Gene detail

Detailed information of FUN_60736-T1 in Siderastrea siderea

Genomic Location: contig_3:16174876...16188480
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_60736-T1

attgttACACGTATATCTTGATCAAGGTATGATTAGAAAATAGTTTGTGAGACTTTTGGTGAAATTTTCACAGAATCCCATAGCAAAAGTTGTTAGCACTTCATCACGCCCTAAGAGCAAGTGGAGACCTCTGCCATTAGACACTGTGGAACTTGAAAAACTGGCCTCCCGAAAGCTGAAAATAAATGCTaaagaaacaatgaaaataGCTGAAAAACTCTACAACCAAGGGTTCATCAGTTATCCGCGCACAGAAACCAACATGTTTCCGAAATCTTTGGACTTGAGGCCTCTTGTTCAAAACCAAACTGTTGATGCTAACTGGGGAGCATTTGCTGCCAGTGTGCTAGAAAGAGGCCCCAACCCTcgtcatggcaacaaaacagACAATGCTCACCCCCCCATCCACCCCACAAAGTACACAGATGGTTTACAGGGCAATGAAAAGAGATTGTATGAGTTTATAGTGAGGCACTTTTTAGCCTGCTGTTCTGAGGATGCAAAAGGTCAAGAGACAAATGTGGAAATTGAGATTGCTGGTGAGAAGTTTACAGCCACAGGACTTATGATCACTGCACGGAACTATCTTGATGTGTATCCATATGACAAGTGGAATGCAAAGACTATTCCAGTGTATAACCAAGGTGAAGAATTTCAACCCAGCTCCATTGAGATGCTCGATGGTGAAACTAAACCTCCTCCACTGTTGACTGAAGCTGACTTGATTGCTTTGATGGAAAAGCATGGTATAGGCACTGATGCTACTCATGCAGAGCACATTGAGACCATAAAGAACAGGTGCTATGTGGGGGTGCAGCAAGATGGGACCTTTCTGCCAGGACAGCTTGGAATGGGACTAGTTGAAGGTTATGATCTGATGGGATTTGAGCTTTCAAAACCAAGACTGAGGGCCGAGCTTGAAGCTGATTTAAAAAGAATTTGTGAAGGAACAAGAAACAAGGATGATGTACTGGTAGAGCAAGTAGCAAAGTACAAGGAGCAGTTTATTCAAGCTGTCCAAGAGGCAGTCAAATTGGATCAGGCATTAGCAAATTATTTTGGGGATCCTCAAGAATTTATCGATGaagTTCTTGGTAGTGAGGATGAAAGAGGACCAGAACCACTTCGTCTTTGTCCAAGGTGCCAAATAGAACAGATGGTTCTCAAGAAAACTAAGGATGGCAGCTACATGATTGGCTGCCAAGGCTACCCAAGATGCCGTTCCAGTGCCTTTTTCCCAAAGTTTGTGACTGAGGCCGCAGTGCACGAGTCTGTGTGTCAAAAGTGCCGACCAGGAGATGTACATAAAATCAGATTTAAATTCTTGAAAGGCTCTGTTCCACCCATGATGCCTTTGGAGTACGTAGGCTGTGTTGGTGGATGTGATGAAACACTTAGAGAATTATTGAACTTGAAAGACTTGACAAGACTACCCTCAGAGTCAGGTGGATCAAATTCATTTGGAAGAGGAGGACGAAACTCTCAGACCAGTAGCAGAGTAAGCCAGCGTTCCATGGGGCGTGGTCAAGGCAATGCTAGCAAAACCAGAGGAGGTGGCAGTAGACCCGCTCCGGCTCAACATGTTACGGGTCCTGTCCAAAGAGGAGGTTCAGGGTTTAATCAGTTTTCTTCGGGAGGATTATTTGGAAGGGATGATAATGAGAACTGTGTGGTTTGCGCTTGTGGACAGCCTGCAAGCCAGTTCACTGTCAAAAAAGATGGACCTAACAAAGGTCGACCATTTTACAAGTGCTCTAACAGAGACAACGGCTGTGGGTTTTTCTTGTGGGCTGACGATGATTCAGGGAGTACCTCCTCATCGTCATTTAGTCATACAGCGCCCCTTGCACCATCCAATAACTTTAACAGGAATAACACAGGTACTTATTTTACTCATTGTTGTCGCACTCCCACCATCACCGTTTTTTTGCGAGGGGCTAAGATTCTGCTAAAGGTAGTTTTACCATTCAAATAACTGTCTTGGTTCTACACATGAACCTGTTTAAATATGGGGACCAAGCTCACCAGAGTTTTCCCTGTAGCTTTATTGTTAGAGTATGCGACCCGTGGTTATGGCTT

