Gene detail

Detailed information of BRAKERKREP00000013832.1 in Hydra viridissima

Genomic Location: QPEY01000075.1:1038327...1052473
NR annotation: XP_047141151.1, DNA-directed RNA polymerase III subunit RPC2 [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

BRAKERKRET00000013832

ATGACTATATTTTCTCATATGGATGATGCATCACCTATAAAAACAGTTGAGtgcaGACTGCGTGACCTCACATATTCTGCTCCAATAACTGTGGATATTGAATATACAAGAGGAAAtcagAGGGTTGTGAGGAATAGTTTGCCGATTGGAAGAATGCCGATAATGTTACGTAGCTCGaattgtgtgcttgctggtaaaaatgaaatagaactAGCAAAGTTAAATGAATGTCCAATTGATCcagGAGGATATTTTGTAGTACGTGGCTCAGAAAAAGTTCTTCTTATTCAAGAGCAGCTGTCAAAAAATCGAATGATTCTTGAACTAGATAGCAAACATCATCTTATCAGCTGCTCTGTTACAAGTGCAACACATGAAGTGAAGAGCAGAACAGCTGTCATACAGAAACATGggaagttttatttgaagcaCAACTCCTTTACTGAGGACATTCCACTTTGCACAATCTTTAAGGCAATGGGTATAGAGTCTGACCAAGAAATTGTTCAAATGATTGGAATTGAGGAGGAAGTGCTTAACTATTTTGCAGCATCTATAGAAGAAGCAAGCATGCtgcaaatatatacaaaaacccagGCTTTAAATCTATTAGCAAGCAAGATTAAGCAACGACAGATGTGGGGTCGTCAAATGTCTAAAATGGATGAATGCAAGCAATTGCTGTTCAAGACATTACTGGCTCACGTTCTTataacaaagaATAATTATCGTGCAAAAGCTGCATATCTTGCTTTGATGGTACGAAGAATTATACTTGCTGTGAAGGGTGTAatcaAAATTGATGATAAAGATTATTATGGAAACAAACGTTTGGAGTTAGCTGGCCAGTTAGTTTCGCTTCTTTTTGAAGACTTGTTCAAGCGCTTTAACATGGAActGAAGAAAATTGCAGATGTCACAATTCCAAAGCCACGTGCTGCTCAGTTTGACATTGTGAAACATATGAGACAAGACTTGATATCGAATGGGCTTACAAATGCTATATCAACAggCAATTGGATTATCAAGAGATTTAACATGCATAGAGTGGGCGTCTCACAAGTTTTATCCCGCCTGTCGTACATTTCTGCTCTAGGAATGATGACAAGGGTTACCAGTCAAtttgaaaaaacacGCAAAGTAAGTGGTCCACGGTCCTTGCAACCATCTCAATGGGGTATTTTATGTCCTTCTGATACCCCTGAAGGTGAAGGGTGTggtttagttaaaaatcttGCACTCATGACTCATGTTACAACAGATCAAGTTCAATATCCAATTAAAAGGTTATTGTGTAACCTTGGAGTTGaggatatcAATCTTTTATCTGGTGAAGAGTTCAGTTCTCCATTAGtacatttggtttttttagaTGGTAATATCATCGGTTTGATTCGTCATCATCGTcgtttgataaaaacatttcgaCTAATGAGAAGAGCTGGTTATATCAATGAGTTTGTTTCTATTTATCCAAGTCATTCTCACAGaTGTGTGTACATTTCATCAGATGGTGGAAGAATGTGCAGgcCTTAcatcattgttaaaaaagggCTTCCATGTGTGACCCAGCAACATATTACTGAATTGTCTCAAGGAAcaagGACATTCGAAGATTTCCTGCACCAAGGATTAATAGAATACTTAGATGTAAATGAACTGAATGACTCTGAGATAGCATTATATGAAGCGGAATGCACAAAAGACACAACACATATGGAGATTGAACCTTTCACTTTACTTGGTGTATGTGTAGGCTTAGTGCCATATCCTCACCACAACCAATCTCCTAGAAATACTTACCAGTGTGCTATGGGTAAACAAGCTATGGGCACTATAGGTTACAATCAGAGAAATCGAATTGATACTTTAATGTACTTGCTTGTTTATCCCCATCAACCTATGGTTAAATCTAAGaCTCTGGACATCattcagtttgaaaaattgcCTGCAGGACAGAATGCAACAGTTGCTGTTATGAGTTATAGTGGTTATGACATAGAGgatGCTTTGATCATCAACAAGTCCTCACTAGACAGAGgtTTTGGAAGGTGTTtggtatataaaaaacaagtttgtaatttaaaaagatatgcAAATCAAacatttgATAGAGTAATGGgTCCAAGTCGTGATGCAAAAACTGGTGAAGTTATTTGGAAACATAATATTTTGGATACAGATGGAATATGTCGAGCTGGAGAACAGGTTTTGGACAAACAAGTTCTAGTAAATAAGTCTATGCCAACTGTTACTAACCAAATGACACAGACATCTGCAGGTCAGCTTGCTCCAACAGAATACAAAGATGTTCCAACATCCTATCATGGACCAATACCATCTTATGTTGAGAAAGTATTAATCAGTTCAACAATGGAAGATGCATTCTTGATAAAGATGCTTATGAGACAAACACGAAGACCTGAAATTGGTGATAAATTTAGTAGTAGGCATGGACAAAAGGGagtttGTGGTTTAATTGTGAATCAAGAAGATATGCCCTTCACTGACCtggGTATATGCCCAGATATAGTAAGTGtttattattaa

