Gene detail

Detailed information of FUN_005045-T1 in Siderastrea siderea

Genomic Location: contig_4:1625779...1660753
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

FUN_005045-T1

ATGGCGGCTGAAACAAGTCCCTTGAAGGATATAATGAATGAGCAAAACACTAATAAAGATGCGTTCGCCACCAAGAAGAAAAAGCGAATGTCAGTGGAGCGAATCTACCAGAAGAAAACCCAGTTGGAACACATACTCTTGCGTCCAGACACGTACATTGGTTCTGTGGAGCCAATCAAGCAGAGCATGTGGGTCTACGATGAAGAGCTGTCAGCCATTGTTAGCAAGGAGATAACATACGTACCTGGTCTGTACAAGATTTTTGATGAATTGTTAGTCAATGCAGCGGACAACAAGCAAAGGGATCCTGCTATGGGCTGTATTAAAATCACCATTGATGCCGAGAATAACACTATCAGTGTTTGGAATGATGGACGTGGAATTCCTGTCGAAATGCATAGGGAGCAGAAAGTCTTTGTACCCACGTTAATATTTGGTCACCTTCTTACGTCGTCTAACTACAACGATGCTGAAAAGAAAGTAACAGGAGGGCGAAACGGCTATGGGGCAAAACTCTGCAACATTTTCAGCACAAAGTTTGTGGTTGAGACCTGTTCCTCTGAATCTGGGAAGAAATTTAAACAGACCTGGACAAACAACATGGGTAAAGCTGCTGAACCAATTGTGAAGGATTTTAGCGGAAAGGATTTCACCTGCATTACATTCAAGCCTGATTTGGCCAAATTTAAAATGGAAACTCTGGACAGTGACACTATCTCACTGCTGTCAAGGAGGGCTTATGATGTAGCTGGCTCTGTGAGGGGAATTGCTGTTTATCTCAATGGCAAGAAATTACCGATTAAATCATTCAAAGATTATGTGGGACTTTATTTGAAAGCCAGAGATGACGAAGAGGAATTAGCCTTGGGTGATgaggaaaatacaaaaaagcCATCAAATTCTGTTGTGCATGAGGTGGTGAACAAACGCTGGGAAGTGTGTGTCACAACAAGTGTGAAAGGCTTCCAGCAAGCCAGCTTTGTGAACAGCATAGCTACCACCAAGGGAGGAACCCATGTTAATTATGTAACTGATCAAATTGTGGACAAGCTTATGGCAGCAGTGAAAAAGAAGAACAAGGGTGGAATAGAAGTAAAGCCATTTCAGATTAAGAACTACCTATGGATTTTCATCAACTGCTTGATTGAAAACCCAACATTTGACTCGCAAACCAAGGAAAATATGACACTAAGGGCCAAGGCATTTGGATCCACATGTGATTTCAGTGACAAGTTTATTAAACAGGTGACACAGTGTGGTGTTGTTGAACACATCATGAACTGGGTGAAATTCAAAGCACAGAGTCAGCTAAACAAGAAATGTCAGAAAACCAAGTCTAGCAAAATCCGTGGAATTCCTAAACTTGATGATGCTAATGATGCAGGAGGTCGGAACTCAAATCAGTGTACGCTCATCCTTACAGAGGGAGACTCAGCTAAGACATTGGCTGTAAGCGGCTTGAGTGTTGTTGGCAAGGATCACTATGGAGTGTTTCCACTGCGTGGCAAACTGCTTAATGTCCGTGATGCTTCGCACAAGCAGATTCTTGAAAATGCAGAGATCAACAATTTAATCAAGATTCTTGGTCTACAATACAACAAGAAGTATGCCTCAGAGGATGATCTCAAGAGCTTGAGATATGGCCATGTCATGATCATGACAGATCAGGACCAGGATGGCTCGCACATCAAAGGACTTCTCATCAATTTTATTCACAGTAACTGGCCCACCTTGACTCGTTTACCATTTTTGGAAGAGTTCATTACTCCAATTGTAAAGGTAAgcaaaggaaaagaagaaaaagccTTTTACAGTATTCCAGAATACGAAGAGTGGAAAAACAGTACAGACAATGCCAAATCATGGAAAGTGAAGTACTATAAGGGGTTGGGTACGAGCACCCCTAAAGAAGCTAAAGAATACTTTGCTGATATGCACCGTCACCAGATTCAGTTCCACCACGAAGGTTCTGCATGCGATGAAGCCATACTCATGGCATTCAGTAAGAAGAAAGTTAATGACAGAAAAGATTGGCTTACCCGTGCCATGGAAGATCGCAAATGGAGAAGACAACAGGGCCTCCCAGAGGTTTACTTGTATGAAAAGGACACAAAGACAGTTTCATACTCAGATTTTGTCAACAAAGaacttattttgttctcaaatgCAGACAATGAAAGATCAATTCCCTGCTTGGTTGATGGCCTAAAACCAGGACAGAGAAAGGTTCTTTTCACCTGCTTAAAGAGGAATGACAAGAGAGAGGTCAAAGTAGCTCAGCTTGCTGGGTCTGTTGCTGAGCTGTCTGCATACCACCATGGTGAGCAAAGTCTTATGGGAACCATCATCAACTTGGCTCAGAATTTTGTCGGCAGCAATAACGTCAACTTGCTGCAACCAATTGGCCAGTTTGGTACCCGCATTCACGGTGGAAAAGATGCTGCCAGTCCTCGTTACATCTTCACCATGCTGAGTCCTCTAACAAAGCTATTGTTCCCTGTGCATGACATGCCAAACCTGACTTACTTGTATGACGACAACCAACCTGTTGAACCAGAATGGTACTGTCCTATACTGCCCACTGTTCTTATTAACGGCGCTGAGGGGATTGGAACTGGTTACAGCACCAAGGTGCCCAATTTTGATGTGCGACAGGTCGTTGACAATCTGAAGAAAATGATCAATGGGGAAGAACCAGAAGAAATGaTGCCGACATACAAGAACTTCACAGGAACTATCACTCAAAATGACAACCAGAAATACACTGTTCGTGGAAACATAGAAGTTGTTGACACCAAAACTGTTGAAATCACTGAGTTACCAATTGGAACCTGGACACAGGCTTACAAAGAGAATGTCTTGGAACCAATGCTTCATGGATCAGAGAAAGTTCCTCCGGTTATAACTGATTACAAGGACCACTACACAGACACGACAGTGAAATTTTTGCTCAGCATGACAGAGGACAAGTTGGCTGAGGCTGAGCAGGCAGGACTACACAAGAAGTTCAAGCTGGAAAGTACAATTGCCACCAGCAATATGGTCTTGTTTGATGCCATGGGCTGTCTGCGCAAGTATGAATCAGCTCTTGATATACTCAAAGAATTTTTTGAGCTTCGCCTGGAAAGATACGCAATCCGCAAAGCTTATTTGGAGGGAATGCTAGCAGCTGAATCTGAGAAACTGAACAGCCAGGCTCGCTTTATTCTGGAAAAGATTGAAGGACATATCATAATTGAGAACAGAACGAAGCGTGATGTAATCACTACCCTTGTGCAGCGAGGTTATCCCTCGGATCCTGTCAAGGCCTGGAAAGAGCTTCAGAAATCAAGCGGACCAGAGGAGGATGTTGACGATGCTTCTAGTGTGGCGAGTTCTGCATCAAGTGCTGGCGGCCCAGACTTCAACTACTTGCTATCCATGTCGCTGCTGTCGCTGTCCAGAGAGAAGAAGGAAGAGCTCCTGAAAGAACGAGATAACAAGGCAGAGGAGCTCCAGGTATTGCGTGGCAAGTCACCTCAAGGCCTGTGGCATGAGGATCTTGATATGTTCATGGAGGAACTGGAGGTTTGTAAAAATAGTAACAACCATCTATTTTCTCGTCACAGTATCGCTACGTGA

