Gene detail

Detailed information of BRAKERNUSP00000029184.1 in Montipora cactus

Genomic Location: BLFO01002536.1:369384...409592
NR annotation: XP_029204996.2, DNA ligase 4-like [Acropora millepora]
Species Montipora cactus · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

BRAKERNUST00000029184

ATGGAGGGAGATTCCAGCGCTGGAGTCGCAGCTCAGGTTCCGTTTTATGATTTATGTTGCTTGTTGGAaaaaatttcggaaacttcaggtactgagaagaaaaagaagattttgtcaaCATTCGTGAGTTCTTGGAGAGAGGCGCATGGCAAGCTTCACAAGGATACTTCGAAAACAACTGATTCGTTTTACTCTGCAATGCGACTCCTGTTACCACAACTGGACAAAGAAAGAGGAGCGTATGGAATAAAGGAGGTTGTACTGGCAAAATATTACATTGATATTCTAAGCATTGGTAAGGATAGTGTGGATGGGCGGAAACTGTTGAATTACAGAGCTCCCAAAAATGCTAAACAGGATTCAGTTGCTGATTTTGCAAGTGTCGCCtactttgttttgaaaaacagaTGTCCAGGGAAGGGAAGtttaaaaattgcTCAAGTTAACAAGCATCTTGATGATGTGGCACAAGCAAATGTTGAACGCAAACGTGAAGATGTCAAGAAAGCCTTACAGCTTCTTCTACGAAACACAAGTGCCCTTGAGCAGAAGTGGTTAATCAGGATTATCTtcaagGAACTGAAGGTTGGCCTTAGTGAGAATTCTGTGTTCAATGTTTTCCATCCTGATGCTGTGGAGCTCTATAGTGTTTGTAACAGTTTGTCCAAGGTAGAAAAGATCATGAAGAATCAAGCATTTTACATAGAAACAAAAATAGATGGAGAAAGGATGCAACTCCACAAAGAAAAAGATGTCTTTATGTACTTTTCTAGAAGTGCAAATGATCACACCCACACATTTGGCGCAAATCCATCTTCAGGAGTTCTCACACCACATATTGCTGGCTGTTTCTCAAGCTCAGTGCATTCCTGTATATTGGATGGTGAAATGATTGTGGTTGATCCTGCAACAGATGTTTGGCTATCAAAAGGGATGAACATGGATGTAAAGTCTTTAACTACTTATGAAAATGGCTACCATCCTTGTTTCGTCGTGTTTGATATCCTTGTTATCAATGACAAGAAACTTGCCAATGTGCCCCTGTGTGAAAGAATCAAAACCATGGAAAAAGTACTGCGACCAAGGTCTGGATATTTTCAGTTTGTCGAAAGGCAGGATGCATCAACGAGAGGAGACGTTGTAAAAGCTCTAAATGAGGCAATCGATAAAAGAGAAGAGGGATTGGTCATCAAATCGCCATCCTCGATTTATAAACCGAACGTGAGAAGTGGAAGTGGCTGGATAAAAATCAAGCCTGAATATGTTGATAGTTTGAGTGATGAGATGGATCTCTTAATCGTTGGGGGCTATTTCGGAGTTGGTcgTCGCAGTGGAATGATATCTCATTTTATGTGTGCCGTGGCAGTGCCATCTGGTATCTCAGGGCAACATCCTTCAGTGTTTCACTCATTTTGCAAGGTTGGAACCGGTTACACAATGAATGAGTTGAACGAACTACATCAATTATTACATCCCTATTGGCGGCCATTTGATACTAAAAAGCCTCCTGATTCAGTTATTTTAGCTTCCGGTTACAAAGAAAAGCCAGATGTTTGGATCGAGCCAACCAAATCAAAAATTGTGCAGGTTAAGGCTGCAGAAATTATCGCTTCAGACAAGTTCAAAACTGGCTTCACACTTCGATTTCCAAGAGTAGAGGCAATAAGGAAAGATAAGATGTGGTACGAATGCTTGAGTTTAAAGGAACTTGAAAAGCTAAAATCGGTGTCGCAAATGTTTGAAGGCAGGGAGTTTTATATTGTCAATGGTCCTTCAACTCATACCAAAGCCATTCTGGAGAAGAAAGTTGCAGAGAACGGAGGTACATTCACTCAAAACCCGTCGCCAGATACATACTGTGTTATTGCCGGAAGAATAAACGTGAGAGTGAAGAACATAATAAGTCAGAAACAATATGATGTTGTACAAGCGTCGTGGCTAATAAAGTGCTTGGAAAATGGACAGGTGGATCCATGGCAACCAAGTGACATGTTGCATTGCTCGCCTGGCACCGCTGACAAGTTCGCAGAGGAATATGATCGCTTTGGTGATAGCTACACTCAGGATGCCACCGTGGAATCTCTCAAAAAAGTTTTTAACAATGTCCAAAATCAGCGCATTCCCAACAGCAGCCTGGAACTTGTTGGCTTGCAAGTTCGCTTGTATGGAGCTCAAACCACGGACACTTTGGATAATAGAGTGACACATATTATTCTTGATGAAAGGTATTCAGATTGA

