Gene detail

Detailed information of g36.t1 in Calvadosia cruxmelitensis

Genomic Location: not available for this species
NR annotation: NCT40930.1, phage tail protein [Alphaproteobacteria 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
Q775C3	Probable portal protein OS=Bordetella phage BPP-1 OX=2885909 GN=bbp21 PE=3 SV=1
P59015	Vacuolar protein sorting-associated protein 18 homolog OS=Danio rerio OX=7955 GN=vps18 PE=2 SV=2
Q9P253	Vacuolar protein sorting-associated protein 18 homolog OS=Homo sapiens OX=9606 GN=VPS18 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000042 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000057 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000081 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000133 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000684 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0002797 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0003515 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0005093 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0008276 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02931 all species →	Neur_chan_LBD	Neurotransmitter-gated ion-channel ligand binding domain	Family	Interproscan
PF02932 all species →	Neur_chan_memb	Neurotransmitter-gated ion-channel transmembrane region	Family	Interproscan
PF00001 all species →	7tm_1	7 transmembrane receptor (rhodopsin family)	Family	Interproscan
PF00431 all species →	CUB	CUB domain	Domain	Interproscan
PF00057 all species →	Ldl_recept_a	Low-density lipoprotein receptor domain class A	Repeat	Interproscan
PF05131 all species →	Pep3_Vps18	Pep3/Vps18/deep orange beta-propeller domain	Repeat	Interproscan
PF10220 all species →	Smg8_Smg9	Smg8_Smg9	Family	Interproscan
PF00643 all species →	zf-B_box	B-box zinc finger	Domain	Interproscan
PF00665 all species →	rve	Integrase core domain	Domain	Interproscan
PF12236 all species →	Head-tail_con	Bacteriophage head to tail connecting protein	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR018000 all species →	Conserved_site	Neurotransmitter-gated ion-channel, conserved site	Interproscan
IPR006202 all species →	Domain	Neurotransmitter-gated ion-channel ligand-binding domain	Interproscan
IPR006029 all species →	Domain	Neurotransmitter-gated ion-channel transmembrane domain	Interproscan
IPR006201 all species →	Family	Neurotransmitter-gated ion-channel	Interproscan
IPR036734 all species →	Homologous_superfamily	Neurotransmitter-gated ion-channel ligand-binding domain superfamily	Interproscan
IPR038050 all species →	Homologous_superfamily	Neuronal acetylcholine receptor	Interproscan
IPR036719 all species →	Homologous_superfamily	Neurotransmitter-gated ion-channel transmembrane domain superfamily	Interproscan
IPR017452 all species →	Domain	GPCR, rhodopsin-like, 7TM	Interproscan
IPR000276 all species →	Family	G protein-coupled receptor, rhodopsin-like	Interproscan
IPR050125 all species →	Family	G-protein coupled receptor opsins	Interproscan
IPR053207 all species →	Family	Non-NMDA Glutamate Receptor Accessory Protein	Interproscan
IPR035914 all species →	Homologous_superfamily	Spermadhesin, CUB domain superfamily	Interproscan
IPR002172 all species →	Repeat	Low-density lipoprotein (LDL) receptor class A repeat	Interproscan
IPR036055 all species →	Homologous_superfamily	LDL receptor-like superfamily	Interproscan
IPR000859 all species →	Domain	CUB domain	Interproscan
IPR035976 all species →	Homologous_superfamily	Sushi/SCR/CCP superfamily	Interproscan
IPR000436 all species →	Domain	Sushi/SCR/CCP domain	Interproscan
IPR023415 all species →	Conserved_site	Low-density lipoprotein (LDL) receptor class A, conserved site	Interproscan
IPR007810 all species →	Domain	Pep3/Vps18/deep orange, beta-propeller domain	Interproscan
IPR000547 all species →	Repeat	Clathrin, heavy chain/VPS, 7-fold repeat	Interproscan
IPR019354 all species →	Family	Nonsense-mediated mRNA decay factor SMG8-like	Interproscan
IPR047153 all species →	Family	TRIM45/56/19	Interproscan
IPR013087 all species →	Domain	Zinc finger C2H2-type	Interproscan
IPR003649 all species →	Domain	B-box, C-terminal	Interproscan
IPR000315 all species →	Domain	B-box-type zinc finger	Interproscan
IPR036236 all species →	Homologous_superfamily	Zinc finger C2H2 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
IPR046373 all species →	Homologous_superfamily	Acyl-CoA oxidase/dehydrogenase, middle domain superfamily	Interproscan
IPR009100 all species →	Homologous_superfamily	Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily	Interproscan
IPR012258 all species →	Family	Acyl-CoA oxidase	Interproscan
IPR020991 all species →	Family	Head-to-tail connector protein, podovirus-type	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR18945 all species →	NEUROTRANSMITTER GATED ION CHANNEL	Interproscan