Transcript

FUN_005045-T1

Protein

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02518 all species →	HATPase_c	Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase	Domain	Interproscan
PF16898 all species →	TOPRIM_C	C-terminal associated domain of TOPRIM	Family	Interproscan
PF01751 all species →	Toprim	Toprim domain	Family	Interproscan
PF00521 all species →	DNA_topoisoIV	DNA gyrase/topoisomerase IV, subunit A	Family	Interproscan
PF00204 all species →	DNA_gyraseB	DNA gyrase B	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR013760 all species →	Homologous_superfamily	DNA topoisomerase, type IIA-like domain superfamily	Interproscan
IPR002205 all species →	Domain	DNA topoisomerase, type IIA, domain A	Interproscan
IPR003594 all species →	Domain	Histidine kinase/HSP90-like ATPase	Interproscan
IPR031660 all species →	Domain	C-terminal associated domain of TOPRIM	Interproscan
IPR006171 all species →	Domain	TOPRIM domain	Interproscan
IPR036890 all species →	Homologous_superfamily	Histidine kinase/HSP90-like ATPase superfamily	Interproscan
IPR050634 all species →	Family	DNA Topoisomerase II Enzyme	Interproscan
IPR013759 all species →	Homologous_superfamily	DNA topoisomerase, type IIA, subunit B, C-terminal	Interproscan
IPR001241 all species →	Family	DNA topoisomerase, type IIA	Interproscan
IPR020568 all species →	Homologous_superfamily	Ribosomal protein uS5 domain 2-type superfamily	Interproscan
IPR018522 all species →	Conserved_site	DNA topoisomerase, type IIA, conserved site	Interproscan
IPR013757 all species →	Homologous_superfamily	DNA topoisomerase, type IIA, alpha-helical domain superfamily	Interproscan
IPR014721 all species →	Homologous_superfamily	Small ribosomal subunit protein uS5 domain 2-type fold, subgroup	Interproscan
IPR001154 all species →	Family	DNA topoisomerase II, eukaryotic-type	Interproscan
IPR013758 all species →	Homologous_superfamily	DNA topoisomerase, type IIA, domain A, alpha-beta	Interproscan
IPR034157 all species →	Domain	DNA topoisomerase 2, TOPRIM domain	Interproscan
IPR013506 all species →	Domain	DNA topoisomerase, type IIA, subunit B, domain 2	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10169 all species →	DNA TOPOISOMERASE/GYRASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003918 all species →	Molecular Function	DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0006265 all species →	Biological Process	DNA topological change	Interproscan
GO:0000712 all species →	Biological Process	resolution of meiotic recombination intermediates	Interproscan
GO:0000819 all species →	Biological Process	sister chromatid segregation	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006259 all species →	Biological Process	DNA metabolic process	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
K03164	TOP2; DNA topoisomerase II	EC:5.6.2.2	Chromosome and associated proteins	ko03036	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_005045-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

15TPM > 0

7Conditions

189.6Max TPM

10.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
holobiont · low.pH_high.temp	20	3	21.58	189.58
holobiont · low.pH Control.temp	20	1	3.38	67.67
holobiont · control.pH_high.temp	20	4	12.75	105.98
holobiont · control.pH Control.temp	19	1	2.88	54.64
Whole organism	4	4	16.80	19.08
unannotated	1	1	15.61	15.61
live coral tissue/skeleton	1	1	19.57	19.57

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR22214402	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	189.58
SRR22214412	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	189.54
SRR22214410	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	52.52
SRR22214403	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214404	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
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
SRR22214407	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214408	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
SRR22214413	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214414	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214415	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
SRR22214418	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
SRR22214420	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214421	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214423	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214429	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	67.67
SRR22214424	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214425	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
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
SRR22214428	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214430	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214431	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
SRR22214435	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214436	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214437	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214438	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
SRR22214442	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214443	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214445	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214464	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	105.98
SRR22214462	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	57.96
SRR22214459	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	57.26
SRR22214446	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	33.84
SRR22214447	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
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
SRR22214451	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
SRR22214453	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214454	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214456	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214457	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214458	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214460	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214461	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214463	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214465	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214467	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
SRR22214468	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	54.64
SRR22214400	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214411	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214422	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214433	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214444	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
SRR22214466	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214469	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
SRR22214481	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
SRR22214506	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214524	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
SRR22214547	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR22214548	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	19.08
SRR14295603	Whole organism	Whole organism	not recorded	not recorded	SRP315757	17.53
SRR14295601	Whole organism	Whole organism	not recorded	not recorded	SRP315757	17.43
SRR14295600	Whole organism	Whole organism	not recorded	not recorded	SRP315757	13.15
ERR12861049	unannotated	not recorded	not recorded	not recorded	ERP159209	15.61
SRR12454619	live coral tissue/skeleton	live coral tissue/skeleton	not recorded	not recorded	SRP277390	19.57

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.