Gene detail

Detailed information of BRAKERKREP00000022679.1 in Hydra viridissima

Genomic Location: not available for this species
NR annotation: WP_086056529.1, polyribonucleotide nucleotidyltransferase [Bordetella genomosp. 9]
Species Hydra viridissima · all data for this species · gene families

Sequence

CDS

BRAKERKRET00000022679

ATGTTTAATAAAGTAACTAAGACCTTTCAATATGGCCAACACACGGTTGTATTAGAAACGGGCGAAATTGCTCGCCAAGCTAATGGCGCCGTGTTGGTGTCCATCGAAGATACGGTCGTGCTTGCCACCGTGGTGGCGGCCAAGAAACCGAAGCCTGGCCAAGATTTTTTTCCGCTTACGGTCGACTACATTGAAAAGACCTACGCTGCAGGCCGGATCCCTGGCGGTTTTTTTAAGCGCGAAGGTAAGCCTACCGAAAAAGAAACTCTCACCTCGCGCCTGATTGATCGTCCATTGCGTCCATTATTCCCTGAAGGGTTTTACAACGACGTCCAGGTTGTGGTGCATACGCTGTCGGTCGATCCTCAAATTGATCCTGACATCGCCGCTATGATTGGTGCCTCAGCCGCGTTGGCCATTTCAGGTATACCCTTCAATGGCCCTATTGGCGCCGCCCGCGTGGGCTATACCCATGGCCAGTACATACTGAATCCAACGGCTGCGCAACTGAAAACTTCCGCTTTGGACTTGGTGGTCGCGGGTACCGAAACCGCGGTGCTAATGGTTGAATCCGAGGCACAGCAGTTGGCTGAAGAAGTAATGCTGGGCGGCGTGATGTTTGGCCATGAGCAAATGCAGGTCGTCATCAACGCCATTCACGACCTGGTGCGAGAGGCCGGCAAGCCCGAATGGGATTGGCAGGCAGGGCCTAAAAACGAAACGCTTATCGCCGCGATCAGCGCTGCTGCGCAAGAAAGACTAGTCGCCGCTTACCAGATTCGCGAAAAACAACTGCGCTCGACCACTCTGCAGCAAATCTATGCTGATGTACACGTTAAGGTCGTCACCCAAGCCACCGATCGAGGGGAGCCTGCGCCGGACAGCATTGCCATTGATAATGTGCTTTTTGATCTAGAAGCTCGCATTGTGCGTGGGCAGATTCTAAACGGCGAGCCGCGTATTGACGGTCGTGACACCCGCACCGTTCGACCCATTAACGTGCGCTTAGGGGTGTTGCCGCGGGCGCATGGTAGCGTTTTATTCACCCGTGGCGAGACCCAAGCACTGGTCGTCGCTACGTTGGGCACCAAGCAGGATGAGCAAATTATTGACGCGCTCATGGGCGAATATCGTGAGCGCTTTATGTTGCACTACAACATGCCACCGTTTGCCACCGGTGAAACCGGGCGCATTGGCGTGCCTAAGCGCCGCGAAATTGGTCATGGTCGCTTGGCCAAGCGGGCGCTGGTGCCCGTGTTGCCAACGCCTGAAGATTTTCAGTACACCGTGCGCCTGGTGTCTGAAATTACTGAGTCCAATGGTTCTTCTTCCATGGCATCGGTGTGCGGCGGCTCGCTGGCGATGATGGATGCGGGCGTGCCCATTACCGATCATGTTGCGGGTGTGGCCATGGGCCTGATTTTGGAGGGCGGCAAGTTCGCTGTCCTAACCGATATTCTGGGTGACGAAGATCACTTGGGTGATATGGACTTCAAAGTGGCCGGTACCGATAAGGGTATTACCGCGCTGCAAATGGATATCAAGATTCAGGGCATTACTAAAGAAATTATGCAAGTGGCATTGGCGCAGGCGCGCGAGGGCCGTTTGCATATTCTTGGCAAAATGCGGGAGGCTCTGGCCCATTCGCGCGTTGAACTGTCTTCTTTCGCGCCGCGCATGCTTACTATTAAGATCAACCCCGAAAAAATTCGCGACGTGATCGGCAAAGGGGGGGCTAACATCCGCGCGCTTACTGAGGAAACGGGCACTCAAATCGACATTTCTGACGATGGCACCATCGTCATCGCTAGTGTCGATGAGGCTCAGGCTAAGGAAGCGCAGCGCCGTATTCTAGAGCTCACTGCCGATGTTGAGGTGGGTCAGGTATATGACGGTTCGGTGCTGCGCCTGCTGGATTTTGGCGCTATCGTACAGGTGCTGCCTGGCCGCGACGGCCTGCTGCACATTTCTGAAATCGCCAACTATCGCATCGCAAATATTACCGACGTGCTTAAGGTTGGGCAGCAAGTTAGGGTCAAAGTTATTGAGGCCGACGATAAGGGCCGACTGCGCCTCTCTATGAAGGCGATTGGTGGTATCGAACAGCAGCCCAGCGAAGCCGGCGAAACAGCGTCGCAGCCGGCGCAGGCCGAATAA

