Gene detail

Detailed information of FUN_048450-T1 in Siderastrea siderea

Genomic Location: contig_70:1782191...1805315
NR annotation: no NCBI-NR hit recorded
Species Siderastrea siderea · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

FUN_048450-T1

TGGTCAGCGGATTTTATAAAACCGCgggaattcaagatggcggtccaGCCAGAAGAAAATGATGCTGCAAATACGATGACAATTCTTGTGGCTACAGATTGCCATCTTGGGTATATGGAAAAAGATCAGGTTAGAGGGAATGATTCACTTGTAACATTTGAGGAAATACTGCAAATAGCAGAAGAGAAGAATgttgattttattttgcttGGTGGGGATCTGTTTCATGAAAACAAACCTTCTCGTAAAACATTACACAGCACCATGGCACTACTTAGGAAGTACTGTCTGGGCGATAAACCTTGCCAGTTAGAGTTCCTCAGTGACCAGTCAGTGAACTTCTCTAATTCTAGGTTTCCTGTGGTTAATTATGAAGATCCAAACTATAACATATCCATTCCAGTGTTCTCAATACATGGAAATCATGATGATCCAGCTGGGGATGGGAACCTTTGTGCCCTGGACTTGCTCAGTGTGTGTGGGTTTGTCAATTACTTTGGAAGAGCGGCGTCAATTGATGACATCACAGTGTCACCCATCTTGATTCAGAAGGGACGTGTCAAACTGGCTCTGTTTGGTTTGGGATCCATCAGAGATGAGCGACTTCACAGGACGTTTTTGAATCAGAGGGTTAAAATGCTAAGACCAAGAGAAGACCCTGACTCTTGGTTCAATGTCTTTGTACTGCATCAAAACAGGTCAAAGCATGGCCTTACTAACTACATCCCAGAAAAGTTCCTGGATGACTTTCTTGATCTTGTGATCTGGGGACACGAACATGAATGCATTATAGATCCAAAGGAACCAGAAGACCCTAACTTGTCTTTTTTCATCAGTCAGCCTGGTTCAAGCGTCGCCACTTCCCTCTGCGAGGGAGAAGCACGAACAAAGCATGTGGGAATCCTTGAAATCACAGAGAACAAAAACTTCCGAATAAACAAGGTGAAATTAAAGACTGTGCGACCTTTCTACATGGAGGATATAGTTTTAAGCAGCACTGACATTGACCCAACCCAGGAAGAGGTGGTAATGGCTTACCTAGTGCAGAAAGTAGAACAATTGATTGAGAAGGCAGAGAGAGAACACTCTGGCAATACTCGGCAGCCTGACAAGCCACTTATAAGGATACGGGTTGATTATAGTGATGGATTCACATCATTTAATATCCGAAGATTTGGACAACAGTTTGTTGACAGGGTGGCCAATCCAAAGGACATTTTACTTTTCTACAGAAGAAAAACACTGCCAGCCAAAGCAGATAAGAAAAACCAGGATGACGTTACACTTCCCCACTTCCGCCCAGAAGCACTAGACACTATCAGAATGGAGGATTTGATCAAAGAATACCTAACATCAAAAGATAATGCATTAGAGCTGCGCATTTTAACAGAGGGCAGAATGGCACAGGCCCTTCGTGAGTTTGTGGAAAAGGATGAAAAAGAAGCCATATCTACACTGGTCAAATGGCAGCTGGATCAAGCACAAAAACACTTGAAGGAAAGGCGCAATGTCCGCGAAGACAACATTGAAGCTGAAGTGTTGAAACACACAGAACAAGTACGACAAAAAGaagatgatgacgacgatgatgatgcaGAAGATATAAGAAGGGTTTTGGCAGAATCTCGTGCCAGCCAACCAAATACTGGACATGATAATGATGGTATGAATGGGAGCAGTGATGACGATAGACCATCTGGGCCAAGTACTAGCAAAGGGAAAAAAGGTGAAGCTGGTACATCTTCAAGGGGTACAGGTGAGGGGCGTGGCAGGGGACGAGGCAGAGGCAGGGGAAGAGGTGGACGTGGACGAGGAAGGGGAGCTTCACAAGCAGCAGCAAACACTTCACGGACTATTATGGACTCATTTAGTTCAGCGTCCAAAAGAAGAAGACAGCCAAGCGATGTAGCAGAGGAAATAATCtctgatgacgatgatgatgaattcAATATTCCTCTGTCATCATCTGTTAAGAAGACAAAGGCTACACAGTAAGTACTTGGCGATAAGAAGTGTAATTAAGTGAAGTTACTCTGCTTAATGAGATTAATAGTCCATAAAAGTGAACTACTGTATGGCCATGTTTGATTCTTTTGTGGACAACCAATAACTCAAATTCATTACACTGAAAAATCACTAAGTTATTCAGGCTTAGTTATCTAATGAAACATTAATGCcatgattttccttttttttttcttgtacaaTTCTTTATTCACCCTTTCATTTCTTTCCTCCTTCCTAATCCACTCTTCATCACCTACCCCGTTACCCTTCCTTTCTTCCATTTTAGTAAACCCCACATCTCCACaagcatattctccttactcttctctatatatttcttatgttactagttgggtgaatttgattaaacagcaacacatttcatgtctggtgattaTTTGCTTTATTCTTCCCTTCTCTTAACCCTATGAGCCCCAATaatgatcagcatcaattttctcctcatcatatcagtgcattataacacataaaggtcatgagaattggggaattgatcactgaagatgaatagtcttgatgtcttaacaagttctcccaattagtactcaatgaaatgtatggagaccagtaaggagaatttgtataatgatactggggcttaaagggttaatgacaTGTTTATACAAaagcattttctttcttttggttgttgttgtttttccacTGTCTGATTTAATGATATTCACTCTATTTATCATCACAGCTTCAtgcaatttttctttgtttgtttgtttttttctactGTCTGATTCAAAGATAAAATACACACTGCTTGAATTTACAGGCCCACACCATCACAGCGGTCAACAACAAGCAGAAACAAGAAAACTGTTGTCAACCTTGCTGATAATGGGGTAAGTTCTTTAATGTTCTGTTTTCAAATTCTTGTGTTGTAGGTTTGTGCTGTGTGTGGTGAAGCAGCATATATAGTGAAGCTACATGTAATGTAGGCCTCAATGATTCCAAGAGAAATTATCCCACTGTTTCTTGTAGGATGAGAGTGACGATTCTGATGATCCATTCTCCATGCAACCAAGCAGTAAAAGAATCAGAAGATAATGCCAGATGAGTCTCGCTAATAATAATTAAGGGTGCATTCTTCAAGGCCTGTTCTGGCTGTTTTTATTCCAGTGTAGATAACTAGTATGGATGTGTGGAATGTCACTTCCCAAAAGAAAGGAATGGGTATTTCTCACAAAAAGAAATTCTTTTGGCAGAGTTGAACTTTAAAGTAACACCTTGAAATAACATGGCCATCTGGGACAAGTCAAGTTTTTCTACCATCTCTGTTACTAGACATCAGATGCCATGccatatttttttgctttaaaagaGTCGTTCCTAGCATTATGGTAGCCACGTGCATGTGTAATTGATTAAAAGTCTAGTAtacttttgtcttcttttttgaAGTGTTTTTTTCATCCTCCTCTTAGGGACAAAAACTGTAAAGAGAATAGCTCTCTTTAataagttaaccctttaagcccaaacagtgacaaaaatggaatttctctttacattattactacttgttcaaacattatattcaagtggtgagaataaaggaagtgttCACCAAGGATATGTCtcgatatttagacaaattcctcttactagttccataagaaatgtatggagaacagtaaggagaatacgcatttttatgtcagggcttaaagggttaaacacaTTTTATTGGCTGTTACAGGCTTATCCCATAATGTTTCTTCTAAGCCTCCAACGTGTGCACCCTGTAATTTTTGATCAGTGATCTTCACCTTGTAAACTTAAGACAGTTTgcacaaagaacaaaaaatgtTGCCATAGTGATTGTTTCCATTTCTCAACACAGAGTTTGATAAACC

