Gene detail

Detailed information of BRAKERKREP00000018013.1 in Hydra viridissima

Genomic Location: QPEY01000132.1:470522...485105
NR annotation: XP_047135064.1, DNA damage-binding protein 1 [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

BRAKERKRET00000018013

atggcATATAACTATGTTGTTACAGCACAAGATGCAACTGCAATTAATGCTACAGTTACTGGTCACTTTACAGGCCCAACAGACTTAAATTTGATACTTGCGAAAAACAATAAGTTAGAGATAAATATGGTAACCCCTGAAGGTTTGCAGCCCaaacttgatttaaatgtttatggACGTGTGGCTGTTATGCAGTTGTTTAGACCTCCAaatgaAAGCCAGgatttgttgtttatattgACAGAGAGATTTCGAACTGCTATATTAGCATATAAACCAGAGACTGGTGATATTATAACAAAAGCTTATGGTGATGTTCAGGATAAAATTGGTCGACTTAGTGATACTGGTATGATTGGTATTATTGACCCACAGTGTCGCATGATTGCATTACACATATATGATGgattgttaaaagttattccTTTGGATCTTGGTTCAAATATGGAATTGAAAGCATTCAATATTAGgcTTGAAGAACTTAATGTTGTTGATATTCAGTTTTTACATGGTTCATTTACACACCCTACTGTAATTCTTGTGTATCAGGACCCACATGGCAGGCATGTTAAAACCTATGGCATCTCACTGGCAGATAAAGAGTTTAAGCGTGGACCATGGAAGCAAGATAATGTTGAGCTAGAAGCTTGTATGCTGATCACAGttCCCAAGCCAATTGAGGGAGCCTTAATAGTTGGACATGAGTCTATTACATATCACAAAGGAGAGACTTATTTAGCTGTTGCACCTCCTGCATTAAAGCAAAGCACATTAAGTTGCTATGGACGAGTTGATAAGGAGGGTCTACGTTATTTACTTGGAGATGCATCTGGTCGTATATTCATGTTGTTCTTGGATTATCAAGCAAAAGCTTCTGAAGTGAAAGATCTCAAATTAGAATTTCTAGGAGAGacATCTATTCCACATTGTTTAACATATCTTGATAATGGAGTTGTTTTCATTGGCTCTTGTCTTGGAGACTCACAAATAGTAAAGTTGAACACAGAGCCAGATGAAAAAGGTTCATTTATTACTATTCTCCGCTCATTCACAAATCTTGGGCCTATTCTTGATATGTGTGTAGTAGATCTCGAAAGACAGGGTCAAGGCCAACTTGTGACATGTTCAGGAGCATTTAAAGATGGCACTCTAAGAATAATTAGAAATGGCATTGGTATAAATGAGCATGCTTCAATTGATTTGGCTGGAATAATGgGATTATGGTGTCTAAAAGTAAACTCAATTGATCTTCATGATACAATGGTTCTCTCGTTTGTTGGTCAATCAAGAGTTCTTTCATTGAGCTCTGATGAAGTTGAAGAAATTGAGTTGGAAGGTTTTTGTAGTGATAAACAAACCACATATTGTgcaaatgtaaattttgatCAGTTGATTCAgGTAACAGATGAATCAATACTGCTTATAAGTTGTTCAACAAGAAAACTTTTGTTTAACTGGTTGCCACCTAACAATAAGCACATCAGTGTGGCAGTATGCAATACTTATCAGATTGTAGTAGCACTGGGAAaggaaataatttatcttgaaGTGCTTGATGGCAGTATTAATCAAATAAGTCATTCAATGGTGGATTTTGAAGTAGCTTGTTTAGATATATCCCCAAAAGCAAATGAAGAGCAGTCTGATCGGTTATGTATTGGTTTGTGGACAGATATCTCTGTACGAATACTTGCATTGCCTACTTTGAAAGAACTTCATGCAGAAAAACTTGGTGGAGAAATGATACCACGTTCCATTCTCATGACAActcttgaagaaaaagaatatttacttTGTGCACTTGGAGATggttctttgttttattttttgctagACCGTGCATCTGGATTTCTTTctgatcaaaaaaaagtgtctCTTGGCACAAAACCCACTGTCATACAGGCATTCAAATCAGGTTCATCCACACATGTGTTTGCTTGCTCTGATCGACCAACTGTAATTTATTCAAGCAACCACAAGCTTGTTTTTTCCAATGTTAACTTAAAGgAAGTAAGCTATATGAGCCCCCTTAACTCACAAGCCTATCCAAACAGtttaGCTATTGCAGATAAGAATTGCCTTTCTATTGGTTCAATTGATGAAATTCAACAGAAGTTACATATAAGATCTGTACCACTATATGAATCTCCCAGgcGTATAGTTTACCAAGAATCAACTCAAACATTTGGTGTTATATCTTCTCGCACTGAAGTTCGAGATCTCAATAGTGGTAAAAATATAGCTCAGCGTCCCTCTGCTAGTATTACTGCATCTTGTATAACATATAGCTCTGGTGACAGTAGTCAGGGAAACCTTACAGGATCTAGTAAAGACTTCGAAGAAGGAGCCATAGGGATGGAAGTTGAAGTTTCATCTTTTCTGGTGTTTGACCAACATACCTTTGAAgttaCGCATGCGCATCAGTTTCTTGAAAATGAATGGGCAACTTCATTAACATCTTGCGTCTTTTCAAATGATCCAACTTCTTACTACTGTGTTGGCACAGCAATGGTATATCCAGAAGAATCTGAACCCAAAGAAggaagaattattttgtttcaactatTTGAAGGAAAACTTGTGCAAGTTGGCAGTAAATCAGTTAACGGATCAGTATACGTTTTGCAGGGTTTTAACGGAAAGTTATTGGCTGGTATCAATAGCTTGGTGTCAGTGTATGAATGGACAAGTGATAAGGAATTAAAACAAGAATGTTGTTATCACAATACCATACTTGCTCtgtatttgaaaacaaaaggcGATTTTATCCTCGTTGGCGATTTAATGCGTTCCATGACACTTTTAGCGTACAAGCCGCTCGGCAGGCTCGAAGAAATTGCTCACGATTTCTCTCCAAATTGGATGACAGCAGTAGAGATTATTGACGACGACACTTTTCTCGGTGCAGAAAATTCCTTTAACTTGTTTACATGTCAAAAAGACAACTCGTCGGTGAACGATGAAGAAAGGCATCATCTGCAAACGATTGGGAAATACCATTTAGgagattttgtaaatgttttcaGACATGgTTCTTTGGTGATGCATCATACCATTGAACAGTTAACACCAATTAGTAGCTCAATATTATACGGAACAGTGCGGGGGGCTATCGGATTAGTTGCTGGTCTTCCTAAGGACACATTTGATTTTCTATCTcaagtacaaaaaaaactttcgaaaattattaaaagcgTCGGCAAAATCGAACATGAATTTTGGCGCTCGTTTTATAACGAACGGAAAACTGATTCAGCAATCGGATGCGTAGACGGAGATCTTATTGAAAGTTGTTTGGATCTGACAAGGTCACAATTACAAGAGGTCGTAGCTGGCTTAGAGaTTGAAGAAGCCGGTATGAAGCGCGAATGTACTGTAGACGATCTTATAAAAGTAGTGGAAGAACTCAGCCGAATTCACTGa

