Gene detail

Detailed information of g876.t1 in Calvadosia cruxmelitensis

Genomic Location: not available for this species
NR annotation: MBT4287848.1, DNA-directed RNA polymerase subunit beta [Deltaproteobacteria bacterium]
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
A7HCH7	DNA-directed RNA polymerase subunit beta OS=Anaeromyxobacter sp. (strain Fw109-5) OX=404589 GN=rpoB PE=3 SV=1
Q1D7U3	DNA-directed RNA polymerase subunit beta OS=Myxococcus xanthus (strain DK1622) OX=246197 GN=rpoB PE=3 SV=1
C6E4R4	DNA-directed RNA polymerase subunit beta OS=Geobacter sp. (strain M21) OX=443144 GN=rpoB PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000708 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0004211 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0004590 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0004928 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0005325 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0006276 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0007804 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0008136 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0010589 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0011766 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0020716 (this species only) · gene tree & orthology
Orthogroup (gene family)	OG0042496 (this species only) · gene tree & orthology
Transcription factor family	Homeobox · all TF in this species
Transcription factor family	SAND · all TF in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF06027 all species →	SLC35F	Solute carrier family 35	Family	Interproscan
PF00562 all species →	RNA_pol_Rpb2_6	RNA polymerase Rpb2, domain 6	Domain	Interproscan
PF04560 all species →	RNA_pol_Rpb2_7	RNA polymerase Rpb2, domain 7	Domain	Interproscan
PF04561 all species →	RNA_pol_Rpb2_2	RNA polymerase Rpb2, domain 2	Domain	Interproscan
PF10385 all species →	RNA_pol_Rpb2_45	RNA polymerase beta subunit external 1 domain	Domain	Interproscan
PF04563 all species →	RNA_pol_Rpb2_1	RNA polymerase beta subunit	Family	Interproscan
PF04565 all species →	RNA_pol_Rpb2_3	RNA polymerase Rpb2, domain 3	Domain	Interproscan
PF05046 all species →	Img2	Mitochondrial large subunit ribosomal protein (Img2)	Domain	Interproscan
PF14622 all species →	Ribonucleas_3_3	Ribonuclease-III-like	Family	Interproscan
PF16878 all species →	SIX1_SD	Transcriptional regulator, SIX1, N-terminal SD domain	Domain	Interproscan
PF05920 all species →	Homeobox_KN	Homeobox KN domain	Family	Interproscan
PF01342 all species →	SAND	SAND domain	Family	Interproscan
PF12895 all species →	ANAPC3	Anaphase-promoting complex, cyclosome, subunit 3	Repeat	Interproscan
PF00001 all species →	7tm_1	7 transmembrane receptor (rhodopsin family)	Family	Interproscan
PF11775 all species →	CobT_C	Cobalamin biosynthesis protein CobT VWA domain	Domain	Interproscan
PF06213 all species →	CobT	Cobalamin biosynthesis protein CobT	Family	Interproscan
PF00486 all species →	Trans_reg_C	Transcriptional regulatory protein, C terminal	Domain	Interproscan
PF00072 all species →	Response_reg	Response regulator receiver domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR052221 all species →	Family	SLC35F Solute Transporter	Interproscan
IPR009262 all species →	Family	Solute carrier family 35 member SLC35F1/F2/F6	Interproscan
IPR015712 all species →	Family	DNA-directed RNA polymerase, subunit 2	Interproscan
IPR007121 all species →	Conserved_site	RNA polymerase, beta subunit, conserved site	Interproscan
IPR037033 all species →	Homologous_superfamily	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily	Interproscan
IPR007120 all species →	Domain	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain	Interproscan
IPR007641 all species →	Domain	RNA polymerase Rpb2, domain 7	Interproscan
IPR010243 all species →	Family	DNA-directed RNA polymerase beta subunit, bacterial-type	Interproscan
IPR014724 all species →	Homologous_superfamily	RNA polymerase Rpb2, OB-fold	Interproscan
IPR042107 all species →	Homologous_superfamily	DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily	Interproscan
IPR007642 all species →	Domain	RNA polymerase Rpb2, domain 2	Interproscan
IPR019462 all species →	Domain	DNA-directed RNA polymerase, beta subunit, external 1 domain	Interproscan
IPR007644 all species →	Domain	RNA polymerase, beta subunit, protrusion	Interproscan
IPR037034 all species →	Homologous_superfamily	RNA polymerase Rpb2, domain 2 superfamily	Interproscan
IPR007645 all species →	Domain	RNA polymerase Rpb2, domain 3	Interproscan
IPR007740 all species →	Family	Large ribosomal subunit protein mL49	Interproscan
IPR036389 all species →	Homologous_superfamily	Ribonuclease III, endonuclease domain superfamily	Interproscan
IPR000999 all species →	Domain	Ribonuclease III domain	Interproscan
IPR009057 all species →	Homologous_superfamily	Homeobox-like domain superfamily	Interproscan
