Gene detail

Detailed information of BRAKERKREP00000019783.1 in Hydra viridissima

Genomic Location: not available for this species
NR annotation: XP_047130973.1, DNA-directed RNA polymerase II subunit RPB1 [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families

Sequence

CDS

BRAKERKRET00000019783

atgccAGGTCCCACAACCCAACTACATTCAAGTGCACCACTGAGATTGgtgaaaaaagttcaattcgGTGTACTCAGTCCTGATGAAATTAGACGCATGTCTGTTACTGATGGTGGAATTCGTTATGCAGAAACTATGGAAGCTGGTAAACCAAAGTTATGTGGTTTAATGGACCCTCGTCAAGGTACAACTGACCGGATGACTCGATGTCAAACATGTGCTGGAAACATGACTGAATGTCCTGGTCACTTTGGGCATATTGAACTCTCAAAGCCTGTGTTTCATATAGGTTTCTTGACAATGACAATTAAGATAATGAGATGCTTTTGTTTCTACTGCTCTAAGTTATTGGTCGATaaaaaTCACCCAAAGCTTTTAGAAATCCTATCTAAAACCAAGTCACAACCAAAGAAAAGATTTCAGCATGTTTATGATTTGTGTAAAGGTAAAAGCATTTGTGAAGGTGGTGATGTAATGGATCAACAATTTGATGCAAATCTGGTTAACAACGAAGAACAAGCTgagaaaaaagGTCATGGTGGTTGCGGGCGATATCAACCCCAAATTCGAAGACAAGGTTTGGATTTAACTGCTGAAtggaaaaatgttaatgaggattctcaagagaaaaaaatttctttaactgcTGAGCGAgtgtatgaaatttttaaacgtaTTTCCGATGATGAATGTGATATTTTGGGCATGGATGCAAAATTTTGTAGGCCTGACTGGCTTATAGTAACTGTTCTTCCAGTACCTCCTTTATCTGTAAGACCAGCTGTTGTGATGAATGGAAGTGCAAGGAACCAGgaTGATCTGACTCACAAACTTGCAGACATTATTAAAGCAAACAACCAGTTAAAACGCAATGAAATGAATGGGGCAGCCGCTCATGTTATTGCACAAGACATGATGATGTTGCAGTTCCATGTTGCAACACTTACTGATAATGAGCTTCCTGGACTTCCAAGGGCTCAGCAAAAATCAGGGAGACCTTTGAAATCAATCAAACAAAGATTAAAGAGTAAGGAAGGTCGTCTAAGAGGTAATTTGATGGGAAAGCGTGTTGATTTTTCAGCTCGTGCTGTTATTACTCCAGATCCTAACTTAGATATAGATCAGGTTGGAACACCAAAAACAATTGCAATGAATCTTACATATCCTGAAATTGTGACACCCTTTAATATTGACAGatTACAAGAGCTTGTACGACGTGGTCCAACTCATTATCCTGGAGCTAAATACATCATTCGTGATAATGGTGAAAGAATAGACTTACGTTTTCACCCAAAAACAAGTGATCTTCATTTGCAGTTTGGATATAAGGTTGAAAGGCATATTATTGATAATGATGTAGTTGTATTTAATCGACAACCTACTCTCCACAAGATGAGCATGATGGGTCATAGAGTTAAAGTACTACCATGGTCTACTTTTCGATTAAATTTAAGTGTGACTACTCCTTATAATGCTGATTTTGATGGAGATGAGATGAACATGCATGTTCCTCAATCAATGGAAACACGAGCAGAGATAACTGAAATTTTGATGGTACCTCGCCAAATTATAACACCACAATCAAACAAGCCATGTATGGGTATTGTGCAGGATTCTTTGTGTGCTGTTCACAAGTTCACTAAAAGAGATGTTTTCTTAGAGAAGGATGTTGTAATGAATCTCCTATTGTGGATTAGAAAATGGGATGGAAAGTTGCCAATTCCGGCTATACTAAAACCTAAGCCATTATGGACTGGAAAAcagatattttctttattgattCCACCAGGAATTAATCATTCTGGTGAGCACAGCACACATCCTGATGATGAATCAAGTGGTCCTTATAGTCACATATCTCCTGGAGATACAAAGGCACAGCCTGGTGAAATGGTTGGTGCCTTAGCTGCTCAATCACTTGGTGAACCTGCAACACAGATGACATTGAATACATTTCATTATGCTGGTGTATCTGCAAAAAATGTAACTCTTGGTGTCCCAaggttaaaagaaattataaatgtttctAAGAAACCAAAAACTCCTTCCCTGACAGTTTTCTTACTTGGTCAAGCTGCTAGAGATGCTGAACATGCTAAGgatGTTCTCTGTCGCTTGGAGCATACGACTCTTCGAAAAGTCACAGCTAATACAGCTATATACTATGATCCTGATCCACAAAATACAGTTATCTCAGAAGATCAAGACTTTGTTAATGTTTACTATGAAATGCCTGATTTTGATCCAGCACGCATGTCTCCATGGTTATTGCGTATAGAACTAGATCGTAAAAGAATGACAGACAGCAAGTTAAGCATGGAACAAATTGCTGATAAAATTAATCAGGGATTTGGAGATGATTTGAACtgcatttttaatgatgataatgCTGAGAAACTAGTGCTCAGAATCCGAATTATGAGTAGTGGTGATGATAGCAAAAATATGGAGgaagAAGAGCAGTTAGACAAGATGGAAGATGATGTATTTCTAAGATGCATTGAAGCCAATATGTTGACAGACATGACCTTACAAGGAATAGAATCTATTGCTAAAGTGTACATGCATTTACCAAGTGAAGAATCAAAAAAGCGTGTTGTATTTAATGCTGATGGAGAGTTCAAGCatttgcaAGAATGGATTTTGGAGACAGATGGTAATGGACTAATGAAAGTCCTTAGTCAGAAAGATATTGATCCAGTAAGAACAACCTCCAATGATATATGCGAGGTCTTCACGATCTTGGGCATTGAAGCTGTAAGAAAAtctgttgaaaaagaaatggatCATGTTATTTCATTTGATGGTTCTTATGTCAACTACAGGCATTTGTCATTATTGTGTGATATAATGACATCAAAAGGTCATTTGATGGCTATTACACGTCATGGTATTAATAGGCAAGAAGTTGGTTGTCTCATGAGATGCTCGTTTGAAGAAACTGTCGATGTCTTGGTTGAAGCAGCATTCCATGCAGAAGCTGATCATTTACGTGGCGTCAGTGAGAATATTATTCTTGGACAGCTTCCACCAGTTGGTACTGGTTGCTTTAATTTGATGCTAGATGctgaaaaatgtaaagagGGAATGGAAATACCTTTAAATATAGGGGAAGGACACGGAATGATGCCAGgtgGTGGTGTTTTTTTTGGCTCATCCGCATCTCCATCAAATGCTATGTCACCCCTGATGACTCCTTGGAATCAAGGTCATACACCTGGCTATGGAGATGTATGGTCTCCAGCCCTAGGCTCTGGAATGACACCTGGAGCTGCTGCTTTTTCACCTTCTGCACTTTCAGACGCAAGTGGATTCAGTCCTGCTGGTGGGTTTAGTCCTGCTTGGAGCCCACAAGATCCTATGTCTTTAGGATCTCCTGACTCGTCGCCGTATATCCCAAGCCCAGCAAGAAATTCTATGAGTCCAAGTTATTCTCCGAATTCTCCCGCGTTTAATCCAACATCACCAGCAATGTCACCTGCATCGCCAGGGTATTCACCTACATCTCCTTCTTATAGTCCGACTTCTCCAGGATATAGCCCAACAAGTCCGAGCTACAGTCCTACTTCTCCTGGTTATAGCCCAACTTCACCGAGTTATTCCCCTACTTCTCCATCCTATTCACCAACATCACCAAGCTATAGTCCAACGAGTCCGAGCTATTCGCCTACTTCTCCGAGCTATAGTCCCACGTCACCAAGTTATTCACCTACATCTCCCTCATATTCGCCAACTTCACCCTCGTATAGTCCAACAAGCCCAAGTTATAGTCCTACGTCACCAAGTTACAGTCCAACCAGTCCAAGTTATAGCCCGACCTCACCTAGTTATAGTCCTACGTCTCCAAGTTATTCACCGACCTCACCTTCTTATTCTCCAACAAGTCCATCTTATTCTCCGACCAGTCCAAAGTACTCTCCTACGTCACCCAGTTACAGTCCAACATCTCCTTCCTACAGCCCTTCTTCTCCTCAATATTCTCCGACCAGTCCATCATATTCGCCTCAATCACCTTCTTATTCACCCTCCTCTCCAAGTTACTCGCCTACTTCACCTAAGTATAGTCCTACATCTCCTAAGTATTCTCCTACCTCTCCCAAATATAGTCCAACCTCACCAATTTATAGCCCCTCATCGCCATCATACTCTCCATCATCTCCGAACTATTCACCTACAAGTCCAACGTACTCACCAACAAGTCCAGCCTACAGCCCAACATCTCCTAAATATAGCCCAACATCACCCATTTATTCACCAACAAGTCCAGCATATTCTCCAACTTCACCAAGATACAGTCCAACATCACCTGAGTATTCTCCTACAAGTCCAAAATACAGTCCTACATCTCCCCAATATTCTCCTACAAGTCCAAAATACAGCCCTGCGTCACCAACTTATTCTCCTAGTACGCCTACAGATAAGTCACTTGGTTCTATAAACTACAGCCCTCTAGAACCTGATTACAGTCCTGGTACACCTACTTACTCACCGGATGGGACTCCAACTTATTCTCTTGAGGGTCGCGGCTATTCGGCACCTAAAAATAAACCTTTGGATTATTCGCCAAGCTCTCCATCAGGTCCCGGTAGTCCTCAAGAACCATCAAAGTTTAAGAAGAgataa