Transcript

BRAKERKRET00000013832

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9NW08	DNA-directed RNA polymerase III subunit RPC2 OS=Homo sapiens OX=9606 GN=POLR3B PE=1 SV=2
P59470	DNA-directed RNA polymerase III subunit RPC2 OS=Mus musculus OX=10090 GN=Polr3b PE=1 SV=2
P25167	DNA-directed RNA polymerase III subunit RPC2 OS=Drosophila melanogaster OX=7227 GN=Polr3B PE=2 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001356 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04566 all species →	RNA_pol_Rpb2_4	RNA polymerase Rpb2, domain 4	Domain	Interproscan
PF00562 all species →	RNA_pol_Rpb2_6	RNA polymerase Rpb2, domain 6	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
PF04561 all species →	RNA_pol_Rpb2_2	RNA polymerase Rpb2, domain 2	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR007646 all species →	Domain	RNA polymerase Rpb2, domain 4	Interproscan
IPR007120 all species →	Domain	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain	Interproscan
IPR007644 all species →	Domain	RNA polymerase, beta subunit, protrusion	Interproscan
IPR007645 all species →	Domain	RNA polymerase Rpb2, domain 3	Interproscan
IPR007642 all species →	Domain	RNA polymerase Rpb2, domain 2	Interproscan
IPR037034 all species →	Homologous_superfamily	RNA polymerase Rpb2, domain 2 superfamily	Interproscan
IPR014724 all species →	Homologous_superfamily	RNA polymerase Rpb2, OB-fold	Interproscan
IPR015712 all species →	Family	DNA-directed RNA polymerase, subunit 2	Interproscan
IPR007121 all species →	Conserved_site	RNA polymerase, beta subunit, conserved site	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR20856 all species →	DNA-DIRECTED RNA POLYMERASE I SUBUNIT 2	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:0001056 all species →	Molecular Function	RNA polymerase III activity	Interproscan
GO:0005666 all species →	Cellular Component	RNA polymerase III complex	Interproscan
GO:0032549 all species →	Molecular Function	ribonucleoside binding	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
K03021	RPC2, POLR3B; DNA-directed RNA polymerase III subunit RPC2	EC:2.7.7.6	Transcription machinery	ko03021	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000013832.1 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

1TPM > 0

7Conditions

0.0Max TPM

0.0Mean TPM

By condition

Condition	Samples	TPM > 0	Max TPM
whole body	18	0	0.00
Whole	6	1	0.02
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	0	0.00
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	0	0.00
symbioic hydra M9 strain · symbioic hydra rep1	1	0	0.00
symbioic hydra M9 strain · symbioic hydra rep2	1	0	0.00
unannotated	1	0	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
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
SRR21134060	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
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	0.02
SRR10058802	Whole	Whole	not recorded	not recorded	SRP220397	0.00
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397	0.00
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	0.00
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	0.00
SRR10058806	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	0.00
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	0.00
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	0.00
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.