Gene detail

Detailed information of g12678.t1 in Montipora capitata

Genomic Location: Sc0000414:169322...177762
NR annotation: XP_029198451.2, RPA-related protein RADX-like [Acropora millepora]
Species Montipora capitata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

g12678.t1

atgatggcggaagacttaacgcaaactgctggttttatttcgcggattaaagccatcgcaggcggggttgaagcacaagaaacctttcaggtgcgagtgttggatatttttaggtacattattgacaagagcttcccgatcgtgaaccccgatttctcggatgctttcgacatactgatcacggatggtcttttcaaaacaaaatgtttgttgtcaccaactctgaattctctcgtttacgacaacaaactgaggaaagactctgtcgtgtcaatcactgaatgcagttccttgatcgacgaagaatcgttggagcaatcaccttgtgttatacttcaaggcatcgagattttagattcagcactgttagacacgcaagatcgttttcaagatattgtgttttgtgaaaatgcaactccaaacgaaaaacaagatttgcctttgttagggtcccgtgggtattacttgccgttgcggaacgatgaagacttttttggatcaaagtggtatactgatccagacttaaaactggtaaatccgataagtaatgcaattacaatcgcagatctcgattctttttggaaagctcttccgcggccatttccagcattgatcggcaggatcgtgagcaaaacaaggctgaatcactacggaaaatcttcagatgaaaagcggagatatccctaccaagtgtccctcgagctagaagataggacagcaactgtaacggtgtgtatctgggattacttgtgtgtcctgctctacaactacctacaagttggcgacattgtagcaattttgaactatcgtgtttcccggaagtttggtcctcgaagtaatgctgtgtacaatacgtgcgatgctgtaaatattgagatctctgtaaatccctcaaacccggttgctgaggtatataaattacccgaggaggaacttggtccagagtggagattaccagatgttccatacagatttataagtaggagatctctgtcaaactatccatcaggattaatctttgatgttgttggaactgtggtgtttgtcggccgtgaaatccgagaaagaaaaggaagtagtacttcattctggacatcaaaatgggttcacctcaaagatggaacaagctctctgccaatcatccttcaactttatggctcttcgcagcctgcacagtttgactccattgcagttggaaacatcctcgttggtgctcgcatgcttctcaaaatagagactctagactcgaaacaccgcaaatgctgcttcttcaccacaacccgtgaaacgcaactatacgttataaagaaaccttccgacgcaaacaacaaaccgttctcgggctttggtgtcatcgaggaatccatcaaatggcggcagtcactcgaggctaaacagctcctaagagagtcttgtaatagcggttattacgactttccaccgttgcctcactcgcttgaatcgtacaagaggatctttcctccagaaaaaccgatggatttgatcacaacagtgaatcttggctttgtgctgaaggagttgcattatcgcgaacgcgtaagactacacattcaagctactattgtagctctggaatttgtgccttttgccagcagcgagacatcttcgcagcaaacgtctggcgaacgtagttgctcgcaactaaatgaagttcatgttgacgatgaaagggagcaagcgtcgccatcggcttgtcccggtattcaatcaagtggcaagaattccacaacttcttcaagccaagaaagcagatcacgatcaagcgctgaatctttcgaaagtgaacgcaagaaactgaaagaaaacaaaacaagtcgaatgcaaacacgcagtatgaaaacgttagttgaaaatgattcagacagcgacgacgaattaactgcttcaattggaaaaacaaagaaagcatctgtcaaagatactaagagagttcttcccagcagaagatgtaaaaaagttttccgtaaacttcctaaacttgtgcgtgggaaaactaaagcaaaacacgaggccgatgaaaatgtacctcccgagagaaaacgtaaaggaaaagaaaaggacattcacttacctagaaaagcgaagaagcaagcagcgacgcggagacccgatacatcactcgatgaaacaaagaaaagaaaaaagttgaaaagtcgtcagcgttcatcaaagaaacgaaaagaagaaatttctcagacaacagaagacaacgagagaaggatctctttaaattcaacccaaccagagaaatattttcccttcaggattttagatgaaacttggctgcagatctcggtagacacaccatacgttggcttgtgcaagcccagctgtcacgacgagacctttccgaggttctgcagtcggggaccacacgagatacgagcggtcccgagtgccgaccgccaaggctttgtaaacagcgaaggttactggcggctcatgttggtgggattgaatcggagaacaattatcaacgctattttcatgccagcagggcctcagaaaactgccgacctatacggagaacccgaagacggtgctttcatgactgcgttaactacgggagcgtttgcaggctggtatcctgtggaagcccttctaaatcgcgcagaagaggagctgaaaggaaggagaatggttttcgtgttggacttatatagtcacggtgaagaaaaagttgaaatagttataaacagggcttattga