IPR001356 all species →	Domain	Homeobox domain	Interproscan
IPR031701 all species →	Domain	Homeobox protein SIX1, N-terminal SD domain	Interproscan
IPR008422 all species →	Domain	Homeobox KN domain	Interproscan
IPR017970 all species →	Conserved_site	Homeobox, conserved site	Interproscan
IPR000770 all species →	Domain	SAND domain	Interproscan
IPR010919 all species →	Homologous_superfamily	SAND-like domain superfamily	Interproscan
IPR011990 all species →	Homologous_superfamily	Tetratricopeptide-like helical domain superfamily	Interproscan
IPR019734 all species →	Repeat	Tetratricopeptide repeat	Interproscan
IPR017452 all species →	Domain	GPCR, rhodopsin-like, 7TM	Interproscan
IPR008365 all species →	Family	Prostanoid receptor	Interproscan
IPR000276 all species →	Family	G protein-coupled receptor, rhodopsin-like	Interproscan
IPR001789 all species →	Domain	Signal transduction response regulator, receiver domain	Interproscan
IPR002035 all species →	Domain	von Willebrand factor, type A	Interproscan
IPR016032 all species →	Homologous_superfamily	Signal transduction response regulator, C-terminal effector	Interproscan
IPR001867 all species →	Domain	OmpR/PhoB-type DNA-binding domain	Interproscan
IPR036465 all species →	Homologous_superfamily	von Willebrand factor A-like domain superfamily	Interproscan
IPR036388 all species →	Homologous_superfamily	Winged helix-like DNA-binding domain superfamily	Interproscan
IPR051928 all species →	Family	NorD/CobT	Interproscan
IPR011006 all species →	Homologous_superfamily	CheY-like superfamily	Interproscan
IPR025861 all species →	Domain	Cobalamin biosynthesis protein CobT VWA domain	Interproscan
IPR006538 all species →	Family	Cobalt chelatase, CobT subunit	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR14233 all species →	DUF914-RELATED	Interproscan
PTHR20856 all species →	DNA-DIRECTED RNA POLYMERASE I SUBUNIT 2	Interproscan
PTHR13477 all species →	MITOCHONDRIAL 39S RIBOSOMAL PROTEIN L49	Interproscan
PTHR10390 all species →	HOMEOBOX PROTEIN SIX	Interproscan
PTHR10417 all species →	GLUCOCORTICOID MODULATORY ELEMENT-BINDING PROTEIN	Interproscan
PTHR12558 all species →	CELL DIVISION CYCLE 16,23,27	Interproscan
PTHR11866 all species →	G-PROTEIN COUPLED RECEPTOR FAMILY 1 MEMBER	Interproscan
PTHR41248 all species →	NORD PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0022857 all species →	Molecular Function	transmembrane transporter activity	Interproscan
GO:0055085 all species →	Biological Process	transmembrane transport	Interproscan
GO:0003899 all species →	Molecular Function	DNA-directed 5'-3' RNA polymerase activity	Interproscan
GO:0006351 all species →	Biological Process	DNA-templated transcription	Interproscan
GO:0032549 all species →	Molecular Function	ribonucleoside binding	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	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:0005762 all species →	Cellular Component	mitochondrial large ribosomal subunit	Interproscan
GO:0004525 all species →	Molecular Function	ribonuclease III activity	Interproscan
GO:0006396 all species →	Biological Process	RNA processing	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:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005667 all species →	Cellular Component	transcription regulator complex	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005680 all species →	Cellular Component	anaphase-promoting complex	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0007091 all species →	Biological Process	metaphase/anaphase transition of mitotic cell cycle	Interproscan
GO:0016567 all species →	Biological Process	protein ubiquitination	Interproscan
GO:0031145 all species →	Biological Process	anaphase-promoting complex-dependent catabolic process	Interproscan
GO:0051301 all species →	Biological Process	cell division	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0006954 all species →	Biological Process	inflammatory response	Interproscan
GO:0007186 all species →	Biological Process	G protein-coupled receptor signaling pathway	Interproscan
GO:0007189 all species →	Biological Process	adenylate cyclase-activating G protein-coupled receptor signaling pathway	Interproscan
GO:0007204 all species →	Biological Process	positive regulation of cytosolic calcium ion concentration	Interproscan
GO:0004930 all species →	Molecular Function	G protein-coupled receptor activity	Interproscan
GO:0000160 all species →	Biological Process	phosphorelay signal transduction system	Interproscan
GO:0009236 all species →	Biological Process	cobalamin biosynthetic process	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
K03043	rpoB; DNA-directed RNA polymerase subunit beta	EC:2.7.7.6	DNA repair and recombination proteins	ko03400	deepkoala
K15287	SLC35F1_2; solute carrier family 35, member F1/2	-	Transporters	ko02000	deepkoala
K17430	MRPL49, NOF1; large subunit ribosomal protein L49	-	Ribosome	ko03011	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 →