Transcript

BRAKERKRET00000019783

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
G3MZY8	DNA-directed RNA polymerase II subunit RPB1 OS=Bos taurus OX=9913 GN=POLR2A PE=1 SV=2
P11414	DNA-directed RNA polymerase II subunit RPB1 OS=Cricetulus griseus OX=10029 GN=POLR2A PE=1 SV=2
P24928	DNA-directed RNA polymerase II subunit RPB1 OS=Homo sapiens OX=9606 GN=POLR2A PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005025 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04998 all species →	RNA_pol_Rpb1_5	RNA polymerase Rpb1, domain 5	Domain	Interproscan
PF04983 all species →	RNA_pol_Rpb1_3	RNA polymerase Rpb1, domain 3	Domain	Interproscan
PF04997 all species →	RNA_pol_Rpb1_1	RNA polymerase Rpb1, domain 1	Domain	Interproscan
PF05001 all species →	RNA_pol_Rpb1_R	RNA polymerase Rpb1 C-terminal repeat	Repeat	Interproscan
PF00623 all species →	RNA_pol_Rpb1_2	RNA polymerase Rpb1, domain 2	Domain	Interproscan
PF04990 all species →	RNA_pol_Rpb1_7	RNA polymerase Rpb1, domain 7	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000684 all species →	Repeat	RNA polymerase II, heptapeptide repeat, eukaryotic	Interproscan
IPR038593 all species →	Homologous_superfamily	RNA polymerase Rpb1, domain 7 superfamily	Interproscan
IPR007081 all species →	Domain	RNA polymerase Rpb1, domain 5	Interproscan
IPR042102 all species →	Homologous_superfamily	RNA polymerase Rpb1, domain 3 superfamily	Interproscan
IPR045867 all species →	Family	DNA-directed RNA polymerase, subunit beta-prime	Interproscan
IPR007066 all species →	Domain	RNA polymerase Rpb1, domain 3	Interproscan
IPR006592 all species →	Domain	RNA polymerase, N-terminal	Interproscan
IPR007080 all species →	Domain	RNA polymerase Rpb1, domain 1	Interproscan
IPR044893 all species →	Homologous_superfamily	RNA polymerase Rpb1, clamp domain superfamily	Interproscan
IPR000722 all species →	Domain	RNA polymerase, alpha subunit	Interproscan
IPR007073 all species →	Domain	RNA polymerase Rpb1, domain 7	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR19376 all species →	DNA-DIRECTED RNA POLYMERASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0006366 all species →	Biological Process	transcription by RNA polymerase II	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:0001055 all species →	Molecular Function	RNA polymerase II activity	Interproscan
GO:0005665 all species →	Cellular Component	RNA polymerase II, core complex	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
K03006	RPB1, POLR2A; DNA-directed RNA polymerase II subunit RPB1	EC:2.7.7.6	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 BRAKERKREP00000019783.1 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

15TPM > 0

7Conditions

37.9Max TPM

10.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	5	4.30	37.93
Whole	6	6	27.77	34.97
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	13.91	13.91
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	1	14.13	14.13
symbioic hydra M9 strain · symbioic hydra rep1	1	1	12.17	12.17
symbioic hydra M9 strain · symbioic hydra rep2	1	1	8.19	8.19
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
SRR21134064	whole body	whole body	not recorded	not recorded	SRP392977	37.93
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977	26.84
SRR21134065	whole body	whole body	not recorded	not recorded	SRP392977	9.36
SRR21134056	whole body	whole body	not recorded	not recorded	SRP392977	1.95
SRR21134052	whole body	whole body	not recorded	not recorded	SRP392977	1.31
SRR21134050	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134051	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
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
SRR21134066	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134067	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR10058802	Whole	Whole	not recorded	not recorded	SRP220397	34.97
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	30.97
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	29.01
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397	26.52
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	24.46
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	20.67
DRR048593	aposymbioic hydra M9 strain · aposymbioic hydra rep1	not recorded	not recorded	aposymbioic hydra rep1	DRP003902	13.91
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	14.13
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	12.17
DRR048596	symbioic hydra M9 strain · symbioic hydra rep2	not recorded	not recorded	symbioic hydra rep2	DRP003902	8.19
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.