Gene detail

Detailed information of BRAKERKREP00000019617.1 in Hydra viridissima

Genomic Location: QPEY01000173.1:276919...278125
NR annotation: XP_047144204.1, DNA ligase 1 isoform X3 [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P51892	DNA ligase 1 OS=Xenopus laevis OX=8355 GN=lig1 PE=2 SV=1
Q9W1H4	DNA ligase 1 OS=Drosophila melanogaster OX=7227 GN=DNAlig1 PE=1 SV=2
P18858	DNA ligase 1 OS=Homo sapiens OX=9606 GN=LIG1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003560 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04679 all species →	DNA_ligase_A_C	ATP dependent DNA ligase C terminal region	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR012340 all species →	Homologous_superfamily	Nucleic acid-binding, OB-fold	Interproscan
IPR012309 all species →	Domain	DNA ligase, ATP-dependent, C-terminal	Interproscan
IPR050191 all species →	Family	ATP-dependent DNA ligase	Interproscan
IPR012310 all species →	Domain	DNA ligase, ATP-dependent, central	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45674 all species →	DNA LIGASE 1/3 FAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003910 all species →	Molecular Function	DNA ligase (ATP) activity	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0006310 all species →	Biological Process	DNA recombination	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005739 all species →	Cellular Component	mitochondrion	Interproscan
GO:0006266 all species →	Biological Process	DNA ligation	Interproscan
GO:0006273 all species →	Biological Process	lagging strand elongation	Interproscan
GO:1903461 all species →	Biological Process	Okazaki fragment processing involved in mitotic DNA replication	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	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 BRAKERKREP00000019617.1.

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000019617.1 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

13TPM > 0

7Conditions

59.8Max TPM

7.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	5	5.48	59.76
Whole	6	5	16.72	25.52
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	9.19	9.19
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	1	10.65	10.65
symbioic hydra M9 strain · symbioic hydra rep1	1	1	6.48	6.48
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
SRR21134051	whole body	whole body	not recorded	not recorded	SRP392977	59.76
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977	20.19
SRR21134064	whole body	whole body	not recorded	not recorded	SRP392977	10.85
SRR21134050	whole body	whole body	not recorded	not recorded	SRP392977	7.69
SRR21134056	whole body	whole body	not recorded	not recorded	SRP392977	0.22
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
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
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
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	25.52
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397	24.54
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	20.27
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	15.45
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	14.55
SRR10058802	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	9.19
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	10.65
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	6.48
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.