Gene detail

Detailed information of g897.t1 in Calvadosia cruxmelitensis

Genomic Location: not available for this species
NR annotation: XP_012555807.1, uncharacterized protein LOC101241166 isoform X1 [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
Q3T0Z8	Small nuclear ribonucleoprotein F OS=Bos taurus OX=9913 GN=SNRPF PE=3 SV=2
P62306	Small nuclear ribonucleoprotein F OS=Homo sapiens OX=9606 GN=SNRPF PE=1 SV=1
P62307	Small nuclear ribonucleoprotein F OS=Mus musculus OX=10090 GN=Snrpf PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000082 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000132 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000181 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000220 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000802 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0001904 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0002852 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0002898 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0006362 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0010379 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0022451 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0030298 (this species only) · gene tree & orthology
Transcription factor family	E2F · all TF in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01423 all species →	LSM	LSM domain	Domain	Interproscan
PF17917 all species →	RT_RNaseH	RNase H-like domain found in reverse transcriptase	Domain	Interproscan
PF00078 all species →	RVT_1	Reverse transcriptase (RNA-dependent DNA polymerase)	Domain	Interproscan
PF00520 all species →	Ion_trans	Ion transport protein	Family	Interproscan
PF07303 all species →	Occludin_ELL	Occludin homology domain	Domain	Interproscan
PF10390 all species →	ELL	RNA polymerase II elongation factor ELL	Family	Interproscan
PF00090 all species →	TSP_1	Thrombospondin type 1 domain	Domain	Interproscan
PF12661 all species →	hEGF	Human growth factor-like EGF	Domain	Interproscan
PF03146 all species →	NtA	Agrin NtA domain	Domain	Interproscan
PF02319 all species →	E2F_TDP	E2F/DP family winged-helix DNA-binding domain	Domain	Interproscan
PF16421 all species →	E2F_CC-MB	E2F transcription factor CC-MB domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001163 all species →	Domain	Sm domain, eukaryotic/archaea-type	Interproscan
IPR047575 all species →	Domain	Sm domain	Interproscan
IPR010920 all species →	Homologous_superfamily	LSM domain superfamily	Interproscan
IPR034100 all species →	Family	Small nuclear ribonucleoprotein F	Interproscan
IPR016487 all species →	Family	Sm-like protein Lsm6/SmF	Interproscan
IPR043128 all species →	Homologous_superfamily	Reverse transcriptase/Diguanylate cyclase domain	Interproscan
IPR050951 all species →	Family	Retrovirus-related Pol polyprotein	Interproscan
IPR041373 all species →	Domain	Reverse transcriptase, RNase H-like domain	Interproscan
IPR000477 all species →	Domain	Reverse transcriptase domain	Interproscan
IPR043502 all species →	Homologous_superfamily	DNA/RNA polymerase superfamily	Interproscan
IPR003968 all species →	Family	Potassium channel, voltage dependent, Kv	Interproscan
IPR005821 all species →	Domain	Ion transport domain	Interproscan
IPR036390 all species →	Homologous_superfamily	Winged helix DNA-binding domain superfamily	Interproscan
IPR042065 all species →	Homologous_superfamily	E3 ubiquitin-protein ligase ELL-like	Interproscan
IPR031176 all species →	Family	ELL/occludin family	Interproscan
IPR010844 all species →	Domain	Occludin homology domain	Interproscan
IPR019464 all species →	Domain	RNA polymerase II elongation factor ELL, N-terminal	Interproscan
IPR045130 all species →	Family	GDP-fucose protein O-fucosyltransferase 2-like	Interproscan
IPR036383 all species →	Homologous_superfamily	Thrombospondin type-1 (TSP1) repeat superfamily	Interproscan
IPR050969 all species →	Family	Developmental Signaling Modulators	Interproscan
IPR000742 all species →	Domain	EGF-like domain	Interproscan
IPR000884 all species →	Repeat	Thrombospondin type-1 (TSP1) repeat	Interproscan
IPR008993 all species →	Homologous_superfamily	Tissue inhibitor of metalloproteinases-like, OB-fold	Interproscan
IPR013032 all species →	Conserved_site	EGF-like, conserved site	Interproscan
IPR004850 all species →	Domain	NtA (N-terminal agrin) domain	Interproscan
