Gene detail

Detailed information of BRAKERKREP00000022984.1 in Hydra viridissima

Genomic Location: not available for this species
NR annotation: WP_038853982.1, DNA ligase D [Bordetella petrii]
Species Hydra viridissima · all data for this species · gene families

Sequence

CDS

BRAKERKRET00000022984

ATGAGAGCAAAAGCGCCTTTGACTGCCTACTGGAAAAAACGCGATTTCGATATGACGAGCGAGCCCAGTGGGCGCGGGCGAAAAAACAAAGAGAACAAGAACACCGATTTATCGTATGTAGTCCAGCGGCACGAGGCGCGCCGGCTGCACTATGACTTTCGGTTGGAATGGGGCGGCGTGCTGATGAGTTGGGCGGTTCCCAAGGGGCCTTCACTAGACCCAGAGGTGAAGCGTCTGGCGATTCAGGTAGAAGACCATCCGCTGGGTTACGCTTCATTTGAGGGCGATATACCTAAAGGTCAATACGGGGCGGGGCATGTGGCCATTTGGGACCGCGGCACCTGGATTCCGCATGGTGATCCCCATAAGGATTTTGCGCAAGGACGCCTACGTTTTGATTTGCAAGGCGATCAACTTAAGGGCGGCTGGTTGCTCTTTCGCACGGACCAGGAAGGCAATCAGTGGATCCTGCGCAAATTGGCAGATCACTTCGCTGTGCCTGGACATGACGCTGAAATGCCGACCGGCAGCGAGGCCGCAACCTGCATAAACACCCAACCCACCAAGGCGGCCGCCGGCCAATTAAAGGGCGTTGCACCGGGCGCTTTGCCTAAACGCATCGAGCCGCAACTCGCCACCTTAGTGGATGAGCCACCGCCTGGAGACCAATGGTCTTATGAAGTGAAATACGACGGTTATCGCATGCTGTGTCGCTTCGATGGCAAAAAAGCAGATTTCGTTAGCCGTAACGACATCGATTGGACCGCTCGTGCAAAAACGTTGGCGCGCGACCTTGCGGCCTTGAAGCTAGGAACCGGTTGGCTCGATGGCGAGATCGTTTGCTTCGATGAGAACGGTGTGTCTAGTTTTCAACAGTTGCAAAATGCGCTGGACGGTGATGTCGGTAACCTGTCTTTTGTGGTCTTCGACGTGCCGTTTTGGGAAGGCCAAGATTTGCGCCAACTGCCGTTGCGTCAACGCCAGGATTTTTTGCTGCAGCTGATGGCTGACTTGCCGGAGAACGCGCCTATTATGTTTACCCAGCGTCTGGGCATGGCCGACGGTACGCGGGCCAATGCGGCGTGGACCGAAGCCTGCCGCTTAGGCCTAGAAGGGCTTATTTGCAAGCGCATCGATGCCCCCTACACGGGCGGTCGTTCCAACACCTGGCTTAAATTGAAATGCAGGCCGCGCCAGGAGTTCGTGGTGGGCGGCTATACCATCAATAGCGTTTCATCTCACAAGTTGCGCTCGCTCATGGTGGGCCTATGGGAGGACGGTAAGTTTGTCTATGCGGGCAAAGTGGGTACGGGATTCAACGCGTCTGCCCACCAGGTGCTAATGAAACGGCTTAAACCCTTGCATATCGACACCATGCCTTTTGATAGCCTGCTGGCGCAAAGCGGGCGCTTCAGCCGACCTGCAGGCGCTAGCGTCTGGGTAAAGCCGGAGGTGGTGGTCGAAGTCGCTTATGCCGGCTGGACCGCCGATAAGTTGCTGCGCCAAGCCTCGTACCTCGGCTTGCGCGAAGACAAGCCGGCCAGCGCGGTGCGCAAAGAAGTGTCATTGGCGACACCGCCGGCTGAACGGATGCCCTCAGTTCGCTCGCGCAAGACCCAGGCGCCGCCAGGATCGGACCGTGTAAGCGGTATCGTTATTTCGCATGCCCAGCGCTTGGTTTATCGCGCGCCCGATATCACAAAATTGCAGCTGGCGCGCTACTACGAAGCCATTGCGCCCCATATGCTGGCACACGTTCGTGGCCGTCGGTTGGCCTTGCTACGCTGTCCTAATGGCACGAGCGCTACctgcttttttcaaaagcactTAAGCGAGAAGCCGCCCGAGGGCGTTGAATTGGACGATGGGTACTTAGTCATTACGTCGGTCGCCGGCATCGTTTCGCTGGTGCAGCGCGGCGTGGTGGAATTTCATACTTGGGGATCGACGAGGCCCCATGCCGATAAGGCCGACCGCATTACGATAGATTTGGACCCAGACCCGAATGTTGCATGGTCTACCGTGGTCGAGGCGGCGCAGCTGACCCGAGCCTTGCTGCAAGCACTGGGTTTAACTTCCTACCTAAAAACCACGGGTGGTAAAGGCCTGCACTTAGTTGCGCCTATTAAACCCACGCATTCCTGGGATGTTATTAAAACCTTTGCGCATAACATTGCCCTGCATCTGGCCACACTCATCCCAGACCGTTTCACCGCCAATATGTCCAAGGGGCGACGTAAAGACAAGATCTTCGTCGATTATTTGCGCAATGGGACGGGTGCGACGGCCATCGCCGCTTTTTCAGCCCGCGCCCGTCAGGGCGCCACGGTGTCGATGCCCATTTTGTGGGACGAACTGGATTCAGACCATGATTTGCGAGGGGCAGCCTTTAATGTGAGCAATGCGTTGGCATACGCCTTAAGCCGGCCCGATCCGTGGGCCGACTATAAAAAGCAAGGCCGCCAAGCCGTGACAGCAAAGATGATGGCTGCGGTGGGGCGCTGA