Transcript

BRAKERKRET00000018013

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q3U1J4	DNA damage-binding protein 1 OS=Mus musculus OX=10090 GN=Ddb1 PE=1 SV=2
Q16531	DNA damage-binding protein 1 OS=Homo sapiens OX=9606 GN=DDB1 PE=1 SV=1
Q5R649	DNA damage-binding protein 1 OS=Pongo abelii OX=9601 GN=DDB1 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003690 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03178 all species →	CPSF_A	CPSF A subunit region	Repeat	Interproscan
PF10433 all species →	MMS1_N	Mono-functional DNA-alkylating methyl methanesulfonate N-term	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR004871 all species →	Domain	Cleavage/polyadenylation specificity factor, A subunit, C-terminal	Interproscan
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	Interproscan
IPR050358 all species →	Family	RSE1/DDB1/CFT1/CPSF1	Interproscan
IPR018846 all species →	Domain	Cleavage/polyadenylation specificity factor, A subunit, N-terminal	Interproscan
IPR011047 all species →	Homologous_superfamily	Quinoprotein alcohol dehydrogenase-like superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10644 all species →	DNA REPAIR/RNA PROCESSING CPSF FAMILY	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0035861 all species →	Cellular Component	site of double-strand break	Interproscan
GO:0043161 all species →	Biological Process	proteasome-mediated ubiquitin-dependent protein 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
K10610	DDB1; DNA damage-binding protein 1	-	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 BRAKERKREP00000018013.1 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.