Protein

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01131 all species →	Topoisom_bac	DNA topoisomerase	Family	Interproscan
PF01396 all species →	zf-C4_Topoisom	Topoisomerase DNA binding C4 zinc finger	Domain	Interproscan
PF06839 all species →	zf-GRF	GRF zinc finger	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR013497 all species →	Domain	DNA topoisomerase, type IA, central	Interproscan
IPR013498 all species →	Domain	DNA topoisomerase, type IA, zn finger	Interproscan
IPR023405 all species →	Homologous_superfamily	DNA topoisomerase, type IA, core domain	Interproscan
IPR013826 all species →	Homologous_superfamily	DNA topoisomerase, type IA, central region, subdomain 3	Interproscan
IPR010666 all species →	Domain	Zinc finger, GRF-type	Interproscan
IPR000380 all species →	Family	DNA topoisomerase, type IA	Interproscan
IPR013824 all species →	Homologous_superfamily	DNA topoisomerase, type IA, central region, subdomain 1	Interproscan
IPR003602 all species →	Domain	DNA topoisomerase, type IA, DNA-binding domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11390 all species →	PROKARYOTIC DNA TOPOISOMERASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0003916 all species →	Molecular Function	DNA topoisomerase activity	Interproscan
GO:0006265 all species →	Biological Process	DNA topological change	Interproscan
GO:0005694 all species →	Cellular Component	chromosome	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0003917 all species →	Molecular Function	DNA topoisomerase type I (single strand cut, ATP-independent) activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	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
K03165	TOP3; DNA topoisomerase III	EC:5.6.2.1	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_60736-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

1,488.4Max TPM

218.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
holobiont · low.pH_high.temp	20	15	304.56	1,488.39
holobiont · low.pH Control.temp	20	15	192.18	639.95
holobiont · control.pH_high.temp	20	17	217.67	961.66
holobiont · control.pH Control.temp	19	14	224.97	766.91
Whole organism	4	4	5.60	7.68
unannotated	1	1	6.65	6.65
live coral tissue/skeleton	1	1	4.33	4.33

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR22214412	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	1,488.39
SRR22214408	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	918.79
SRR22214423	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	511.68
SRR22214402	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	495.95
SRR22214407	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	489.17
SRR22214414	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	433.27
SRR22214421	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	393.91
SRR22214403	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	364.68
SRR22214417	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	245.27
SRR22214419	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	176.93
SRR22214409	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	171.11
SRR22214418	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	134.09
SRR22214413	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	122.78
SRR22214415	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	83.55
SRR22214404	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	61.71
SRR22214405	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214406	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214410	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
SRR22214420	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214443	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	639.95
SRR22214445	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	622.58
SRR22214434	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	345.30
SRR22214441	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	288.82
SRR22214429	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	287.02
SRR22214430	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	283.61
SRR22214436	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	245.98
SRR22214439	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	209.13
SRR22214440	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	207.00
SRR22214425	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	166.07
SRR22214424	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	156.22
SRR22214438	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	156.10
SRR22214431	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	104.26
SRR22214428	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	92.74
SRR22214437	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	38.72
SRR22214426	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214427	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
SRR22214435	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214442	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214456	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	961.66
SRR22214467	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	615.79
SRR22214453	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	379.92
SRR22214463	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	355.83
SRR22214465	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	343.74
SRR22214462	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	278.66
SRR22214457	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	247.89
SRR22214458	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	243.09
SRR22214447	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	242.75
SRR22214461	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	182.81
SRR22214452	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	125.75
SRR22214446	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	122.77
SRR22214460	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	85.51
SRR22214459	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	54.45
SRR22214451	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	45.50
SRR22214464	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	35.74
SRR22214454	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	31.48
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
SRR22214450	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214548	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	766.91
SRR22214547	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	691.63
SRR22214481	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	474.01
SRR22214444	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	411.34
SRR22214492	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	326.79
SRR22214400	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	270.65
SRR22214524	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	263.92
SRR22214468	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	239.21
SRR22214506	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	231.55
SRR22214469	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	222.50
SRR22214411	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	136.85
SRR22214422	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	94.77
SRR22214455	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	78.39
SRR22214466	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	65.85
SRR22214433	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214470	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214471	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214535	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
SRR14295600	Whole organism	Whole organism	not recorded	not recorded	SRP315757	7.68
SRR14295601	Whole organism	Whole organism	not recorded	not recorded	SRP315757	6.21
SRR14295603	Whole organism	Whole organism	not recorded	not recorded	SRP315757	5.04
SRR14295604	Whole organism	Whole organism	not recorded	not recorded	SRP315757	3.47
ERR12861049	unannotated	not recorded	not recorded	not recorded	ERP159209	6.65
SRR12454619	live coral tissue/skeleton	live coral tissue/skeleton	not recorded	not recorded	SRP277390	4.33

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.