Gene detail

Detailed information of g21669.t1 in Montipora capitata

Genomic Location: Sc0001460:17361...53820
NR annotation: XP_029205270.2, DNA repair protein RAD50-like [Acropora millepora]
Species Montipora capitata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

g21669.t1

atgaagatccaaggaatccgtagttactcgcacagtgaaccgtctatcatagaattccagaagccactgacattgattgttggaccaaatggagcaggcaaaacgtctgtcatagaatgcctcaactacatggctactggagacatgccccctggcagcaaagggaatctgtttgttcacgacccaaagattgcaggtgagcttgaggtcaagggtcaaataaaattgagattcagggatgttactggaaatacaattgtcgtcacaagaactctggtgtctgaacaaaagggaaaaaagttgcaaacaagaactatggaaggaaacataatgcgagaagttcatggggagagacgaagcttaagctcaaaatgtgctgacatcaatagagagatgatatccttccttggagtatctaaggctgtgttggataatgtgattttctgtcatcaagaagagtctaactggccacttagtgagggcaaagtactaaagcaaaaatttgatgatatttttgctgcaacaaggtacatcaaagcactggaagctattcgcaaatttcgacaggaacaggctcagactgtaaaggagtatgcaatagacctgagtcatctcaaagcaaataaggagaaagcagatcagatagcagatgaactcgcccaaacccaggggaaagttgctgcaacggaggataaagtcaaggaactgaatgaaaagattaaaccaaccgagttgaggctggctgaactggcatgtatcgctgatgatgtctttgagttggagaaaaaagttgaatccttgtctacggaaagaagacaactcttgaaagtagaagctgatcttaaggaaaagatcatcaacctcttcaacgggcctgtggaggaactgcacaaaatatattcagattttcagaaaagagttatggaaaaggaaaacaccttgagagacgatgagtgcataatccataagctaggcgaagatcagcaaaaattgaccgctgcaaagaaccaacttcacgtggaaggaggaagacttgaacaacaagctcataggcacaaacagaacgtttctgatagagacaatgctgttatagatctggcaacggagcataacttcaaaggctacgaaaaaggccctttctcaaaagacggcgtggatcagttcttggaggaaatgaagagaaaatatcaaaacatcattgatgacacaaagcgtaagagggaagtgttcgaaaaaaagtcgaacgaactgcagaaaaagattgacgatatgaagaagaaccaagcacagtgtgaggaaactattcgcctcaagaaaaacttcatgagggaaaaccagcagaagttgaggcagattgggctcgacttgaaaagtgtggatgcttcagctaacagccttaaaaccctcgagggtgacctacaaagagcggaaagagaacttaaaatggctcacgacagtggaaatgtgagcgagttgggaagagaaattggcgaacttcagtcagagaaacgtcaagttgacaacggactacgtcagttaagggaagagcagcaagctatgcatatgcaatccaaaacacaagctgaactggacatgatgaccaaagagaaaagtaacaaggaagaagccatccaacaaatcatggaacgtcatgaggaagacctgaagactacactcggtacacgaggtacaacagagagtcttcacacaagactgaaggagcacttgaaagagaaggaaaaggagctaaaagaaactactaagaatctgcagaaactgaaggaacagttatcatccaaacaaacacgcaaacggatgatcgtagacagtttagcagacaaagagaatcgagtccaggaacacaaacgacaaatttcggaggcgtgtggcgagaatgactataacaccacaaaagaagtcattaagaacaacattgactctctgcaagatgaacgaggtataattgggtctttggaaaaaatttattccaagtttgtgtcgaagctggagagcagtgatgtacatagcagcggatgtcctctgtgtcatcgaacattcaatactaacagagagattgacgaactcgcaacagagctgaggaacaaaattcgaactcttcctgaacgtcgtgtggcgaatgaaagaagcctgaatcaagagcaaaatcgttatgatcacattcttaaactggctccggctaaagaaactctggaatctctagagaacaatgagattcctgacataaaatccaagttggatgcgataaaggctgaagagcaaagaattcaagatgagatcaccgaagtatgtgaagtcaagttcatttttttttctcttttgcacaaattgcaattaaaagaattttcagatcctcccagtttggtttttggacttatgtcccccgtgtgtttttatcgttcagtttatgcacatgtaaacgtagaagtcgtgcataggttgagcgcaaagggcattttagaaaaacagtctaagaaaaaggcaaccttcaaggaatga

