Gene detail

Detailed information of BRAKERKREP00000012482.1 in Hydra viridissima

Genomic Location: QPEY01000063.1:979055...979258
NR annotation: XP_033110777.1, DNA-directed RNA polymerases I, II, and III subunit RPABC5 [Anneissia japonica]
Species Hydra viridissima · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q32P78	DNA-directed RNA polymerases I, II, and III subunit RPABC5 OS=Bos taurus OX=9913 GN=POLR2L PE=1 SV=1
Q6QN04	DNA-directed RNA polymerases I, II, and III subunit RPABC5 OS=Chinchilla lanigera OX=34839 GN=POLR2L PE=3 SV=1
Q9VC49	DNA-directed RNA polymerases I, II, and III subunit RPABC5 OS=Drosophila melanogaster OX=7227 GN=Polr2L PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0011929 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01194 all species →	RNA_pol_N	RNA polymerases N / 8 kDa subunit	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000268 all species →	Family	DNA-directed RNA polymerase subunit RPABC5/Rpb10	Interproscan
IPR023580 all species →	Homologous_superfamily	RNA polymerase subunit RPB10	Interproscan
IPR020789 all species →	Binding_site	RNA polymerases, subunit N, zinc binding site	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23431 all species →	DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5 FAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	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: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: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:0006360 all species →	Biological Process	transcription by RNA polymerase I	Interproscan
GO:0006366 all species →	Biological Process	transcription by RNA polymerase II	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0042797 all species →	Biological Process	tRNA transcription by RNA polymerase III	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
K03007	RPABC5, RPB10, POLR2L; DNA-directed RNA polymerases I, II, and III subunit RPABC5	-	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 BRAKERKREP00000012482.1 across 29 RNA-seq samples of Hydra viridissima. 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.

29Samples

8TPM > 0

7Conditions

5.1Max TPM

1.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	1	0.28	5.05
Whole	6	4	3.10	5.08
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	3.21	3.21
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	1	3.14	3.14
symbioic hydra M9 strain · symbioic hydra rep1	1	1	1.72	1.72
symbioic hydra M9 strain · symbioic hydra rep2	1	0	0.00	0.00
unannotated	1	0	0.00	0.00

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977	5.05
SRR21134050	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134051	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134052	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134053	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134054	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134055	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134056	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134057	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134058	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134059	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134061	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134062	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134063	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134064	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134065	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134066	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134067	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	5.08
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397	4.83
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	4.38
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	4.31
SRR10058802	Whole	Whole	not recorded	not recorded	SRP220397	0.00
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	0.00
DRR048593	aposymbioic hydra M9 strain · aposymbioic hydra rep1	not recorded	not recorded	aposymbioic hydra rep1	DRP003902	3.21
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	3.14
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	1.72
DRR048596	symbioic hydra M9 strain · symbioic hydra rep2	not recorded	not recorded	symbioic hydra rep2	DRP003902	0.00
ERR13389755	unannotated	not recorded	not recorded	not recorded	ERP162636	0.00

Source: CnidoSite RNA-seq expression matrices (HVIRI_TPM, StringTie quantification over 29 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.