Gene detail

Detailed information of XP_068721827.1 in Montipora capricornis

Genomic Location: chr10:17392501...17405360
NR annotation: XP_029181177.2, DNA repair protein XRCC4-like isoform X1 [Acropora millepora]
Species Montipora capricornis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_068865726.1

TAGCGCCTGTCAGAAGTGCACATGACTCAGAGATTGAAACGATTGCTTCACTTGAATATTTACTAAAATGCCACAGACGTTCACCAGGATAGAATATGGGGAAGAGAAATACTATCTCTTGGCGGATCTATTTGAGGGAGGTGAAGGCGGATTCAATCTGACGATTTGCAACGGGAGGCAACTTTGGCGCGAAACTGTGTCTTCATCAGTGGTGCAATCAATGGCCAAAGCTGCAGATATGAGTGTTTCTGAATTTGCTGCACAGACAGGCAGAGCATTGACAGGGCAGACCACACGACAGGATAACTTTGTTTACCAAACAAAGCTTAGGGGAACAGATTTACAGttttcttggaagaaaaataTTGGAGATGGAGTTAAGTTTCAGCTGGGGTCATTAATATTGGCTGAAGTTGACAACTGTGTCCCTATCACGATAGGCGTTTTTGACCTTGCAGTTGATCAGATGTCACAGCTTAAGGAAGAAATTACATCTCTAATGTCAGAAAATGCCAGGCTTTCTTCAGAAAGGGAAGAAGCCCTTAAGCTTTTGAATGAATGTGTGACAGCAAAAGAGCATATGGAAACAGATTTATTTGAAAAGttTGCTGCAGTTCTTAACGAGAAAAAAGCCAAGATCAGACAACTAAAGGAAGCAGTTCATGAAACGGCAATGGCAGCTGCCGCTGACGCTGTGAAAGCTAAGAAACCCTCAGATTCAAGCAAAAGCCAGGACAAAGGCAAGTCCAGTTGGGCATCAAAGAGGTCAGATGATACAGATGATGATACCGATGATGATAATACTGATGATGATAATACACAAGCAAGAGATGTAGATACACGAAACAAAcaagaaggaaggaaggagaaGGAACCTAAAACTACGGCGTTCAGTCCGTCCCTTTTGCCTgaggaagaagatgaagaaattGAACTGACAGTTAAAAGACGCCGCCGAAGAGAACCAAAGCCGAGAAAATCGCCAGCGGCCAAACTTGTTTTGCCCAAAGTTACCCCCGTTAGAAAGACACCAAGCACTTCTTCAGGGGAAAGtgTAACTCCAGTTCGACCGCGTCGACAAGCCTCTGACAAGTCTCCTCCTGATGCTGACGACCTGATGGCTGAGATGTAAATGTGAATCCTTTGTTTGAGTTTTTGGGAAAtattcaatgaaatgaaatcgCCAGAACTATGACAGAGAAGCCTTCGGTTGCACCTCGCCTTCTTCGTGAGGGAAGGGCTATCAGCCGACCGAGAAAATATCCCTCTAGGCAGGTAGGATTAGTCACTTGCGCAACTTGTAGAGCTTACGAAGTCCAGCTACAAAGTGTACTCGCACTATTTTCTGAGTTCCCTTCGAAAAacatttattattaaattttcaacctcggatattgcgtttctaacGTTTCTAgattggctcactcaatctcCGTTAGCAGCTCgtataccgtatgacctaatatggaaacggattttgtcaagtgttgccaagctggaaactgaaTTGGCTTTTATGTCCAAGTGACCATGCGTTCAGAATTTAGggaaattttaataaaacaattattccattcgtgcttgttggatattaGACTGGTTCAGGATAGCCAACTCGGTgcggctatttaccatctcatttCCAAGGAGGGCTCATAGGTTGATTATGataattttatcttcacttcAAATGCGAGATCTCGACAATTTCAGTCCTAGAAGCTTAACTGGACGATTGCCACCTGTACCTATATTATTGCTGAACTCCCACTTGTCTCCAATAGCTCATTGAGATGGTATCCGCATTTGTAACAGGAAGATGATAGATTAAATTCACATTGGgagaactcggatttttccgagtatccttGACTCACCATcggaaaaaaaatcatcttttcATACAGTTTTGTAATTTCTAGGAAGAAACAGAGAGTCATGGGGAGTTTTATTTTGGCAATTGTTGACTTTGTAAAAGAAGGGTAGTCAATCCCGTTGCATTATTTCCTCGGGGGTATCGCACTACAGTTTTTTTCTAATTAGCACAGGATGTAAAATGATATTGGTTCAAGAAAGATTGGGCTGTACGTCTAGACACCACATCATGATCAGATCCAGTTTGTGATGACCTCGGTCCGAATTTCTTCTTGAAGGGTGAAACGTTGCACGAGGCTGCAGCTGTGGTCGGTTGTGTACTAAGTGATTAACTCCTCGAGTAGTATTTTTTTCGAAGACCATTTGAATCTATCTATTGCTTAACGACAAACCAAGGTTTTTAAATTGCACGCTAATAGATTTTGGAAAGTCGCCTGATCGACTTTTTTCAGGACATAGTTACTCTAAGCAAAGAGTAAAGAGCTCTTTACACTATAATTTTGGTTTGTAATTAATGAACTCTTAAAGTTAATGCGGCCCTGAACAGGATTCGATCGTAGTAAGTGTGCGTTGGGGCGTTACCACACCAACTTAGTTGTGAATGTTACAATCTTACTTCTAAGGAAATATTTTTCAGGCATGTTCCACTCGTTGAATAAAGTCAAGTAAAACCCTTA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q924T3	DNA repair protein XRCC4 OS=Mus musculus OX=10090 GN=Xrcc4 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006671 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF06632 all species →	XRCC4	DNA double-strand break repair and V(D)J recombination protein XRCC4	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR009089 all species →	Homologous_superfamily	XRCC4, N-terminal domain superfamily	Interproscan
IPR014751 all species →	Homologous_superfamily	DNA repair protein XRCC4-like, C-terminal	Interproscan
IPR010585 all species →	Family	DNA repair protein XRCC4	Interproscan
IPR038051 all species →	Homologous_superfamily	XRCC4-like, N-terminal domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR28559 all species →	DNA REPAIR PROTEIN XRCC4	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006302 all species →	Biological Process	double-strand break repair	Interproscan
GO:0006310 all species →	Biological Process	DNA recombination	Interproscan
GO:0005958 all species →	Cellular Component	DNA-dependent protein kinase-DNA ligase 4 complex	Interproscan
GO:0006303 all species →	Biological Process	double-strand break repair via nonhomologous end joining	Interproscan
GO:0010165 all species →	Biological Process	response to X-ray	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:0051351 all species →	Biological Process	positive regulation of ligase activity	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
K10886	XRCC4; DNA-repair protein XRCC4	-	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 XP_068721827.1 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

