Gene detail

Detailed information of XP_068761471.1 in Montipora capricornis

Genomic Location: chr8:43407222...43424622
NR annotation: XP_044184001.1, DNA ligase 1-like isoform X2 [Acropora millepora]
Species Montipora capricornis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_068905370.1

cttttcctttttgtagAGTTTCCGCCCCCATTGATTGACAATGCTAAGAATTTTTCTGGGGAAGAGTTGAAGAAGAAGCAAGATGAAGCTGCTTTGATAGTTAAGACTTGTTACTGTGAAATGCCCAACTATAATAAACTAATTCCATCTATTTTGGAGCATGGGTTAGAAGCACTGCCACGTTACTGTCATCTCACGCCTGGTATCCCACTCAAACCAATGTTGGCACATCCATCTAAGGGAGTGGAAGAAGTGTTTAAACGATTTGAAAATGCAGAATTTACTTGCGAGTTTAAGTATGATGGAGAACGTGCTCAGATTCATGTTTTGGAAAATGGAGAAATTCACATTTACAGCAGAAACCAAGAAAATAATACCTCCAAGTATCCTGACATCATTGCAAGAATGACGAAGGTTTTAGGAGATGGAATCAAATCCTGCATCATAGATACAGAGGCAGTAGCATGGGATCGCGAGAAGAGGCAGATTTTACCCTTCCAGATTCTTagcacaagaaaaagaaagGATGCTGATGCCTCAGAAATTAAAGTTCAAGTTTGTGTATATGCATTTGATCTGTTATACCTCAACGGAAAAtCTTACGTAAAAGAACCTTTCCGTGTTCGCAGAGAAGCATTGCGATCTTCTTTCACAGAAATCGAAGGGGAATTCATGTTTGCTCAGAGTTCTGACTCTGTAAACACGGACGACATAGCGGAATTTTTAGACGAGTCTATCAAGGGAAACTGCGAAGGGCTGATGGTGAAAACTCTTGAAGTGGACGCCACTTACGAAATTGCCAAACGTTCACATAACTGGttaaaaTTGAAGAAGGACTACCTGGCTGGCGTCGGAGATACGTTAGATGTGGTGGTGATTGGTGGGTATCTTGGTAAAGGCAAAAGGACCGGTTCATACGGAGGCTATCTTTTAGCTTGCTATGATCCTGAAAGTGAGGAGTTCCAGACCATATGTAAGATTGGAACTGGCTTTACCGACGAACTTCTCGACCAACATCACCAGTTTTTCAAGGATCACGTGATTTCACAACCAAAGGCGTACTATCGCTATGACGACAATTTGGCGCCTGATCATTGGTTCGACCCAGTGCAGGTGTGGGAGATAAGAGCAGCGGATCTTTCGATTTCTCCTGTGCATAAAGCAGCAGTTGGCCTGGTTGATCCTGTTAAGGGAATTTCGTTACGATTTCCACGCTTCCTTAGAATCCGAGACGACAAAACGCCAGAGCAAGCTACAGACAGTTCACAAGTGGCAGAAATGTACAGAAGCCAGGAAACTGTGAAGAATAACACCAATCCTCCTGCTGTCCCGGATGCGGATGACTTTTATTGAGAATTAAGGATGATGCCAAAGGAAACTTTTGGTGGCTTTACAGCATTCACGGACGAAGTGTTCTAACCTATAAGACTTCGATTGCTGTAGTGACTAAGTAGTCCGCCATGCGTTACCTTCCATTCGATTGAGAATCATCAACGCGCTGTTTTTGCGCGAAGATTATTGCAGCTGTCCAACGAGGGACAATGAGGAAGGCTAATACTAGAACTTCATCCGTAACTTTCCGGGAAAAATGGACATCCTTCGAAGGTTGTCttctttttccactttttaCCGAAACGACCGCAATTTTCTGTACCATTTATTTGCACCACTAAAACCAGGCTCCGATGCGAGGATTAAACCGCTTCACTTACCGGGCTTTTGGCCGCCCGCCACATTTATTTGTACCCAGACTCTTCCATCATTCGGAAATGGACTCAAATTCTTTTCTCACCGAAAATTccgttaaggtaattccctatccagattttttcaaacttggcacaattgatattcatacacagaacattttaaaaaatgtaataaaaagattgggtcactgtgcttgttttcgcgcagtatgccctttattttaagtgtttttttaccgaattacgcgagaagcgttcgaaactacagatcaaccggaaaaatttgTTGTCATGTAGCAAAAGCTATCgagtattactgaaaacttgaacttatttgtttgtccGGGGTATAATCTTTTAAGTAAAGTAATTTCAAATTGCttaatcttgcaaagaaatgtaagcaaatcgGACCGCTACAGTCATCGCCTTGCACCCCatgtctggctccaaatgcagtttcacgtcatttatatgtaaatactacaacttctactatccaactttttttcgcCTTAaaatgttttccgtgtacctattaagagtaaataaaaccattaaaaatgaa