Transcript

BRAKERKRET00000022984

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9I1X7	Multifunctional non-homologous end joining protein LigD OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=ligD PE=1 SV=1
P9WNV3	Multifunctional non-homologous end joining DNA repair protein LigD OS=Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) OX=83332 GN=ligD PE=1 SV=1
P59971	Multifunctional non-homologous end joining protein LigD OS=Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97) OX=233413 GN=ligD PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0041577 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01068 all species →	DNA_ligase_A_M	ATP dependent DNA ligase domain	Domain	Interproscan
PF04679 all species →	DNA_ligase_A_C	ATP dependent DNA ligase C terminal region	Family	Interproscan
PF13298 all species →	LigD_N	DNA polymerase Ligase (LigD)	Family	Interproscan
PF21686 all species →	LigD_Prim-Pol	LigD, primase-polymerase domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR052171 all species →	Family	Non-homologous end joining protein LigD	Interproscan
IPR012340 all species →	Homologous_superfamily	Nucleic acid-binding, OB-fold	Interproscan
IPR014146 all species →	Domain	DNA ligase D, ligase domain	Interproscan
IPR014143 all species →	Domain	DNA ligase D	Interproscan
IPR012310 all species →	Domain	DNA ligase, ATP-dependent, central	Interproscan
IPR012309 all species →	Domain	DNA ligase, ATP-dependent, C-terminal	Interproscan
IPR014145 all species →	Domain	DNA ligase D, polymerase domain	Interproscan
IPR014144 all species →	Domain	DNA ligase D, 3'-phosphoesterase domain	Interproscan
IPR033651 all species →	Domain	LigD polymerase domain, PaeLigD-type	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR42705 all species →	BIFUNCTIONAL NON-HOMOLOGOUS END JOINING PROTEIN LIGD	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003910 all species →	Molecular Function	DNA ligase (ATP) activity	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0006310 all species →	Biological Process	DNA recombination	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
K01971	ligD; bifunctional non-homologous end joining protein LigD	EC:6.5.1.1	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 BRAKERKREP00000022984.1 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

7TPM > 0

7Conditions

0.4Max TPM

0.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	0	0.00	0.00
Whole	6	4	0.06	0.27
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	0.28	0.28
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	1	0.05	0.05
symbioic hydra M9 strain · symbioic hydra rep1	1	1	0.38	0.38
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
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
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	0.27
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	0.03
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	0.03
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	0.01
SRR10058802	Whole	Whole	not recorded	not recorded	SRP220397	0.00
SRR10058803	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	0.28
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	0.05
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	0.38
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.