28TPM > 0

1Conditions

25.5Max TPM

8.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
Polyps	36	28	8.55	25.48

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR12959229	Polyps	Polyps	E3 day3	not recorded	SRP199550	25.48
SRR12904783	Polyps	Polyps	not recorded	not recorded	SRP199550	18.54
SRR27940191	Polyps	Polyps	not recorded	not recorded	SRP199550	18.39
SRR12786896	Polyps	Polyps	OA3 day0	not recorded	SRP199550	16.69
SRR12786897	Polyps	Polyps	OA3 day0	not recorded	SRP199550	15.78
SRR12904781	Polyps	Polyps	not recorded	not recorded	SRP199550	15.75
SRR27940193	Polyps	Polyps	not recorded	not recorded	SRP199550	15.33
SRR12904782	Polyps	Polyps	not recorded	not recorded	SRP199550	14.97
SRR12786898	Polyps	Polyps	OA3 day0	not recorded	SRP199550	14.23
SRR12959183	Polyps	Polyps	E3 day0	not recorded	SRP199550	13.46
SRR12959182	Polyps	Polyps	E3 day0	not recorded	SRP199550	13.39
SRR12959184	Polyps	Polyps	E3 day0	not recorded	SRP199550	12.93
SRR12959202	Polyps	Polyps	E3 day15	not recorded	SRP199550	12.35
SRR12959203	Polyps	Polyps	E3 day15	not recorded	SRP199550	11.94
SRR12959201	Polyps	Polyps	E3 day15	not recorded	SRP199550	11.78
SRR12959230	Polyps	Polyps	E3 day3	not recorded	SRP199550	10.81
SRR12959215	Polyps	Polyps	E3 day9	not recorded	SRP199550	8.49
SRR12959216	Polyps	Polyps	E3 day9	not recorded	SRP199550	8.33
SRR12959214	Polyps	Polyps	E3 day9	not recorded	SRP199550	7.64
SRR12710858	Polyps	Polyps	OA3 day9	not recorded	SRP199550	6.20
SRR12959188	Polyps	Polyps	E3 day21	not recorded	SRP199550	6.00
SRR12710855	Polyps	Polyps	OA3 day9	not recorded	SRP199550	4.77
SRR12710857	Polyps	Polyps	OA3 day9	not recorded	SRP199550	4.67
SRR12959189	Polyps	Polyps	E3 day21	not recorded	SRP199550	4.64
SRR12710848	Polyps	Polyps	OA3 day3	not recorded	SRP199550	4.47
SRR12959190	Polyps	Polyps	E3 day21	not recorded	SRP199550	4.44
SRR12710846	Polyps	Polyps	OA3 day3	not recorded	SRP199550	3.43
SRR12710847	Polyps	Polyps	OA3 day3	not recorded	SRP199550	3.02
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
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.