Gene detail

Detailed information of g769.t1 in Calvadosia cruxmelitensis

Genomic Location: not available for this species
NR annotation: XP_047123860.1, structural maintenance of chromosomes protein 2-like [Hydra vulgaris]
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
Q9C5Y4	Structural maintenance of chromosomes protein 2-1 OS=Arabidopsis thaliana OX=3702 GN=SMC2-1 PE=2 SV=2
Q8CG48	Structural maintenance of chromosomes protein 2 OS=Mus musculus OX=10090 GN=Smc2 PE=1 SV=2
Q90988	Structural maintenance of chromosomes protein 2 OS=Gallus gallus OX=9031 GN=SMC2 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000068 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000463 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000846 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0003207 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0003515 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0003899 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0004156 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0004793 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0009397 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0042559 (this species only) · gene tree & orthology
Transcription factor family	zf-C2H2 · all TF in this species
Transcription factor family	zf-BED · all TF in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02463 all species →	SMC_N	RecF/RecN/SMC N terminal domain	Domain	Interproscan
PF06470 all species →	SMC_hinge	SMC proteins Flexible Hinge Domain	Domain	Interproscan
PF05131 all species →	Pep3_Vps18	Pep3/Vps18/deep orange beta-propeller domain	Repeat	Interproscan
PF00366 all species →	Ribosomal_S17	Ribosomal protein S17	Domain	Interproscan
PF00096 all species →	zf-C2H2	Zinc finger, C2H2 type	Domain	Interproscan
PF00012 all species →	HSP70	Hsp70 protein	Family	Interproscan
PF14961 all species →	BROMI	Broad-minded protein	Family	Interproscan
PF00106 all species →	adh_short	short chain dehydrogenase	Domain	Interproscan
PF07648 all species →	Kazal_2	Kazal-type serine protease inhibitor domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR003395 all species →	Domain	RecF/RecN/SMC, N-terminal	Interproscan
IPR010935 all species →	Domain	SMCs flexible hinge	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR036277 all species →	Homologous_superfamily	SMCs flexible hinge superfamily	Interproscan
IPR011010 all species →	Homologous_superfamily	DNA breaking-rejoining enzyme, catalytic core	Interproscan
IPR000020 all species →	Domain	Anaphylatoxin/fibulin	Interproscan
IPR018081 all species →	Homologous_superfamily	Anaphylatoxin, complement system	Interproscan
IPR007810 all species →	Domain	Pep3/Vps18/deep orange, beta-propeller domain	Interproscan
IPR000266 all species →	Family	Small ribosomal subunit protein uS17	Interproscan
IPR012340 all species →	Homologous_superfamily	Nucleic acid-binding, OB-fold	Interproscan
IPR013087 all species →	Domain	Zinc finger C2H2-type	Interproscan
IPR050752 all species →	Family	C2H2-type zinc-finger domain-containing protein	Interproscan
IPR036236 all species →	Homologous_superfamily	Zinc finger C2H2 superfamily	Interproscan
IPR029047 all species →	Homologous_superfamily	Heat shock protein 70kD, peptide-binding domain superfamily	Interproscan
IPR013126 all species →	Family	Heat shock protein 70 family	Interproscan
IPR050451 all species →	Family	Heat Shock Protein 70 (HSP70)	Interproscan
IPR043129 all species →	Homologous_superfamily	ATPase, nucleotide binding domain	Interproscan
IPR029048 all species →	Homologous_superfamily	Heat shock protein 70kD, C-terminal domain superfamily	Interproscan
IPR032735 all species →	Family	Protein broad-minded	Interproscan
IPR016024 all species →	Homologous_superfamily	Armadillo-type fold	Interproscan
IPR036291 all species →	Homologous_superfamily	NAD(P)-binding domain superfamily	Interproscan
IPR002347 all species →	Family	Short-chain dehydrogenase/reductase SDR	Interproscan
IPR020904 all species →	Conserved_site	Short-chain dehydrogenase/reductase, conserved site	Interproscan
IPR002350 all species →	Domain	Kazal domain	Interproscan
IPR011061 all species →	Homologous_superfamily	Hirudin/antistatin	Interproscan
IPR036058 all species →	Homologous_superfamily	Kazal domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR43977 all species →	STRUCTURAL MAINTENANCE OF CHROMOSOMES PROTEIN 3	Interproscan
PTHR24384 all species →	FINGER PUTATIVE TRANSCRIPTION FACTOR FAMILY-RELATED	Interproscan
PTHR45639 all species →	HSC70CB, ISOFORM G-RELATED	Interproscan
PTHR43313 all species →	SHORT-CHAIN DEHYDROGENASE/REDUCTASE FAMILY 9C	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0005694 all species →	Cellular Component	chromosome	Interproscan
GO:0051276 all species →	Biological Process	chromosome organization	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0005576 all species →	Cellular Component	extracellular region	Interproscan
GO:0003735 all species →	Molecular Function	structural constituent of ribosome	Interproscan
GO:0005840 all species →	Cellular Component	ribosome	Interproscan
GO:0006412 all species →	Biological Process	translation	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:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0140662 all species →	Molecular Function	ATP-dependent protein folding chaperone	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0006457 all species →	Biological Process	protein folding	Interproscan
GO:0008202 all species →	Biological Process	steroid metabolic process	Interproscan
GO:0016491 all species →	Molecular Function	oxidoreductase activity	Interproscan
GO:0043231 all species →	Cellular Component	intracellular membrane-bounded organelle	Interproscan
GO:0004857 all species →	Molecular Function	enzyme inhibitor activity	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
K06674	SMC2; structural maintenance of chromosome 2	-	Chromosome and associated proteins	ko03036	deepkoala
K09489	HSPA4; heat shock 70kDa protein 4	-	Chaperones and folding catalysts	ko03110	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 →