Transcript

BRAKERNUST00000029184

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q90YB1	DNA ligase 4 OS=Gallus gallus OX=9031 GN=LIG4 PE=2 SV=2
G3GTP0	DNA ligase 4 OS=Cricetulus griseus OX=10029 GN=LIG4 PE=1 SV=1
Q8BTF7	DNA ligase 4 OS=Mus musculus OX=10090 GN=Lig4 PE=2 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002879 (this species only) · gene tree & orthology

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
PF11411 all species →	DNA_ligase_IV	DNA ligase IV	Family	Interproscan
PF04675 all species →	DNA_ligase_A_N	DNA ligase N terminus	Family	Interproscan
PF16589 all species →	BRCT_2	BRCT domain, a BRCA1 C-terminus domain	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036420 all species →	Homologous_superfamily	BRCT domain superfamily	Interproscan
IPR012310 all species →	Domain	DNA ligase, ATP-dependent, central	Interproscan
IPR029710 all species →	Family	DNA ligase 4	Interproscan
IPR012309 all species →	Domain	DNA ligase, ATP-dependent, C-terminal	Interproscan
IPR001357 all species →	Domain	BRCT domain	Interproscan
IPR036599 all species →	Homologous_superfamily	DNA ligase, ATP-dependent, N-terminal domain superfamily	Interproscan
IPR012340 all species →	Homologous_superfamily	Nucleic acid-binding, OB-fold	Interproscan
IPR000977 all species →	Family	DNA ligase, ATP-dependent	Interproscan
IPR044125 all species →	Domain	DNA Ligase 4, adenylation domain	Interproscan
IPR021536 all species →	Domain	DNA ligase IV domain	Interproscan
IPR012308 all species →	Domain	DNA ligase, ATP-dependent, N-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45997 all species →	DNA LIGASE 4	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
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0005958 all species →	Cellular Component	DNA-dependent protein kinase-DNA ligase 4 complex	Interproscan
GO:0006297 all species →	Biological Process	nucleotide-excision repair, DNA gap filling	Interproscan
GO:0006303 all species →	Biological Process	double-strand break repair via nonhomologous end joining	Interproscan
GO:0032807 all species →	Cellular Component	DNA ligase IV complex	Interproscan
GO:0051103 all species →	Biological Process	DNA ligation involved in DNA repair	Interproscan
GO:0071897 all species →	Biological Process	DNA biosynthetic 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
K10777	LIG4, DNL4; DNA ligase 4	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.

Co-expression network

Genes whose expression across the transcriptome samples of Montipora cactus tracks this one. Counts are over the whole network; the network view itself draws at most 100 partners per query gene (CNIDO_NET_TOP_K), so a hub gene can show fewer edges than the number below.

No co-expression network has been built for this species, so this gene has no partners to show. Networks are available for the species listed on the Network Analysis page.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Montipora cactus, and in which cell types it is a marker. Expression is stored per cell, so the violin plot and the cell-type means are computed in the viewer — open a dataset to see them.

No single-cell dataset has been published for this species. The atlases that do exist are listed in the Cell Atlas.

Epigenetic marks

Chromatin and DNA-methylation data covering this gene. Peak calls are listed per sample with the genomic region the peak falls in; DNA methylation is listed as sample availability only, because those tables are queried by the DNA Methylation page itself.

No epigenomic data has been deposited for this species. The assays that exist across the site are described in the Epigenomic Data module.

What you can do with this gene

Every tool below opens with this gene already entered, so you land on the analysis rather than on an empty form. Links open in a new tab.

Analysis	What it does	Status
Primer design	Design PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.	template found	open →
BLAST	Search this gene’s sequence against the CnidoSite BLAST databases. The query is filled in and the species’ database is preselected — press Run to start.	template found	open →
Expression heatmap	Draw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it.	no expression matrix	–
Gene family / orthogroup	Look this gene up in the single-copy orthogroups built from the high-quality cnidarian genomes, and see which other species carry an orthologue.		open →
Gene set analysis	Start a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.		open →