Gene detail

Detailed information of g459.t1 in Calvadosia cruxmelitensis

Genomic Location: not available for this species
NR annotation: CAH3142330.1, unnamed protein product [Pocillopora meandrina]
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
Q3TX08	tRNA (guanine(26)-N(2))-dimethyltransferase OS=Mus musculus OX=10090 GN=Trmt1 PE=1 SV=3
Q9NXH9	tRNA (guanine(26)-N(2))-dimethyltransferase OS=Homo sapiens OX=9606 GN=TRMT1 PE=1 SV=1
Q9VK89	tRNA (guanine(26)-N(2))-dimethyltransferase OS=Drosophila melanogaster OX=7227 GN=Trm1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000050 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000123 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000130 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000428 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000769 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0001538 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0003241 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0005064 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0005784 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0037163 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13499 all species →	EF-hand_7	EF-hand domain pair	Domain	Interproscan
PF07741 all species →	BRF1	Brf1-like TBP-binding domain	Domain	Interproscan
PF16837 all species →	SF3A3	Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9	Domain	Interproscan
PF12108 all species →	SF3a60_bindingd	Splicing factor SF3a60 binding domain	Domain	Interproscan
PF11931 all species →	SF3a60_Prp9_C	SF3a60/Prp9 C-terminal	Family	Interproscan
PF13297 all species →	SDE2_2C	Replication stress response SDE2 C-terminal	Domain	Interproscan
PF01590 all species →	GAF	GAF domain	Domain	Interproscan
PF00233 all species →	PDEase_I	3'5'-cyclic nucleotide phosphodiesterase	Domain	Interproscan
PF03982 all species →	DAGAT	Diacylglycerol acyltransferase	Family	Interproscan
PF02005 all species →	TRM	N2,N2-dimethylguanosine tRNA methyltransferase	Family	Interproscan
PF20519 all species →	Polycystin_dom	Polycystin domain	Domain	Interproscan
PF01477 all species →	PLAT	PLAT/LH2 domain	Domain	Interproscan
PF02010 all species →	REJ	REJ domain	Family	Interproscan
PF08016 all species →	PKD_channel	Polycystin cation channel	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002048 all species →	Domain	EF-hand domain	Interproscan
IPR011992 all species →	Homologous_superfamily	EF-hand domain pair	Interproscan
IPR051111 all species →	Family	Calcium-binding regulatory protein	Interproscan
IPR018247 all species →	Binding_site	EF-Hand 1, calcium-binding site	Interproscan
IPR011665 all species →	Domain	Brf1, TBP-binding domain	Interproscan
IPR000690 all species →	Domain	Matrin/U1-C, C2H2-type zinc finger	Interproscan
IPR051421 all species →	Family	RNA Processing and DNA Damage Response Regulator	Interproscan
IPR031774 all species →	Domain	SF3A3 domain	Interproscan
IPR021966 all species →	Domain	Splicing factor SF3a60 binding domain	Interproscan
IPR024598 all species →	Domain	Splicing factor SF3a60 /Prp9 subunit, C-terminal	Interproscan
IPR025086 all species →	Domain	SDE2-like, C-terminal domain	Interproscan
IPR002073 all species →	Domain	3'5'-cyclic nucleotide phosphodiesterase, catalytic domain	Interproscan
IPR023174 all species →	Conserved_site	3'5'-cyclic nucleotide phosphodiesterase, conserved site	Interproscan
IPR003607 all species →	Domain	HD/PDEase domain	Interproscan
IPR003018 all species →	Domain	GAF domain	Interproscan
IPR029016 all species →	Homologous_superfamily	GAF-like domain superfamily	Interproscan
IPR023088 all species →	Family	3'5'-cyclic nucleotide phosphodiesterase	Interproscan
IPR036971 all species →	Homologous_superfamily	3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily	Interproscan