Transcript

BRAKERKRET00000022679

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q7WCQ0	Polyribonucleotide nucleotidyltransferase OS=Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50) OX=257310 GN=pnp PE=3 SV=1
Q7W570	Polyribonucleotide nucleotidyltransferase OS=Bordetella parapertussis (strain 12822 / ATCC BAA-587 / NCTC 13253) OX=257311 GN=pnp PE=3 SV=1
Q7VZU0	Polyribonucleotide nucleotidyltransferase OS=Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251) OX=257313 GN=pnp PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004215 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03725 all species →	RNase_PH_C	3' exoribonuclease family, domain 2	Domain	Interproscan
PF03726 all species →	PNPase	Polyribonucleotide nucleotidyltransferase, RNA binding domain	Domain	Interproscan
PF00013 all species →	KH_1	KH domain	Domain	Interproscan
PF01138 all species →	RNase_PH	3' exoribonuclease family, domain 1	Domain	Interproscan
PF00575 all species →	S1	S1 RNA binding domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR027408 all species →	Homologous_superfamily	PNPase/RNase PH domain superfamily	Interproscan
IPR012340 all species →	Homologous_superfamily	Nucleic acid-binding, OB-fold	Interproscan
IPR003029 all species →	Domain	S1 domain	Interproscan
IPR015847 all species →	Domain	Exoribonuclease, phosphorolytic domain 2	Interproscan
IPR036345 all species →	Homologous_superfamily	Exoribonuclease, PH domain 2 superfamily	Interproscan
IPR015848 all species →	Domain	Polyribonucleotide nucleotidyltransferase, RNA-binding domain	Interproscan
IPR020568 all species →	Homologous_superfamily	Ribosomal protein uS5 domain 2-type superfamily	Interproscan
IPR004088 all species →	Domain	K Homology domain, type 1	Interproscan
IPR036612 all species →	Homologous_superfamily	K Homology domain, type 1 superfamily	Interproscan
IPR036456 all species →	Homologous_superfamily	Polyribonucleotide nucleotidyltransferase, RNA-binding domain superfamily	Interproscan
IPR001247 all species →	Domain	Exoribonuclease, phosphorolytic domain 1	Interproscan
IPR012162 all species →	Family	Polyribonucleotide nucleotidyltransferase	Interproscan
IPR004087 all species →	Domain	K Homology domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11252 all species →	POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0006396 all species →	Biological Process	RNA processing	Interproscan
GO:0000175 all species →	Molecular Function	3'-5'-RNA exonuclease activity	Interproscan
GO:0004654 all species →	Molecular Function	polyribonucleotide nucleotidyltransferase activity	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0006401 all species →	Biological Process	RNA catabolic process	Interproscan
GO:0006402 all species →	Biological Process	mRNA catabolic process	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
K00962	pnp, PNPT1; polyribonucleotide nucleotidyltransferase	EC:2.7.7.8	Transfer RNA biogenesis	ko03016	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000022679.1 across 29 RNA-seq samples of Hydra viridissima. This gene has no row in the species' RNA-seq expression matrix, so every value below is shown as zero — the matrix simply does not cover this transcript. 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

0TPM > 0

7Conditions

0.0Max TPM

0.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
whole body	18	0	0.00	0.00
Whole	6	0	0.00	0.00
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	0	0.00	0.00
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	0	0.00	0.00
symbioic hydra M9 strain · symbioic hydra rep1	1	0	0.00	0.00
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
SRR21134050	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134051	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134052	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134053	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134054	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134055	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134056	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134057	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134058	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134059	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134061	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134062	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134063	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134064	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134065	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134066	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134067	whole body	whole body	not recorded	not recorded	SRP392977
SRR10058802	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397
DRR048593	aposymbioic hydra M9 strain · aposymbioic hydra rep1	not recorded	not recorded	aposymbioic hydra rep1	DRP003902
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902
DRR048596	symbioic hydra M9 strain · symbioic hydra rep2	not recorded	not recorded	symbioic hydra rep2	DRP003902
ERR13389755	unannotated	not recorded	not recorded	not recorded	ERP162636

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.