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P51892	DNA ligase 1 OS=Xenopus laevis OX=8355 GN=lig1 PE=2 SV=1
P37913	DNA ligase 1 OS=Mus musculus OX=10090 GN=Lig1 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)	OG0003742 (this species only)

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
PF01068 all species →	DNA_ligase_A_M	ATP dependent DNA ligase domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR016059 all species →	Conserved_site	DNA ligase, ATP-dependent, conserved site	Interproscan
IPR012309 all species →	Domain	DNA ligase, ATP-dependent, C-terminal	Interproscan
IPR036599 all species →	Homologous_superfamily	DNA ligase, ATP-dependent, N-terminal domain superfamily	Interproscan
IPR012310 all species →	Domain	DNA ligase, ATP-dependent, central	Interproscan
IPR000977 all species →	Family	DNA ligase, ATP-dependent	Interproscan
IPR050191 all species →	Family	ATP-dependent DNA ligase	Interproscan
IPR012340 all species →	Homologous_superfamily	Nucleic acid-binding, OB-fold	Interproscan

PANTHER

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

Gene Ontology

GO term	Category	Description	Source
GO:0003909 all species →	Molecular Function	DNA ligase activity	Interproscan
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:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0071897 all species →	Biological Process	DNA biosynthetic process	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

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 XP_068761471.1.

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

Expression pattern (RNA-seq)

Transcript abundance of XP_068761471.1 across 36 RNA-seq samples of Montipora capricornis. 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.

36Samples

27TPM > 0

1Conditions

26.5Max TPM

6.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
Polyps	36	27	6.05	26.47

Per sample · hover a bar for the full sample record · show / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR12904781	Polyps	Polyps	not recorded	not recorded	SRP199550	26.47
SRR12904782	Polyps	Polyps	not recorded	not recorded	SRP199550	26.00
SRR27940193	Polyps	Polyps	not recorded	not recorded	SRP199550	25.67
SRR12904783	Polyps	Polyps	not recorded	not recorded	SRP199550	21.51
SRR27940191	Polyps	Polyps	not recorded	not recorded	SRP199550	21.35
SRR12959182	Polyps	Polyps	E3 day0	not recorded	SRP199550	9.42
SRR12959183	Polyps	Polyps	E3 day0	not recorded	SRP199550	9.15
SRR12786896	Polyps	Polyps	OA3 day0	not recorded	SRP199550	8.15
SRR12959184	Polyps	Polyps	E3 day0	not recorded	SRP199550	7.69
SRR12786898	Polyps	Polyps	OA3 day0	not recorded	SRP199550	7.64
SRR12786897	Polyps	Polyps	OA3 day0	not recorded	SRP199550	6.76
SRR12959203	Polyps	Polyps	E3 day15	not recorded	SRP199550	5.96
SRR12959202	Polyps	Polyps	E3 day15	not recorded	SRP199550	5.54
SRR12959201	Polyps	Polyps	E3 day15	not recorded	SRP199550	5.50
SRR12959229	Polyps	Polyps	E3 day3	not recorded	SRP199550	4.76
SRR12959216	Polyps	Polyps	E3 day9	not recorded	SRP199550	3.44
SRR12959214	Polyps	Polyps	E3 day9	not recorded	SRP199550	3.14
SRR12959215	Polyps	Polyps	E3 day9	not recorded	SRP199550	2.81
SRR12710858	Polyps	Polyps	OA3 day9	not recorded	SRP199550	2.78
SRR12710855	Polyps	Polyps	OA3 day9	not recorded	SRP199550	2.45
SRR12959189	Polyps	Polyps	E3 day21	not recorded	SRP199550	2.12
SRR12959188	Polyps	Polyps	E3 day21	not recorded	SRP199550	1.87
SRR12710848	Polyps	Polyps	OA3 day3	not recorded	SRP199550	1.81
SRR12710847	Polyps	Polyps	OA3 day3	not recorded	SRP199550	1.75
SRR12710846	Polyps	Polyps	OA3 day3	not recorded	SRP199550	1.57
SRR12959190	Polyps	Polyps	E3 day21	not recorded	SRP199550	1.40
SRR12710857	Polyps	Polyps	OA3 day9	not recorded	SRP199550	1.21
SRR12807381	Polyps	Polyps	OA3 day0	not recorded	SRP199550	0.00
SRR12849113	Polyps	Polyps	OA3 day0	not recorded	SRP199550	0.00
SRR12927880	Polyps	Polyps	E3 day0	not recorded	SRP199550	0.00
SRR12959227	Polyps	Polyps	E3 day3	not recorded	SRP199550	0.00
SRR12959230	Polyps	Polyps	E3 day3	not recorded	SRP199550	0.00
SRR12963484	Polyps	Polyps	E3 day0	not recorded	SRP199550	0.00
SRR27940192	Polyps	Polyps	not recorded	not recorded	SRP199550	0.00
SRR9129316	Polyps	Polyps	not recorded	not recorded	SRP199550	0.00
SRR9613519	Polyps	Polyps	not recorded	not recorded	SRP199550	0.00

Source: CnidoSite RNA-seq expression matrices (MCAPR_TPM, StringTie quantification over 36 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.