Transcript

g12678.t1

ATGATGGCGGAAGACTTAACGCAAACTGCTGGTTTTATTTCGCGGATTAAAGCCATCGCAGGCGGGGTTGAAGCACAAGAAACCTTTCAGGTGCGAGTGTTGGATATTTTTAGGTACATTATTGACAAGAGCTTCCCGATCGTGAACCCCGATTTCTCGGATGCTTTCGACATACTGATCACGGATGgtcttttcaaaacaaaatgtttgttGTCACCAACTCTGAATTCTCTCGTTTACGACAACAAACTGAGGAAAGACTCTGTCGTGTCAATCACTGAATGCAGTTCCTTGATCGACGAAGAATCGTTGGAGCAATCACCTTGTGTTATACTTCAAGGCATCGAGATTTTAGATTCAGCACTGTTAGACACGCAAGATCGTTTTCAAGATATTGTGTTTTGTGAAAATGCAACTCCAAACGAAAAACAAGATTTGCCTTTGTTAGGGTCCCGTGGGTATTACTTGCCGTTGCGGAACGATGAAGACTTTTTTGGATCAAAGTGGTATACTGATCCAGACTTAAAACTGGTAAATCCGATAAGTAATGCAATTACAATCGCAGATCTCGATTCTTTTTGGAAAGCTCTTCCGCGGCCATTTCCAGCATTGATCGGCAGGATCGTGAGCAAAACAAGGCTGAATCACTACGGAAAATCTTCAGATGAAAAGCGGAGATATCCCTACCAAGTGTCCCTCGAGCTAGAAGATAGGACAGCAACTGTAACGGTGTGTATCTGGGATTACTTGTGTGTCCTGCTCTACAACTACCTACAAGTTGGCGACATTGTAGCAATTTTGAACTATCGTGTTTCCCGGAAGTTTGGTCCTCGAAGTAATGCTGTGTACAATACGTGCGATGCTGTAAATATTGAGATCTCTGTAAATCCCTCAAACCCGGTTGCTGAGGTATATAAATTACCCGAGGAGGAACTTGGTCCAGAGTGGAGATTACCAGATGTTCCATACAGATTTATAAGTAGGAGATCTCTGTCAAACTATCCATCAGGATTAATCTTTGATGTTGTTGGAACTGTGGTGTTTGTCGGCCGTGAAATCCGAGAAAGAAAAGGAAGTAGTACTTCATTCTGGACATCAAAATGGGTTCACCTCAAAGATGGAACAAGCTCTCTGCCAATCATCCTTCAACTTTATGGCTCTTCGCAGCCTGCACAGTTTGACTCCATTGCAGTTGGAAACATCCTCGTTGGTGCTCGCATGCTTCTCAAAATAGAGACTCTAGACTCGAAACACCGCAAATGCTGCTTCTTCACCACAACCCGTGAAACGCAACTATACGTTATAAAGAAACCTTCCGACGCAAACAACAAACCGTTCTCGGGCTTTGGTGTCATCGAGGAATCCATCAAATGGCGGCAGTCACTCGAGGCTAAACAGCTCCTAAGAGAGTCTTGTAATAGCGGTTATTACGACTTTCCACCGTTGCCTCACTCGCTTGAATCGTACAAGAGGATCTTTCCTCCAGAAAAACCGATGGATTTGATCACAACAGTGAATCTTGGCTTTGTGCTGAAGGAGTTGCATTATCGCGAACGCGTAAGACTACACATTCAAGCTACTATTGTAGCTCTGGAATTTGTGCCTTTTGCCAGCAGCGAGACATCTTCGCAGCAAACGTCTGGCGAACGTAGTTGCTCGCAACTAAATGAAGTTCATGTTGACGATGAAAGGGAGCAAGCGTCGCCATCGGCTTGTCCCGGTATTCAATCAAGTGGCAAGAATTCCACAACTTCTTCAAGCCAAGAAAGCAGATCACGATCAAGCGCTGAATCTTTCGAAAGTGAACGCAagaaactgaaagaaaacaaaacaagtcgAATGCAAACACGCAGTATGAAAACGTTAGTTGAAAATGATTCAGACAGCGACGACGAATTAACTGCTTCAattggaaaaacaaagaaagcatCTGTCAAAGATACTAAGAGAGTTCTTCCCAGCAGAAGATGTAAAAAAGTTTTCCGTAAACTTCCTAAACTTGTGCGTGGGAAAACTAAAGCAAAACACGAGGCCGATGAAAATGTACCTCCCGAGAGAAAacgtaaaggaaaagaaaaggacaTTCACTTACCTAGAAAAGCGAAGAAGCAAGCAGCGACGCGGAGACCCGATACATCACTcgatgaaacaaagaaaagaaaaaagttgaaaagtcGTCAGCGTTCATCAAAGAAACGAAAAGAAGAAATTTCTCAGACAACAGAAGACAACGAGAGAAGGATCTCTTTAAATTCAACCCAACCAGAGAAATATTTTCCCTTCAGGATTTTAGATGAAACTTGGCTGCAGATCTCGGTAGACACACCATACGTTGGCTTGTGCAAGCCCAGCTGTCACGACGAGACCTTTCCGAGGTTCTGCAGTCGGGGACCACACGAGATACGAGCGGTCCCGAGTGCCGACCGCCAAGGCTTTGTAAACAGCGAAGGTTACTGGCGGCTCATGTTGGTGGGATTGAATCGGAGAACAATTATCAACGCTATTTTCATGCCAGCAGGGCCTCAGAAAACTGCCGACCTATACGGAGAACCCGAAGACGGTGCTTTCATGACTGCGTTAACTACGGGAGCGTTTGCAGGCTGGTATCCTGTGGAAGCCCTTCTAAATCGCGCAGAAGAGGAGCTGAAAGGAAGGAGAATGGTTTTCGTGTTGGACTTATATAGTCACGGTgaagaaaaagttgaaatagttATAAACAGGGCTTATTGA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q6NSI4	RPA-related protein RADX OS=Homo sapiens OX=9606 GN=RADX PE=1 SV=2
B2GV47	RPA-related protein RADX OS=Rattus norvegicus OX=10116 GN=Radx PE=2 SV=1
Q8C779	RPA-related protein RADX OS=Mus musculus OX=10090 GN=Radx PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0009950 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF17659 all species →	DUF5521	Family of unknown function (DUF5521)	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR012340 all species →	Homologous_superfamily	Nucleic acid-binding, OB-fold	Interproscan
IPR040893 all species →	Family	RPA-related protein RADX	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR14944 all species →	RPA-RELATED PROTEIN RADX	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003697 all species →	Molecular Function	single-stranded DNA binding	Interproscan
GO:0005657 all species →	Cellular Component	replication fork	Interproscan
GO:0006282 all species →	Biological Process	regulation of DNA repair	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 g12678.t1.