PTHR38681 all species →	RETROVIRUS-RELATED POL POLYPROTEIN FROM TRANSPOSON 412-LIKE PROTEIN-RELATED	Interproscan
PTHR24240 all species →	OPSIN	Interproscan
PTHR47537 all species →	CUBILIN	Interproscan
PTHR23323 all species →	VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN	Interproscan
PTHR13091 all species →	AMPLIFIED IN BREAST CANCER 2-RELATED	Interproscan
PTHR25462 all species →	BONUS, ISOFORM C-RELATED	Interproscan
PTHR42648 all species →	TRANSPOSASE, PUTATIVE-RELATED	Interproscan
PTHR10909 all species →	ELECTRON TRANSPORT OXIDOREDUCTASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005230 all species →	Molecular Function	extracellular ligand-gated monoatomic ion channel activity	Interproscan
GO:0006811 all species →	Biological Process	monoatomic ion transport	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0004888 all species →	Molecular Function	transmembrane signaling receptor activity	Interproscan
GO:0005216 all species →	Molecular Function	monoatomic ion channel activity	Interproscan
GO:0034220 all species →	Biological Process	monoatomic ion transmembrane transport	Interproscan
GO:0005231 all species →	Molecular Function	excitatory extracellular ligand-gated monoatomic ion channel activity	Interproscan
GO:0005887 all species →	Cellular Component	plasma membrane	Interproscan
GO:0007165 all species →	Biological Process	signal transduction	Interproscan
GO:0007268 all species →	Biological Process	chemical synaptic transmission	Interproscan
GO:0030594 all species →	Molecular Function	neurotransmitter receptor activity	Interproscan
GO:0042391 all species →	Biological Process	regulation of membrane potential	Interproscan
GO:0043005 all species →	Cellular Component	neuron projection	Interproscan
GO:0045202 all species →	Cellular Component	synapse	Interproscan
GO:0050877 all species →	Biological Process	nervous system process	Interproscan
GO:1904315 all species →	Molecular Function	transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential	Interproscan
GO:0004930 all species →	Molecular Function	G protein-coupled receptor activity	Interproscan
GO:0007186 all species →	Biological Process	G protein-coupled receptor signaling pathway	Interproscan
GO:0007602 all species →	Biological Process	phototransduction	Interproscan
GO:0008020 all species →	Molecular Function	G protein-coupled photoreceptor activity	Interproscan
GO:0071482 all species →	Biological Process	cellular response to light stimulus	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0006886 all species →	Biological Process	intracellular protein transport	Interproscan
GO:0016192 all species →	Biological Process	vesicle-mediated transport	Interproscan
GO:0005768 all species →	Cellular Component	endosome	Interproscan
GO:0006904 all species →	Biological Process	vesicle docking involved in exocytosis	Interproscan
GO:0007032 all species →	Biological Process	endosome organization	Interproscan
GO:0007033 all species →	Biological Process	vacuole organization	Interproscan
GO:0007040 all species →	Biological Process	lysosome organization	Interproscan
GO:0008333 all species →	Biological Process	endosome to lysosome transport	Interproscan
GO:0030674 all species →	Molecular Function	protein-macromolecule adaptor activity	Interproscan
GO:0030897 all species →	Cellular Component	HOPS complex	Interproscan
GO:0048284 all species →	Biological Process	organelle fusion	Interproscan
GO:0000184 all species →	Biological Process	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0015074 all species →	Biological Process	DNA integration	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0016627 all species →	Molecular Function	oxidoreductase activity, acting on the CH-CH group of donors	Interproscan
GO:0003997 all species →	Molecular Function	acyl-CoA oxidase activity	Interproscan
GO:0005504 all species →	Molecular Function	fatty acid binding	Interproscan
GO:0005777 all species →	Cellular Component	peroxisome	Interproscan
GO:0006631 all species →	Biological Process	fatty acid metabolic process	Interproscan
GO:0016402 all species →	Molecular Function	pristanoyl-CoA oxidase activity	Interproscan
GO:0033540 all species →	Biological Process	fatty acid beta-oxidation using acyl-CoA oxidase	Interproscan
GO:0050660 all species →	Molecular Function	flavin adenine dinucleotide binding	Interproscan
GO:0055088 all species →	Biological Process	lipid homeostasis	Interproscan
GO:0071949 all species →	Molecular Function	FAD 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
K05312	CHRNN; nicotinic acetylcholine receptor, invertebrate	-	Ion channels	ko04040	deepkoala
K18734	SMG8; protein SMG8	-	Messenger RNA biogenesis	ko03019	deepkoala
K20181	VPS18, PEP3; vacuolar protein sorting-associated protein 18	-	Membrane trafficking	ko04131	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 →