IPR013320 all species →	Homologous_superfamily	Concanavalin A-like lectin/glucanase domain superfamily	Interproscan
IPR003316 all species →	Domain	E2F/DP family, winged-helix DNA-binding domain	Interproscan
IPR037241 all species →	Homologous_superfamily	E2F-DP heterodimerization region	Interproscan
IPR032198 all species →	Domain	E2F transcription factor, CC-MB domain	Interproscan
IPR015633 all species →	Family	E2F Family	Interproscan
IPR036388 all species →	Homologous_superfamily	Winged helix-like DNA-binding domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11021 all species →	SMALL NUCLEAR RIBONUCLEOPROTEIN F SNRNP-F	Interproscan
PTHR37984 all species →	PROTEIN CBG26694	Interproscan
PTHR11537 all species →	VOLTAGE-GATED POTASSIUM CHANNEL	Interproscan
PTHR23288 all species →	OCCLUDIN AND RNA POLYMERASE II ELONGATION FACTOR ELL	Interproscan
PTHR13398 all species →	GDP-FUCOSE PROTEIN O-FUCOSYLTRANSFERASE 2	Interproscan
PTHR14949 all species →	EGF-LIKE-DOMAIN, MULTIPLE 7, 8	Interproscan
PTHR46880 all species →	RAS-ASSOCIATING DOMAIN-CONTAINING PROTEIN	Interproscan
PTHR12081 all species →	TRANSCRIPTION FACTOR E2F	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0000387 all species →	Biological Process	spliceosomal snRNP assembly	Interproscan
GO:0005681 all species →	Cellular Component	spliceosomal complex	Interproscan
GO:0000398 all species →	Biological Process	mRNA splicing, via spliceosome	Interproscan
GO:0005685 all species →	Cellular Component	U1 snRNP	Interproscan
GO:0034715 all species →	Cellular Component	pICln-Sm protein complex	Interproscan
GO:0071013 all species →	Cellular Component	catalytic step 2 spliceosome	Interproscan
GO:0005249 all species →	Molecular Function	voltage-gated potassium channel activity	Interproscan
GO:0008076 all species →	Cellular Component	voltage-gated potassium channel complex	Interproscan
GO:0016021 all species →	Cellular Component	membrane	Interproscan
GO:0071805 all species →	Biological Process	potassium ion transmembrane transport	Interproscan
GO:0006813 all species →	Biological Process	potassium ion transport	Interproscan
GO:0005216 all species →	Molecular Function	monoatomic ion channel activity	Interproscan
GO:0006811 all species →	Biological Process	monoatomic ion transport	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0055085 all species →	Biological Process	transmembrane transport	Interproscan
GO:0000987 all species →	Molecular Function	cis-regulatory region sequence-specific DNA binding	Interproscan
GO:0008023 all species →	Cellular Component	transcription elongation factor complex	Interproscan
GO:0032968 all species →	Biological Process	positive regulation of transcription elongation by RNA polymerase II	Interproscan
GO:0042795 all species →	Biological Process	snRNA transcription by RNA polymerase II	Interproscan
GO:0006368 all species →	Biological Process	transcription elongation by RNA polymerase II	Interproscan
GO:0036066 all species →	Biological Process	protein O-linked fucosylation	Interproscan
GO:0046922 all species →	Molecular Function	peptide-O-fucosyltransferase activity	Interproscan
GO:0005102 all species →	Molecular Function	signaling receptor binding	Interproscan
GO:0005576 all species →	Cellular Component	extracellular region	Interproscan
GO:0009986 all species →	Cellular Component	cell surface	Interproscan
GO:0048856 all species →	Biological Process	anatomical structure development	Interproscan
GO:0043113 all species →	Biological Process	receptor clustering	Interproscan
GO:0043236 all species →	Molecular Function	laminin binding	Interproscan
GO:0005667 all species →	Cellular Component	transcription regulator complex	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0046983 all species →	Molecular Function	protein dimerization activity	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:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:0090575 all species →	Cellular Component	RNA polymerase II transcription regulator complex	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
K04889	KCNC3, KV3.3; potassium voltage-gated channel Shaw-related subfamily C member 3	-	Ion channels	ko04040	deepkoala
K11098	SNRPF, SMF; small nuclear ribonucleoprotein F	-	DNA replication proteins	ko03032	deepkoala
K15183	ELL; RNA polymerase II elongation factor ELL	-	Transcription machinery	ko03021	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 →