Gene detail

Detailed information of g993.t1 in Calvadosia cruxmelitensis

Genomic Location: not available for this species
NR annotation: CAH3040744.1, unnamed protein product [Porites lobata]
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
Q2T9S3	DNA-directed RNA polymerase III subunit RPC6 OS=Bos taurus OX=9913 GN=POLR3F PE=2 SV=1
Q9H1D9	DNA-directed RNA polymerase III subunit RPC6 OS=Homo sapiens OX=9606 GN=POLR3F PE=1 SV=1
Q921X6	DNA-directed RNA polymerase III subunit RPC6 OS=Mus musculus OX=10090 GN=Polr3f PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000031 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000042 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000311 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0000539 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0001272 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0002046 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0002192 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0003774 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0007315 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0007817 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00055 all species →	Laminin_N	Laminin N-terminal (Domain VI)	Domain	Interproscan
PF05158 all species →	RNA_pol_Rpc34	RNA polymerase Rpc34 subunit	Family	Interproscan
PF21033 all species →	RMD1-3	Regulator of microtubule dynamics protein 1-3	Repeat	Interproscan
PF03128 all species →	CXCXC	CXCXC repeat	Repeat	Interproscan
PF13895 all species →	Ig_2	Immunoglobulin domain	Domain	Interproscan
PF00089 all species →	Trypsin	Trypsin	Domain	Interproscan
PF09380 all species →	FERM_C	FERM C-terminal PH-like domain	Domain	Interproscan
PF00373 all species →	FERM_M	FERM central domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR008211 all species →	Domain	Laminin, N-terminal	Interproscan
IPR050440 all species →	Family	Laminin/Netrin Extracellular Matrix	Interproscan
IPR036397 all species →	Homologous_superfamily	Ribonuclease H superfamily	Interproscan
IPR012337 all species →	Homologous_superfamily	Ribonuclease H-like superfamily	Interproscan
IPR007832 all species →	Family	RNA polymerase Rpc34	Interproscan
IPR036388 all species →	Homologous_superfamily	Winged helix-like DNA-binding domain superfamily	Interproscan
IPR016049 all species →	Family	RNA polymerase Rpc34-like	Interproscan
IPR036390 all species →	Homologous_superfamily	Winged helix DNA-binding domain superfamily	Interproscan
IPR024857 all species →	Family	Cappuccino	Interproscan
IPR019734 all species →	Repeat	Tetratricopeptide repeat	Interproscan
IPR049039 all species →	Repeat	Regulator of microtubule dynamics protein 1-3, alpha helical repeats	Interproscan
IPR011990 all species →	Homologous_superfamily	Tetratricopeptide-like helical domain superfamily	Interproscan
IPR029034 all species →	Homologous_superfamily	Cystine-knot cytokine	Interproscan
IPR004153 all species →	Repeat	CXCXC repeat	Interproscan
IPR040247 all species →	Family	Protein of unknown function DUF5524	Interproscan
IPR003599 all species →	Domain	Immunoglobulin subtype	Interproscan
IPR013783 all species →	Homologous_superfamily	Immunoglobulin-like fold	Interproscan
IPR007110 all species →	Domain	Immunoglobulin-like domain	Interproscan
IPR003598 all species →	Domain	Immunoglobulin subtype 2	Interproscan
IPR051275 all species →	Family	Cellular adhesion and signaling domain-containing protein	Interproscan
IPR036179 all species →	Homologous_superfamily	Immunoglobulin-like domain superfamily	Interproscan
IPR001254 all species →	Domain	Serine proteases, trypsin domain	Interproscan
IPR018114 all species →	Active_site	Serine proteases, trypsin family, histidine active site	Interproscan
IPR001314 all species →	Family	Peptidase S1A, chymotrypsin family	Interproscan
IPR050127 all species →	Family	Serine Proteases (Peptidase S1 Family)	Interproscan
IPR009003 all species →	Homologous_superfamily	Peptidase S1, PA clan	Interproscan
IPR043504 all species →	Homologous_superfamily	Peptidase S1, PA clan, chymotrypsin-like fold	Interproscan
IPR011993 all species →	Homologous_superfamily	PH-like domain superfamily	Interproscan
IPR018980 all species →	Domain	FERM, C-terminal PH-like domain	Interproscan
IPR035963 all species →	Homologous_superfamily	FERM superfamily, second domain	Interproscan
IPR014352 all species →	Homologous_superfamily	FERM/acyl-CoA-binding protein superfamily	Interproscan
IPR019748 all species →	Domain	FERM central domain	Interproscan
IPR000299 all species →	Domain	FERM domain	Interproscan
IPR052074 all species →	Family	Non-receptor Tyrosine-protein Phosphatases	Interproscan
IPR019749 all species →	Domain	Band 4.1 domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10574 all species →	NETRIN/LAMININ-RELATED	Interproscan
PTHR42648 all species →	TRANSPOSASE, PUTATIVE-RELATED	Interproscan
PTHR12780 all species →	RNA POLYMERASE III DNA DIRECTED , 39KD SUBUNIT-RELATED	Interproscan
PTHR16230 all species →	CAPPUCCINO	Interproscan
PTHR16056 all species →	REGULATOR OF MICROTUBULE DYNAMICS PROTEIN	Interproscan
PTHR11633 all species →	PLATELET-DERIVED GROWTH FACTOR	Interproscan
PTHR31097 all species →	SI:DKEY-276J7.1	Interproscan
PTHR11640 all species →	NEPHRIN	Interproscan
PTHR24264 all species →	TRYPSIN-RELATED	Interproscan
PTHR46900 all species →	TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 13	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005604 all species →	Cellular Component	basement membrane	Interproscan
GO:0009887 all species →	Biological Process	animal organ morphogenesis	Interproscan
GO:0009888 all species →	Biological Process	tissue development	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0005666 all species →	Cellular Component	RNA polymerase III complex	Interproscan
GO:0006383 all species →	Biological Process	transcription by RNA polymerase III	Interproscan
GO:0031083 all species →	Cellular Component	BLOC-1 complex	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0005739 all species →	Cellular Component	mitochondrion	Interproscan
GO:0005876 all species →	Cellular Component	spindle microtubule	Interproscan
GO:0008017 all species →	Molecular Function	microtubule binding	Interproscan
GO:0097431 all species →	Cellular Component	mitotic spindle pole	Interproscan
GO:0005615 all species →	Cellular Component	extracellular space	Interproscan
GO:0008284 all species →	Biological Process	positive regulation of cell population proliferation	Interproscan
GO:0031954 all species →	Biological Process	positive regulation of protein autophosphorylation	Interproscan
GO:0070851 all species →	Molecular Function	growth factor receptor binding	Interproscan
GO:0005887 all species →	Cellular Component	plasma membrane	Interproscan
GO:0005911 all species →	Cellular Component	cell-cell junction	Interproscan
GO:0050839 all species →	Molecular Function	cell adhesion molecule binding	Interproscan
GO:0098609 all species →	Biological Process	cell-cell adhesion	Interproscan
GO:0004252 all species →	Molecular Function	serine-type endopeptidase activity	Interproscan
GO:0006508 all species →	Biological Process	proteolysis	Interproscan
GO:0005856 all species →	Cellular Component	cytoskeleton	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
K03025	RPC6, POLR3F; DNA-directed RNA polymerase III subunit RPC6	-	Transcription machinery	ko03021	deepkoala
K08366	BLOC1S4, CNO; biogenesis of lysosome-related organelles complex 1 subunit 4	-	Membrane trafficking	ko04131	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 →