Transcript

g21669.t1

ATGAAGATCCAAGGAATCCGTAGTTACTCGCACAGTGAACCGTCTATCATAGAATTCcagaagccactgacattgatTGTTGGACCAAATGGAGCAGGCAAAAcgTCTGTCATAGAATGCCTCAACTACATGGCTACTGGAGACATGCCCCCTGGCAGCAAAGGGAATCTGTTTGTTCACGACCCAAAGATTGCAGGTGAGCTTGAGGTCAAGGGTCAAATAAAATTGAGATTCAGGGATGTTACTGGAAATACAATTGTCGTCACAAGAACTCTGGTGTCTGAACAAAAGGGAAAAAAGTTGCAAACAAGAACTATGGAAGGAAACATAATGCGAGAAGTTCATGGGGAGAGACGAAGCTTAAGCTCAAAATGTGCTGACATCAATAGAGAGatgaTATCCTTCCTTGGAGTATCTAAGGCTGTGTTGGATAATGTGATTTTCTGTCATCAAGAAGAGTCTAACTGGCCACTTAGTGAGGGCAAAGTACTAAAGCAAAAATTTGATGATATTTTTGCTGCAACAAGGTACATCAAAGCACTGGAAGCTATTCGCAAATTTCGACAGGAACAGGCTCAGACTGTAAAGGAGTATGCAATAGACCTGAGTCATCTCAAAGCAAATAAGGAGAAAGCAGATCAgATAGCAGATGAACTCGCCCAAACCCAGGGGAAAGTTGCTGCAACGGAGGATAAAGTCAAGGAACTGAATGAAAAGATTAAACCAACCGAGTTGAGGCTGGCTGAACTGGCATGTATCGCTGATGATGTCTTTGAGTTGGAGAAAAAAGTTGAATCCTTGTCTACGGAAAGAAGACAACTCTTGAAAGTAGAAGCTGATCTTAAGGAAAAGATCATCAACCTCTTCAACGGGCCTGTGGAGGAACTGCACAAAATATATTCAGATTTTCAGAAAAGAGttatggaaaaggaaaacaccTTGAGAGACGATGAGTGCATAATCCATAAGCTAGGCGAAGATCAGCAAAAATTGACCGCTGCAAAGAACCAACTTCACGTGGAAGGAGGAAGACTTGAACAACAAGCTCATaGGCACAAACAGAACGTTTCTGATAGAGACAATGCTGTTATAGATCTGGCAACGGAGCATAACTTCAAAGGCTACGAAAAAGGCCCTTTCTCAAAAGACGGCGTGGATCAGTTCTTGGAGGAAATGAAGAGAAAATATCAAAACATCATTGATGACACAAAGCGTAAGAGGGAAGTGTTCGAAAAAAAGTCGAACGAACTGCAGAAAAAGATTGACGATATGAAGAAGAACCAAGCACAGTGTGAGGAAACTATTCGCCTCAAGAAAAACTTCATGAGGGAAAACCAGCAGAAGTTGAGGCAGATTGGGCTCGACTTGAAAAGTGTGGATGCTTCAGCTAACAGCCTTAAAACCCTCGAGGGTGACCTACAAAGAGCGGAAAGAGAACTTAAAATGGCTCACGACAGTGGAAATGTGAGCGAGTTGGGAAGAGAAATTGGCGAACTTCAGTCAGAGAAACGTCAAGTTGACAACGGACTACGTCAGTTAAGGGAAGAGCAGCAAGCTATGCATATGCAATCCAAAACACAAGCTGAACTGGACATGATGACCAAAGAGAAAAGTAACAAGGAAGAAGCCATCCAACAAATcATGGAACGTCATGAGGAAGACCTGAAGACTACACTCGGTACACGAGGTACAACAGAGAGTCTTCACACAAGACTGAAGGAGCACTtgaaagagaaggaaaaggaGCTAAAAGAAACTACTAAGAATCTGCAGAAACTGAAGGAACAGTTATCATCCAAACAAACACGCAAACGGATGATCGTAGACAGTTTAGCAGACAAAGAGAATCGAGTCCAGGAACACAAACGACAAATTTCGGAGGCGTGTGGCGAGAATGACTATAACACCACAAAAGAAGTCATTAAGAACAACATTGACTCTCTGCAAGATGAACGAGGTATAATTGGGTCTTTGGAAAAAATTTATTCCAAGTTTGTGTCGAAGCTGGAGAGCAGTGATGTACATAGCAGCGGATGTCCTCTGTGTCATCGAACATTCAATACTAACAGAGAGATTGACGAACTCGCAACAGAGCTGAGGAACAAAATTCGAACTCTTCCTGAACGTCGTGTGGCGAATGAAAGAAGCCTGAATCAAGAGCAAAATCGTTATGATCACATTCTTAAACTGGCTCCGGCTAAAGAAACTCTGGAATCTCTAGAGAACAATGAGATTCCTGACATAAAATCCAAGTTGGATGCGATAAAGGCTGAAGAGCAAAGAATTCAAGATGAGATCACCGAAGTATGTGAAgtcaagttcatttttttttctcttttgcacAAATTGCAATTAAAAGAATTTTCAGATCCTCCCAGTTTGGTTTTTGGACTTATGTCCCCCGTGTGTTTTTATCGTTCAGTTTATGCACATGTAAACGTAGAAGTCGTGCATAGGTTGAGCGCAAAGGGCATTTTAGAAAAACAGTCTAAGAAAAAGGCAACCTTCAAGGAATGA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q92878	DNA repair protein RAD50 OS=Homo sapiens OX=9606 GN=RAD50 PE=1 SV=1
Q9JIL8	DNA repair protein RAD50 OS=Rattus norvegicus OX=10116 GN=Rad50 PE=1 SV=1
P70388	DNA repair protein RAD50 OS=Mus musculus OX=10090 GN=Rad50 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001873 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04423 all species →	Rad50_zn_hook	Rad50 zinc hook motif	Motif	Interproscan
PF13476 all species →	AAA_23	AAA domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR004584 all species →	Family	DNA repair protein Rad50, eukaryotes	Interproscan
IPR013134 all species →	Domain	RAD50, zinc hook	Interproscan
IPR038729 all species →	Domain	Rad50/SbcC-type AAA domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR18867 all species →	RAD50	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000723 all species →	Biological Process	telomere maintenance	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006281 all species →	Biological Process	DNA repair	Interproscan
GO:0016887 all species →	Molecular Function	ATP hydrolysis activity	Interproscan
GO:0030870 all species →	Cellular Component	Mre11 complex	Interproscan
GO:0000722 all species →	Biological Process	telomere maintenance via recombination	Interproscan
GO:0000794 all species →	Cellular Component	condensed nuclear chromosome	Interproscan
GO:0003691 all species →	Molecular Function	double-stranded telomeric DNA binding	Interproscan
GO:0006302 all species →	Biological Process	double-strand break repair	Interproscan
GO:0007004 all species →	Biological Process	telomere maintenance via telomerase	Interproscan
GO:0032508 all species →	Biological Process	DNA duplex unwinding	Interproscan
GO:0043047 all species →	Molecular Function	single-stranded telomeric DNA binding	Interproscan
GO:0051880 all species →	Molecular Function	G-quadruplex DNA binding	Interproscan
GO:0070192 all species →	Biological Process	chromosome organization involved in meiotic cell cycle	Interproscan
GO:0090305 all species →	Biological Process	obsolete nucleic acid phosphodiester bond hydrolysis	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
K10866	RAD50; DNA repair protein RAD50	EC:3.6.-.-	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 g21669.t1 across 48 RNA-seq samples of Montipora capitata. 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.

