Gene detail

Detailed information of CAB3984624.1 in Paramuricea clavata

Genomic Location: not available for this species
NR annotation: CAB3984624.1, DNA-directed RNA polymerases I, II, and III subunit RPABC1 [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Sequence

No sequence record for CAB3984624.1 in PCLAV (the gene ID may belong to a different isoform naming scheme). Try the gene search.

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q80UW8	DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Mus musculus OX=10090 GN=Polr2e PE=1 SV=1
Q5R587	DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Pongo abelii OX=9601 GN=POLR2E PE=2 SV=1
B0BNE2	DNA-directed RNA polymerases I, II, and III subunit RPABC1 OS=Rattus norvegicus OX=10116 GN=Polr2e PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006699 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01191 all species →	RNA_pol_Rpb5_C	RNA polymerase Rpb5, C-terminal domain	Domain	Interproscan
PF03871 all species →	RNA_pol_Rpb5_N	RNA polymerase Rpb5, N-terminal domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR035913 all species →	Homologous_superfamily	RPB5-like RNA polymerase subunit superfamily	Interproscan
IPR020608 all species →	Conserved_site	RNA polymerase, subunit H/Rpb5, conserved site	Interproscan
IPR014381 all species →	Family	DNA-directed RNA polymerase subunit Rpo5/Rpb5	Interproscan
IPR000783 all species →	Domain	RNA polymerase, subunit H/Rpb5 C-terminal	Interproscan
IPR036710 all species →	Homologous_superfamily	RNA polymerase Rpb5, N-terminal domain superfamily	Interproscan
IPR005571 all species →	Domain	RNA polymerase, Rpb5, N-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10535 all species →	DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0001054 all species →	Molecular Function	RNA polymerase I activity	Interproscan
GO:0001055 all species →	Molecular Function	RNA polymerase II activity	Interproscan
GO:0001056 all species →	Molecular Function	RNA polymerase III activity	Interproscan
GO:0003899 all species →	Molecular Function	DNA-directed 5'-3' RNA polymerase activity	Interproscan
GO:0005665 all species →	Cellular Component	RNA polymerase II, core complex	Interproscan
GO:0005666 all species →	Cellular Component	RNA polymerase III complex	Interproscan
GO:0005736 all species →	Cellular Component	RNA polymerase I complex	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0006351 all species →	Biological Process	DNA-templated transcription	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
K03013	RPABC1, RPB5, POLR2E; DNA-directed RNA polymerases I, II, and III subunit RPABC1	-	DNA repair and recombination proteins	ko03400	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of CAB3984624.1 across 21 RNA-seq samples of Paramuricea clavata. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.

21Samples

15TPM > 0

4Conditions

64.0Max TPM

16.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	5	23.57	55.88
apical branchlet · Temperature treatment at T0	6	6	19.65	47.44
apical branchlet · Temperature treatment at T25	5	3	15.31	64.01
apical branchlet · Control at T0	4	1	2.60	10.40

Per sample · hover a bar for the full sample record · show / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	55.88
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	29.62
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	27.91
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	16.12
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	11.89
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.00
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	47.44
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	28.34
SRR19977436	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	20.07
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	12.66
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	6.69
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	2.69
SRR19977463	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	64.01
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	11.43
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	1.11
SRR19977432	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	0.00
SRR19977434	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	0.00
SRR19977443	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	10.40
SRR19977442	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	0.00
SRR19977445	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	0.00
SRR19977446	apical branchlet · Control at T0	apical branchlet	not recorded	Control at T0	SRP384900	0.00

Source: CnidoSite RNA-seq expression matrices (PCLAV_TPM, StringTie quantification over 21 runs), joined to SRA sample metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped by the descriptor carried in the expression matrix itself.