Gene detail

Detailed information of CAB4000690.1 in Paramuricea clavata

Genomic Location: not available for this species
NR annotation: CAB4000690.1, DNA-directed RNA polymerases I, II, and III subunit RPABC4 [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families

Sequence

No sequence record for CAB4000690.1 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
Q3ZBC0	DNA-directed RNA polymerases I, II, and III subunit RPABC4 OS=Bos taurus OX=9913 GN=POLR2K PE=1 SV=1
P53803	DNA-directed RNA polymerases I, II, and III subunit RPABC4 OS=Homo sapiens OX=9606 GN=POLR2K PE=1 SV=1
Q63871	DNA-directed RNA polymerases I, II, and III subunit RPABC4 OS=Mus musculus OX=10090 GN=Polr2k PE=3 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0013047 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03604 all species →	DNA_RNApol_7kD	DNA directed RNA polymerase, 7 kDa subunit	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR029040 all species →	Homologous_superfamily	RNA polymerase subunit RPABC4/transcription elongation factor Spt4	Interproscan
IPR039747 all species →	Family	DNA-directed RNA polymerases I, II, and III subunit RPABC4	Interproscan
IPR006591 all species →	Family	RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12056 all species →	DNA-DIRECTED RNA POLYMERASES I, II, AND III	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:0008270 all species →	Molecular Function	zinc ion binding	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
K03009	RPABC4, RPB12, POLR2K; DNA-directed RNA polymerases I, II, and III subunit RPABC4	-	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 CAB4000690.1 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

12TPM > 0

4Conditions

118.0Max TPM

35.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
apical branchlet · Control at T25	6	5	66.97	118.03
apical branchlet · Temperature treatment at T0	6	4	25.05	87.89
apical branchlet · Temperature treatment at T25	5	2	25.32	76.09
apical branchlet · Control at T0	4	1	17.18	68.70

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR19977441	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	118.03
SRR19977455	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	90.16
SRR19977439	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	79.29
SRR19977444	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	75.70
SRR19977440	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	38.64
SRR19977433	apical branchlet · Control at T25	apical branchlet	not recorded	Control at T25	SRP384900	0.00
SRR19977427	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	87.89
SRR19977438	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	31.32
SRR19977428	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	20.85
SRR19977437	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	10.24
SRR19977426	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.00
SRR19977436	apical branchlet · Temperature treatment at T0	apical branchlet	not recorded	Temperature treatment at T0	SRP384900	0.00
SRR19977435	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	76.09
SRR19977463	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	50.48
SRR19977425	apical branchlet · Temperature treatment at T25	apical branchlet	not recorded	Temperature treatment at T25	SRP384900	0.00
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	68.70
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.