48Samples

48TPM > 0

3Conditions

18.6Max TPM

7.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole organisms · ambient pH treatment	21	21	6.97	18.59
whole organisms · low pH treatment	15	15	8.06	16.31
whole organisms · extra low pH treatment pH treatment	12	12	7.64	12.82

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11452263	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	18.59
SRR11452250	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	12.79
SRR11452246	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	10.96
SRR11452254	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	10.12
SRR11452217	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	9.50
SRR11452252	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	8.68
SRR11452251	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	8.65
SRR11452230	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	8.28
SRR11452262	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	7.58
SRR11452240	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	7.32
SRR11452222	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	6.31
SRR11452260	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	5.98
SRR11452259	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	5.60
SRR11452228	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	5.42
SRR11452232	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	5.10
SRR11452243	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	4.80
SRR11452237	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	3.46
SRR11452231	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	2.72
SRR11452242	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	2.34
SRR11452233	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	1.62
SRR11452234	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	0.59
SRR11452229	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	16.31
SRR11452247	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	13.91
SRR11452249	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	12.08
SRR11452245	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	11.40
SRR11452218	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	10.84
SRR11452216	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	8.79
SRR11452253	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	6.28
SRR11452224	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	6.22
SRR11452221	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	6.09
SRR11452238	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	5.92
SRR11452223	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	5.72
SRR11452255	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	4.55
SRR11452236	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	4.48
SRR11452258	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	4.46
SRR11452241	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	3.85
SRR11452219	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	12.82
SRR11452248	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	12.27
SRR11452244	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	10.56
SRR11452257	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	9.64
SRR11452227	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	7.77
SRR11452261	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	7.24
SRR11452225	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	6.98
SRR11452226	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	6.83
SRR11452256	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	5.52
SRR11452239	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	4.40
SRR11452220	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	4.24
SRR11452235	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	3.35

Source: CnidoSite RNA-seq expression matrices (MCAPI_TPM, StringTie quantification over 48 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.