Protein

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04152 all species →	Mre11_DNA_bind	Mre11 DNA-binding presumed domain	Domain	Interproscan
PF00149 all species →	Metallophos	Calcineurin-like phosphoesterase	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR007281 all species →	Domain	Mre11, DNA-binding	Interproscan
IPR038487 all species →	Homologous_superfamily	Mre11, capping domain	Interproscan
IPR003701 all species →	Family	DNA double-strand break repair protein Mre11	Interproscan
IPR029052 all species →	Homologous_superfamily	Metallo-dependent phosphatase-like	Interproscan
IPR041796 all species →	Domain	Mre11 nuclease, N-terminal metallophosphatase domain	Interproscan
IPR004843 all species →	Domain	Calcineurin-like phosphoesterase domain, ApaH type	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10139 all species →	DOUBLE-STRAND BREAK REPAIR PROTEIN MRE11	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004519 all species →	Molecular Function	endonuclease activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006302 all species →	Biological Process	double-strand break repair	Interproscan
GO:0030145 all species →	Molecular Function	manganese ion binding	Interproscan
GO:0004520 all species →	Molecular Function	DNA endonuclease activity	Interproscan
GO:0008296 all species →	Molecular Function	3'-5'-DNA exonuclease activity	Interproscan
GO:0030870 all species →	Cellular Component	Mre11 complex	Interproscan
GO:0016787 all species →	Molecular Function	hydrolase activity	Interproscan
GO:0000014 all species →	Molecular Function	single-stranded DNA endodeoxyribonuclease activity	Interproscan
GO:0000723 all species →	Biological Process	telomere maintenance	Interproscan
GO:0000724 all species →	Biological Process	double-strand break repair via homologous recombination	Interproscan
GO:0006303 all species →	Biological Process	double-strand break repair via nonhomologous end joining	Interproscan
GO:0007095 all species →	Biological Process	mitotic G2 DNA damage checkpoint signaling	Interproscan
GO:0031573 all species →	Biological Process	mitotic intra-S DNA damage checkpoint signaling	Interproscan
GO:0035861 all species →	Cellular Component	site of double-strand break	Interproscan
GO:0042138 all species →	Biological Process	meiotic DNA double-strand break formation	Interproscan
GO:0097552 all species →	Biological Process	mitochondrial double-strand break repair via homologous recombination	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
K10865	MRE11; double-strand break repair protein MRE11	-	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 FUN_048450-T1 across 85 RNA-seq samples of Siderastrea siderea. 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.

85Samples

67TPM > 0

7Conditions

500.8Max TPM

91.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
holobiont · low.pH_high.temp	20	15	73.53	187.63
holobiont · low.pH Control.temp	20	14	92.88	361.51
holobiont · control.pH_high.temp	20	17	114.43	500.77
holobiont · control.pH Control.temp	19	15	111.19	358.33
Whole organism	4	4	8.73	15.01
unannotated	1	1	7.43	7.43
live coral tissue/skeleton	1	1	11.34	11.34

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR22214420	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	187.63
SRR22214414	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	140.56
SRR22214403	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	131.58
SRR22214407	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	128.59
SRR22214421	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	115.20
SRR22214402	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	115.04
SRR22214413	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	106.77
SRR22214406	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	101.94
SRR22214410	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	93.29
SRR22214418	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	91.93
SRR22214412	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	76.25
SRR22214423	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	70.19
SRR22214415	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	61.65
SRR22214404	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	29.51
SRR22214408	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	20.44
SRR22214405	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214409	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214416	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214417	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214419	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214425	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	361.51
SRR22214435	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	239.89
SRR22214424	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	238.65
SRR22214431	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	147.66
SRR22214443	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	141.43
SRR22214442	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	137.34
SRR22214428	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	121.03
SRR22214445	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	118.42
SRR22214429	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	97.02
SRR22214438	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	90.16
SRR22214437	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	67.52
SRR22214436	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	48.37
SRR22214427	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	30.24
SRR22214430	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	18.28
SRR22214426	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214432	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214434	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214439	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214440	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214441	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214451	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	500.77
SRR22214462	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	303.17
SRR22214450	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	163.05
SRR22214454	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	156.81
SRR22214447	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	137.66
SRR22214465	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	127.66
SRR22214446	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	126.98
SRR22214467	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	116.68
SRR22214453	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	103.47
SRR22214456	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	97.61
SRR22214464	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	94.82
SRR22214457	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	91.56
SRR22214459	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	79.40
SRR22214460	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	59.47
SRR22214458	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	51.88
SRR22214461	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	42.89
SRR22214463	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	34.68
SRR22214448	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214449	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214452	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214444	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	358.33
SRR22214524	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	269.25
SRR22214469	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	230.95
SRR22214481	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	181.28
SRR22214468	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	172.94
SRR22214506	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	151.17
SRR22214466	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	137.38
SRR22214471	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	135.49
SRR22214470	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	108.99
SRR22214547	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	106.70
SRR22214411	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	90.47
SRR22214422	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	55.59
SRR22214548	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	55.00
SRR22214535	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	35.12
SRR22214400	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	23.99
SRR22214433	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214455	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214492	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214546	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR14295604	Whole organism	Whole organism	not recorded	not recorded	SRP315757	15.01
SRR14295603	Whole organism	Whole organism	not recorded	not recorded	SRP315757	8.62
SRR14295601	Whole organism	Whole organism	not recorded	not recorded	SRP315757	5.80
SRR14295600	Whole organism	Whole organism	not recorded	not recorded	SRP315757	5.50
ERR12861049	unannotated	not recorded	not recorded	not recorded	ERP159209	7.43
SRR12454619	live coral tissue/skeleton	live coral tissue/skeleton	not recorded	not recorded	SRP277390	11.34

Source: CnidoSite RNA-seq expression matrices (SSIDE_TPM, StringTie quantification over 85 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.