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

Expression pattern (RNA-seq)

Transcript abundance of g12678.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

47TPM > 0

3Conditions

35.6Max TPM

13.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole organisms · ambient pH treatment	21	21	13.32	35.60
whole organisms · low pH treatment	15	14	15.18	35.60
whole organisms · extra low pH treatment pH treatment	12	12	13.05	30.92

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11452250	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	35.60
SRR11452254	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	32.81
SRR11452259	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	32.24
SRR11452260	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	28.91
SRR11452246	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	28.79
SRR11452252	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	26.18
SRR11452242	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	12.09
SRR11452243	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	10.56
SRR11452237	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	10.22
SRR11452234	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	9.11
SRR11452233	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	7.97
SRR11452232	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	7.69
SRR11452231	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	5.69
SRR11452222	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	5.45
SRR11452263	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	4.69
SRR11452228	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	4.68
SRR11452230	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	4.45
SRR11452262	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	4.28
SRR11452240	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	4.06
SRR11452251	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	2.43
SRR11452217	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	1.86
SRR11452247	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	35.60
SRR11452253	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	35.43
SRR11452249	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	30.86
SRR11452258	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	26.03
SRR11452245	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	25.86
SRR11452255	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	19.03
SRR11452238	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	13.54
SRR11452236	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	11.94
SRR11452241	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	11.89
SRR11452218	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	4.60
SRR11452221	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	4.01
SRR11452224	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	3.24
SRR11452223	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	3.13
SRR11452216	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	2.49
SRR11452229	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	0.00
SRR11452244	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	30.92
SRR11452248	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	29.05
SRR11452257	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	26.51
SRR11452256	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	24.28
SRR11452239	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	13.70
SRR11452235	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	12.08
SRR11452227	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	4.73
SRR11452226	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	4.58
SRR11452225	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	4.05
SRR11452219	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	3.33
SRR11452261	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	2.55
SRR11452220	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	0.84

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.