Gene detail

Detailed information of g103.t1 in Calvadosia cruxmelitensis

Genomic Location: not available for this species
NR annotation: WP_076717168.1, TRAP transporter substrate-binding protein [Motiliproteus sp. MSK22-1]
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
Q8YSQ6	Monocarboxylate 2-oxoacid-binding periplasmic protein all3028 OS=Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) OX=103690 GN=all3028 PE=1 SV=1
Q3J1R2	Alpha-keto acid-binding periplasmic protein TakP OS=Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.) OX=272943 GN=takP PE=1 SV=1
Q5U5A6	Notch-regulated ankyrin repeat-containing protein OS=Xenopus laevis OX=8355 GN=nrarp PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000005 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000051 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000201 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0001176 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0001325 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0002261 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0002440 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0002476 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0004193 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0005367 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0021115 (this species only) · gene tree & orthology
Transcription factor family	Homeobox · all TF in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00046 all species →	Homeodomain	Homeodomain	Domain	Interproscan
PF00582 all species →	Usp	Universal stress protein family	Domain	Interproscan
PF03480 all species →	DctP	Bacterial extracellular solute-binding protein, family 7	Family	Interproscan
PF02145 all species →	Rap_GAP	Rap/ran-GAP	Family	Interproscan
PF12796 all species →	Ank_2	Ankyrin repeats (3 copies)	Repeat	Interproscan
PF01465 all species →	GRIP	GRIP domain	Family	Interproscan
PF13418 all species →	Kelch_4	Galactose oxidase, central domain	Repeat	Interproscan
PF03067 all species →	LPMO_10	Lytic polysaccharide mono-oxygenase, cellulose-degrading	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR009057 all species →	Homologous_superfamily	Homeobox-like domain superfamily	Interproscan
IPR017970 all species →	Conserved_site	Homeobox, conserved site	Interproscan
IPR001356 all species →	Domain	Homeobox domain	Interproscan
IPR050674 all species →	Family	Msh Homeobox Transcriptional Regulators	Interproscan
IPR020479 all species →	Domain	Homeobox domain, metazoa	Interproscan
IPR000047 all species →	Conserved_site	Helix-turn-helix motif	Interproscan
IPR006015 all species →	Family	Universal stress protein A family	Interproscan
IPR014729 all species →	Homologous_superfamily	Rossmann-like alpha/beta/alpha sandwich fold	Interproscan
IPR006016 all species →	Domain	UspA	Interproscan
IPR051688 all species →	Family	Universal stress protein A	Interproscan
IPR018389 all species →	Family	TRAP transporter solute receptor DctP	Interproscan
IPR026289 all species →	Family	Solute binding protein, TakP-like	Interproscan
IPR038404 all species →	Homologous_superfamily	TRAP transporter solute receptor DctP superfamily	Interproscan
IPR027107 all species →	Family	Tuberin/Ral GTPase-activating protein subunit alpha	Interproscan
IPR035974 all species →	Homologous_superfamily	Rap/Ran-GAP superfamily	Interproscan
IPR000331 all species →	Domain	Rap/Ran-GAP domain	Interproscan
IPR002110 all species →	Repeat	Ankyrin repeat	Interproscan
IPR000237 all species →	Domain	GRIP domain	Interproscan
IPR036770 all species →	Homologous_superfamily	Ankyrin repeat-containing domain superfamily	Interproscan
IPR051952 all species →	Family	Golgi-associated and autophagy-related protein	Interproscan
IPR015915 all species →	Homologous_superfamily	Kelch-type beta propeller	Interproscan
IPR052456 all species →	Family	CTLH complex component protein	Interproscan
IPR011043 all species →	Homologous_superfamily	Galactose oxidase/kelch, beta-propeller	Interproscan
IPR004302 all species →	Domain	Cellulose/chitin-binding protein, N-terminal	Interproscan
IPR052282 all species →	Family	Starch-active lytic polysaccharide monooxygenase	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR47027 all species →	REVERSE TRANSCRIPTASE DOMAIN-CONTAINING PROTEIN	Interproscan
PTHR24338 all species →	HOMEOBOX PROTEIN MSX	Interproscan
PTHR43010 all species →	UNIVERSAL STRESS PROTEIN SLR1230	Interproscan
PTHR33376 all species →	-	Interproscan
PTHR10063 all species →	TUBERIN	Interproscan
PTHR23157 all species →	GRIP AND COILED-COIL DOMAIN-CONTAINING PROTEIN 1	Interproscan
PTHR35169 all species →	FE2OG DIOXYGENASE DOMAIN-CONTAINING PROTEIN	Interproscan
PTHR15526 all species →	MUSKELIN	Interproscan
PTHR36575 all species →	BINDING PROTEIN, PUTATIVE (AFU_ORTHOLOGUE AFUA_1G14430)-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000981 all species →	Molecular Function	DNA-binding transcription factor activity, RNA polymerase II-specific	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0000977 all species →	Molecular Function	RNA polymerase II transcription regulatory region sequence-specific DNA binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:0048598 all species →	Biological Process	embryonic morphogenesis	Interproscan
GO:0055085 all species →	Biological Process	transmembrane transport	Interproscan
GO:0031317 all species →	Cellular Component	tripartite ATP-independent periplasmic transporter complex	Interproscan
GO:0005096 all species →	Molecular Function	GTPase activator activity	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0032007 all species →	Biological Process	negative regulation of TOR signaling	Interproscan
GO:0033596 all species →	Cellular Component	TSC1-TSC2 complex	Interproscan
GO:0043547 all species →	Biological Process	positive regulation of GTPase activity	Interproscan
GO:0051056 all species →	Biological Process	regulation of small GTPase mediated signal transduction	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005794 all species →	Cellular Component	Golgi apparatus	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
K09341	MSX; homeobox protein MSX	-	Transcription factors	ko03000	deepkoala
K11688	dctP; C4-dicarboxylate-binding protein DctP	-	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 →