Gene detail

Detailed information of g779.t1 in Calvadosia cruxmelitensis

Genomic Location: not available for this species
NR annotation: AAG34890.1, T-box protein AmphiTbx6/16, partial [Branchiostoma floridae]
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
O73718	T-box transcription factor TBX3 (Fragment) OS=Gallus gallus OX=9031 GN=TBX3 PE=2 SV=1
Q7ZTU9	T-box transcription factor TBX2b OS=Danio rerio OX=7955 GN=tbx2b PE=1 SV=4
Q9IAK8	T-box transcription factor TBX5-A OS=Danio rerio OX=7955 GN=tbx5a PE=2 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000006 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000042 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000326 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000437 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000501 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0002375 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0003869 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0007187 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0007515 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0014232 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0026063 (this species only) · gene tree & orthology
Transcription factor family	T-box · all TF in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF05699 all species →	Dimer_Tnp_hAT	hAT family C-terminal dimerisation region	Domain	Interproscan
PF05041 all species →	Pecanex_C	Pecanex protein (C-terminus)	Family	Interproscan
PF00907 all species →	T-box	T-box	Domain	Interproscan
PF00168 all species →	C2	C2 domain	Domain	Interproscan
PF05970 all species →	PIF1	PIF1-like helicase	Family	Interproscan
PF00654 all species →	Voltage_CLC	Voltage gated chloride channel	Family	Interproscan
PF21056 all species →	ZSWIM1-3_RNaseH-like	Zinc finger SWIM domain-containing protein 1/3, RNaseH-like domain	Domain	Interproscan
PF07727 all species →	RVT_2	Reverse transcriptase (RNA-dependent DNA polymerase)	Family	Interproscan
PF06396 all species →	AGTRAP	Angiotensin II, type I receptor-associated protein (AGTRAP)	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR052035 all species →	Family	Zinc finger BED domain-containing	Interproscan
IPR012337 all species →	Homologous_superfamily	Ribonuclease H-like superfamily	Interproscan
IPR008906 all species →	Domain	HAT, C-terminal dimerisation domain	Interproscan
IPR013087 all species →	Domain	Zinc finger C2H2-type	Interproscan
IPR007735 all species →	Domain	Pecanex, C-terminal	Interproscan
IPR039797 all species →	Family	Protein Pecanex	Interproscan
IPR046360 all species →	Domain	T-box transcription factor, DNA-binding domain	Interproscan
IPR008967 all species →	Homologous_superfamily	p53-like transcription factor, DNA-binding domain superfamily	Interproscan
IPR001699 all species →	Family	T-box transcription factor	Interproscan
IPR018186 all species →	Conserved_site	Transcription factor, T-box, conserved site	Interproscan
IPR036960 all species →	Homologous_superfamily	T-box superfamily	Interproscan
IPR000008 all species →	Domain	C2 domain	Interproscan
IPR035892 all species →	Homologous_superfamily	C2 domain superfamily	Interproscan
IPR010285 all species →	Family	DNA helicase Pif1-like	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR001807 all species →	Family	Chloride channel, voltage gated	Interproscan
IPR014743 all species →	Homologous_superfamily	Chloride channel, core	Interproscan
IPR048324 all species →	Domain	ZSWIM1/3, RNaseH-like domain	Interproscan
IPR052579 all species →	Family	Zinc finger SWIM domain-containing protein	Interproscan
IPR013103 all species →	Domain	Reverse transcriptase, RNA-dependent DNA polymerase	Interproscan
IPR043502 all species →	Homologous_superfamily	DNA/RNA polymerase superfamily	Interproscan
IPR009436 all species →	Family	Type-1 angiotensin II receptor-associated protein	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46481 all species →	ZINC FINGER BED DOMAIN-CONTAINING PROTEIN 4	Interproscan
PTHR12372 all species →	PECANEX	Interproscan
PTHR11267 all species →	T-BOX PROTEIN-RELATED	Interproscan
PTHR10024 all species →	SYNAPTOTAGMIN	Interproscan
PTHR10492 all species →	UNCHARACTERIZED	Interproscan
PTHR45711 all species →	CHLORIDE CHANNEL PROTEIN	Interproscan
PTHR31569 all species →	SWIM-TYPE DOMAIN-CONTAINING PROTEIN	Interproscan
PTHR16521 all species →	TYPE-1 ANGIOTENSIN II RECEPTOR-ASSOCIATED PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0046983 all species →	Molecular Function	protein dimerization activity	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0003700 all species →	Molecular Function	DNA-binding transcription factor activity	Interproscan
GO:0045893 all species →	Biological Process	positive regulation of DNA-templated transcription	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	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:0001708 all species →	Biological Process	cell fate specification	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0000149 all species →	Molecular Function	SNARE binding	Interproscan
GO:0001786 all species →	Molecular Function	phosphatidylserine binding	Interproscan
GO:0005509 all species →	Molecular Function	calcium ion binding	Interproscan
GO:0005544 all species →	Molecular Function	calcium-dependent phospholipid binding	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0014059 all species →	Biological Process	regulation of dopamine secretion	Interproscan
GO:0017156 all species →	Biological Process	calcium-ion regulated exocytosis	Interproscan
GO:0017158 all species →	Biological Process	regulation of calcium ion-dependent exocytosis	Interproscan
GO:0030276 all species →	Molecular Function	clathrin binding	Interproscan
GO:0070382 all species →	Cellular Component	exocytic vesicle	Interproscan
GO:0071277 all species →	Biological Process	cellular response to calcium ion	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:0005247 all species →	Molecular Function	voltage-gated chloride channel activity	Interproscan
GO:0006821 all species →	Biological Process	chloride transport	Interproscan
GO:0055085 all species →	Biological Process	transmembrane transport	Interproscan
GO:0005769 all species →	Cellular Component	early endosome	Interproscan
GO:0005794 all species →	Cellular Component	Golgi apparatus	Interproscan
GO:0005887 all species →	Cellular Component	plasma membrane	Interproscan
GO:0015299 all species →	Molecular Function	obsolete solute:proton antiporter activity	Interproscan
GO:0038166 all species →	Biological Process	angiotensin-activated signaling pathway	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
K24637	ZBED1; zinc finger BED domain-containing protein 1 (E3 SUMO-protein ligase ZBED1)	EC:2.3.2.-	Ubiquitin system	ko04121	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 →