Gene detail

Detailed information of BRAKERKREP00000023637.1 in Hydra viridissima

Genomic Location: not available for this species
NR annotation: AXA72315.1, 23S rRNA pseudouridylate synthase B [Achromobacter insolitus]
Species Hydra viridissima · all data for this species · gene families

Sequence

CDS

BRAKERKRET00000023637

ATGGACGAGAGCGAGGCAATCCTCGTGTTGGAAACGGCGCTTTTGTGCGCGGCCCAGCCTATGCAATTGGCTGAAATACGCAAGCTGTTCGGCGATGAAGAGCCCTACGACCTCCATGGGTTGCGCGGGCTGCTAGAGACACTGCAGATGGCGTGGGCAGACCGTGGGCTGGAATTGGTGGAACTCGCTGGCGGCTGGCGTTTTCAGAGTAAGCCTCTGATGCAGCGTTACTTGGAGCGGCTTAACCCGGATAAGCCGCCTAAGTATTCCCGCGCTGTGATGGAGACCTTGGCGATTGTGGCTTGGCGGCAACCCGTGACGCGTGGCGACATTGAAGATATACGCGGTGTCACCGTGTCGTCGCAAATCATCAAGACGCTCGAAGATCGCGGCTGGATCGAAGTCATTGGTCACCGCGATGCGCCTGGGCGGCCAGCGCTGTTCGGAACCACTCGCCAGTTTCTTGACGATCTCGGCCTGCGCGCATTGGACGAGCTACCGCCGCTCGAGTCGTCCGAAGCCGCTGTGGCGTTGGCCAATCTGGATCTGAGCGACGCGCAAGCTGCGGTTAATTTTGAGGTGACCACGAATACGACAGTGCAAGACGAAATTCGCCAAATCAATGAGAACCAAGAGGCAGTAGAAGCGCCTACGCCGGAGTCTCCCGCGCGGCGGCAAGCGGCGGGGGGCGAGCAGGCACCTCGTGGTCGCGGCCGCAAGCTGCGTACGCCGTTTCGCCGCCGTCGTGGCGATGCTGCCACGGGTGAACAACCAAGCGCTGGGCCGCCTACGCCAGCTGTGCACGAAGATGCCGGCGCAGCCATTACAGGGGTAGAGGCGGCTGACGCGCGTGAAGCCGAGCAGGCGCTATCTTATTTGGAAAACGCCGCTCGAATGGAACAGCGTCTAGGAAAATATCTGAGCAGTGAAGCCATCATGCCGAAGCTGCACAAGGTATTGGCTGAGGCGGGTATTGGCTCGCGCCGGGATATGGAAGAACTCATTGTGGCGGGCCGTGTCTCGGTTAACGGAGAGCCTGCCCATATCGGCCAACGTGTGGCGCCGTCTGACCAAGTAAGGGTGAACGGCAAGATCATCGCGCGCGCGCCTGCGCGCAAGCTCCCCCGCGTCGTCCTATACCACAAGCCGGCAGGTGAAATCGTTAGCCATAATGATCCGGGTGGGCGTGCCACTGTCTTTACGCGGCTGCCCAAACTGCGCACTGGCAAGTGGCTTTCTGTAGGCCGACTCGATTTAAACACCGAAGGTTTATTGATCTTTACGACGTCCGGTGATATGGCCAATCGCATTATGCATCCGCGCTATGGTAATGAGCGCGAGTATGCGGTACGCGTGTTAGGTGAAATGGATGAGACGCAGCGTAAGTCTTTGGTCGAGGGCATTGAGCTGGAAGACGGCCTTGCCGCTTTCGGTGCGCTGGATTATCTAGGTGGCGAAGGCAGTAATCGTTGGTATCGCGTCACTTTACAGGAAGGGCGTAACCGCGAAGTACGACGCATGTTTGAGGCTGCCGGTGTTACCGTCAGCCGCCTTATCCGTACGCGCTTTGGCGATATTGTTTTACCGCGTAGCCTGCGCCGCGGTCGCTGGGAGGAACTAGACGGCACACTCGTGACCGCGCTTCTGGTTCAGCTTGGGCTGCTGCGTGAGGACGGCGAGGGAGAGGGCCGCCGGCGTTCCAAGCAGCCCCAGTCACACGACAGCGCTTTGCCACCTGGCTTTGGCACACTGGAGCGGAATGGCACCAATGGCGCCCGCGTCGGCCGCCGCGGTAAGGTACAGGGCGGACGGCCTGGCAATAGTCATGGCTCAGGCGCCGTCTATCCTTCCGATCCCTTTGGTACTGGGCTGATGATCACCGGCGGTTATGCAAATGGCCATCCCTTGGAAGCCGGCGCGCGCAGCAAAGGGCGTGGTAAGCCCGGCGGAAAGCCCGGTATGAAGGCGGGTGGGGCGCGACCTGGCTCCCGTAATAAAGCTGCCGGCAAGTCGCGCGGCGCACTGGCCCCGGCGGGCACTAGCAACCTGCCGGCTGATCCCTCCGCTGCATCGGGTACGACCGGTGGAAAGTCTGCTGGACCCAGAAAAGCAGGCAGACCAACCGGTCCGCGTGGGGCTGCCAAAGCTGGCGCTGCGAGCGGTAAGCCGAGGACGCTGCGCGGCGACGATTGGCAGCCGAAGAGCGCTTCGGCGCACGAGTCGCGCCTGGGCGTCGTGGCAAATCGCGGCCGCAACGGGCGCTAA

Transcript

BRAKERKRET00000023637

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q8X4Q8	Ribosomal large subunit pseudouridine synthase B OS=Escherichia coli O157:H7 OX=83334 GN=rluB PE=3 SV=1
P59815	Ribosomal large subunit pseudouridine synthase B OS=Shigella flexneri OX=623 GN=rluB PE=3 SV=1
Q8FHV4	Ribosomal large subunit pseudouridine synthase B OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) OX=199310 GN=rluB PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0013472 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00849 all species →	PseudoU_synth_2	RNA pseudouridylate synthase	Family	Interproscan
PF01479 all species →	S4	S4 domain	Domain	Interproscan
PF04079 all species →	SMC_ScpB	Segregation and condensation complex subunit ScpB	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR005234 all species →	Family	Chromosome segregation/condensation protein ScpB	Interproscan
IPR036390 all species →	Homologous_superfamily	Winged helix DNA-binding domain superfamily	Interproscan
IPR042092 all species →	Homologous_superfamily	Pseudouridine synthase, RsuA/RluB/E/F, catalytic domain	Interproscan
IPR006145 all species →	Domain	Pseudouridine synthase, RsuA/RluA-like	Interproscan
IPR002942 all species →	Domain	RNA-binding S4 domain	Interproscan
IPR000748 all species →	Family	Pseudouridine synthase, RsuA/RluB/E/F	Interproscan
IPR036388 all species →	Homologous_superfamily	Winged helix-like DNA-binding domain superfamily	Interproscan
IPR036986 all species →	Homologous_superfamily	RNA-binding S4 domain superfamily	Interproscan
IPR018496 all species →	Conserved_site	Pseudouridine synthase, RsuA/RluB/E/F, conserved site	Interproscan
IPR020094 all species →	Homologous_superfamily	Pseudouridine synthase TruA/RsuA/RluB/E/F, N-terminal	Interproscan
IPR020103 all species →	Homologous_superfamily	Pseudouridine synthase, catalytic domain superfamily	Interproscan
IPR050343 all species →	Family	Ribosomal RNA Pseudouridine Synthase RsuA	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR47683 all species →	PSEUDOURIDINE SYNTHASE FAMILY PROTEIN-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0051304 all species →	Biological Process	chromosome separation	Interproscan
GO:0001522 all species →	Biological Process	pseudouridine synthesis	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0009451 all species →	Biological Process	RNA modification	Interproscan
GO:0009982 all species →	Molecular Function	pseudouridine synthase activity	Interproscan
GO:0016866 all species →	Molecular Function	intramolecular transferase activity	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

No KEGG orthology assignment for BRAKERKREP00000023637.1.

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000023637.1 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

18TPM > 0

7Conditions

16.4Max TPM

5.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	9	6.27	16.42
Whole	6	6	7.13	9.03
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	4.57	4.57
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	1	0.08	0.08
symbioic hydra M9 strain · symbioic hydra rep1	1	1	0.05	0.05
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
SRR21134055	whole body	whole body	not recorded	not recorded	SRP392977	16.42
SRR21134066	whole body	whole body	not recorded	not recorded	SRP392977	15.66
SRR21134057	whole body	whole body	not recorded	not recorded	SRP392977	14.95
SRR21134054	whole body	whole body	not recorded	not recorded	SRP392977	14.24
SRR21134053	whole body	whole body	not recorded	not recorded	SRP392977	14.05
SRR21134056	whole body	whole body	not recorded	not recorded	SRP392977	11.82
SRR21134052	whole body	whole body	not recorded	not recorded	SRP392977	10.02
SRR21134064	whole body	whole body	not recorded	not recorded	SRP392977	7.99
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977	7.69
SRR21134050	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134051	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
SRR21134065	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134067	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	9.03
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	8.36
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	8.26
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397	8.22
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	8.10
SRR10058802	Whole	Whole	not recorded	not recorded	SRP220397	0.82
DRR048593	aposymbioic hydra M9 strain · aposymbioic hydra rep1	not recorded	not recorded	aposymbioic hydra rep1	DRP003902	4.57
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	0.08
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	0.05
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.