IPR007130 all species →	Family	Diacylglycerol acyltransferase	Interproscan
IPR029063 all species →	Homologous_superfamily	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Interproscan
IPR002905 all species →	Family	tRNA methyltransferase, Trm1	Interproscan
IPR042296 all species →	Homologous_superfamily	tRNA methyltransferase, Trm1, C-terminal	Interproscan
IPR000571 all species →	Domain	Zinc finger, CCCH-type	Interproscan
IPR046338 all species →	Homologous_superfamily	GAIN domain superfamily	Interproscan
IPR036392 all species →	Homologous_superfamily	PLAT/LH2 domain superfamily	Interproscan
IPR000203 all species →	Conserved_site	GPS motif	Interproscan
IPR001024 all species →	Domain	PLAT/LH2 domain	Interproscan
IPR051223 all species →	Family	Polycystin	Interproscan
IPR003915 all species →	Family	Polycystic kidney disease type 2 protein	Interproscan
IPR046791 all species →	Domain	Polycystin domain	Interproscan
IPR002859 all species →	Domain	PKD/REJ-like domain	Interproscan
IPR013122 all species →	Domain	Polycystin cation channel, PKD1/PKD2	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46311 all species →	CALCIUM-BINDING PROTEIN 8-RELATED	Interproscan
PTHR12786 all species →	SPLICING FACTOR SF3A-RELATED	Interproscan
PTHR11347 all species →	CYCLIC NUCLEOTIDE PHOSPHODIESTERASE	Interproscan
PTHR12317 all species →	DIACYLGLYCEROL O-ACYLTRANSFERASE	Interproscan
PTHR31912 all species →	IP13529P	Interproscan
PTHR10631 all species →	N 2 ,N 2 -DIMETHYLGUANOSINE TRNA METHYLTRANSFERASE	Interproscan
PTHR10877 all species →	POLYCYSTIN FAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005509 all species →	Molecular Function	calcium ion binding	Interproscan
GO:0032588 all species →	Cellular Component	trans-Golgi network membrane	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0000398 all species →	Biological Process	mRNA splicing, via spliceosome	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0005681 all species →	Cellular Component	spliceosomal complex	Interproscan
GO:0004114 all species →	Molecular Function	3',5'-cyclic-nucleotide phosphodiesterase activity	Interproscan
GO:0007165 all species →	Biological Process	signal transduction	Interproscan
GO:0008081 all species →	Molecular Function	phosphoric diester hydrolase activity	Interproscan
GO:0004118 all species →	Molecular Function	3',5'-cGMP-stimulated cyclic-nucleotide phosphodiesterase activity	Interproscan
GO:0010754 all species →	Biological Process	negative regulation of cGMP-mediated signaling	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0008374 all species →	Molecular Function	O-acyltransferase activity	Interproscan
GO:0008033 all species →	Biological Process	tRNA processing	Interproscan
GO:0160102 all species →	Molecular Function	tRNA (guanine(10)-N2)-methyltransferase activity	Interproscan
GO:0002940 all species →	Biological Process	tRNA N2-guanine methylation	Interproscan
GO:0004809 all species →	Molecular Function	obsolete tRNA (guanine-N2-)-methyltransferase activity	Interproscan
GO:0046872 all species →	Molecular Function	metal ion binding	Interproscan
GO:0005262 all species →	Molecular Function	calcium channel activity	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0050982 all species →	Biological Process	detection of mechanical stimulus	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
K00555	TRMT1, trm1; tRNA (guanine26-N2/guanine27-N2)-dimethyltransferase	EC:2.1.1.215 EC:2.1.1.216	Transfer RNA biogenesis	ko03016	deepkoala
K04988	PKD1L2; polycystin 1L2	-	Ion channels	ko04040	deepkoala
K12827	SF3A3, SAP61, PRP9; splicing factor 3A subunit 3	-	Spliceosome	ko03041	deepkoala
K18438	PDE10; cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10	EC:3.1.4.17 EC:3.1.4.35	Morphine addiction	ko05032	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 →