfamily	Interproscan
IPR050951 all species →	Family	Retrovirus-related Pol polyprotein	Interproscan
IPR020458 all species →	Conserved_site	Zinc finger, DksA/TraR C4-type conserved site	Interproscan
IPR000962 all species →	Domain	Zinc finger, DksA/TraR C4-type	Interproscan
IPR037187 all species →	Homologous_superfamily	DksA, N-terminal domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR28583 all species →	ACID AMIDASE	Interproscan
PTHR13132 all species →	ALPHA- 1,6 -FUCOSYLTRANSFERASE	Interproscan
PTHR23112 all species →	G PROTEIN-COUPLED RECEPTOR 157-RELATED	Interproscan
PTHR12533 all species →	NFAT	Interproscan
PTHR13134 all species →	UNCHARACTERIZED	Interproscan
PTHR10877 all species →	POLYCYSTIN FAMILY MEMBER	Interproscan
PTHR11070 all species →	UVRD / RECB / PCRA DNA HELICASE FAMILY MEMBER	Interproscan
PTHR15454 all species →	NISCHARIN RELATED	Interproscan
PTHR12629 all species →	DIPHOSPHOINOSITOL POLYPHOSPHATE PHOSPHOHYDROLASE	Interproscan
PTHR45746 all species →	LP21163P	Interproscan
PTHR37984 all species →	PROTEIN CBG26694	Interproscan
PTHR33823 all species →	RNA POLYMERASE-BINDING TRANSCRIPTION FACTOR DKSA-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005764 all species →	Cellular Component	lysosome	Interproscan
GO:0006631 all species →	Biological Process	fatty acid metabolic process	Interproscan
GO:0017064 all species →	Molecular Function	fatty acid amide hydrolase activity	Interproscan
GO:0016810 all species →	Molecular Function	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	Interproscan
GO:0006487 all species →	Biological Process	protein N-linked glycosylation	Interproscan
GO:0036071 all species →	Biological Process	N-glycan fucosylation	Interproscan
GO:0046921 all species →	Molecular Function	alpha-(1->6)-fucosyltransferase activity	Interproscan
GO:0004930 all species →	Molecular Function	G protein-coupled receptor activity	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0007189 all species →	Biological Process	adenylate cyclase-activating G protein-coupled receptor signaling pathway	Interproscan
GO:0000978 all species →	Molecular Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	Interproscan
GO:0000981 all species →	Molecular Function	DNA-binding transcription factor activity, RNA polymerase II-specific	Interproscan
GO:0003700 all species →	Molecular Function	DNA-binding transcription factor activity	Interproscan
GO:0005667 all species →	Cellular Component	transcription regulator complex	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:0008134 all species →	Molecular Function	transcription factor binding	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:1990072 all species →	Cellular Component	TRAPPIII protein complex	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005262 all species →	Molecular Function	calcium channel activity	Interproscan
GO:0050982 all species →	Biological Process	detection of mechanical stimulus	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0016787 all species →	Molecular Function	hydrolase activity	Interproscan
GO:0000725 all species →	Biological Process	recombinational repair	Interproscan
GO:0003678 all species →	Molecular Function	DNA helicase activity	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0033202 all species →	Cellular Component	DNA helicase complex	Interproscan
GO:0043138 all species →	Molecular Function	3'-5' DNA helicase activity	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0000298 all species →	Molecular Function	endopolyphosphatase activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0008486 all species →	Molecular Function	diphosphoinositol-polyphosphate diphosphatase activity	Interproscan
GO:0034431 all species →	Molecular Function	bis(5'-adenosyl)-hexaphosphatase activity	Interproscan
GO:0034432 all species →	Molecular Function	bis(5'-adenosyl)-pentaphosphatase activity	Interproscan
GO:0050072 all species →	Molecular Function	obsolete m7G(5')pppN diphosphatase activity	Interproscan
GO:0071543 all species →	Biological Process	diphosphoinositol polyphosphate metabolic process	Interproscan
GO:1901907 all species →	Biological Process	diadenosine pentaphosphate catabolic process	Interproscan
GO:1901909 all species →	Biological Process	diadenosine hexaphosphate catabolic process	Interproscan
GO:1901911 all species →	Biological Process	adenosine 5'-(hexahydrogen pentaphosphate) catabolic process	Interproscan
GO:0005096 all species →	Molecular Function	GTPase activator activity	Interproscan
GO:0008277 all species →	Biological Process	regulation of G protein-coupled receptor signaling pathway	Interproscan
GO:0043547 all species →	Biological Process	positive regulation of GTPase activity	Interproscan
GO:0015074 all species →	Biological Process	DNA integration	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	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
K04988	PKD1L2; polycystin 1L2	-	Ion channels	ko04040	deepkoala
K06204	dksA; RNA polymerase-binding transcription factor	-	Ribosome biogenesis	ko03009	deepkoala
K13720	NAAA; N-(long-chain-acyl)ethanolamine deacylase	EC:3.5.1.60	Peptidases and inhibitors	ko01002	deepkoala
K16449	RGS; regulator of G-protein signaling	-	Signaling proteins	-	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 →