Gene detail

Detailed information of FUN_057216-T1 in Siderastrea siderea

Genomic Location: contig_119:232263...241127
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_057216-T1

ATGTCTGCGATAGAAATAATCACATCAAaggagaaagaaataaaaattacgGATAAGCAAACCGGAAAGGAGAAAGTGGTGACTGTCAAACTATGGAACGAAACAGTCTCGAATTTAACTCTTATGGCACTTGGTTCATCAGCGCCCGAAATTCTGCTCTCAGCAATTGAAATCTGCGGGAACAATTTTGACGCTGGTGAGCTCGGTCCGTCGACAATTGTCGGTTCTGCAGCGTTCAACCTGCTGGTTATTATTGCAGTGTGTGTTTATGTTATTCCCGATGGCGAGGTCCGCCGAATCAAACATCTCCGAGTATTTGCTATCACAGCGTCCACGTCGGTCCTTGCTTACATCTGGTTATATATTATCCTGGCGGTCTCTTCGAAGGGTGAAGTGGAGATATGGGAAGCTCTTTTAACTTTTGCCTTCTTCCCAATGATGGTCATCGCTGCTTACGTTGCGGATCGCAGGCTGCTCTTCTACAGAGCCTTACGAAAGAGGCAAAGAAGGCAGAAGCGTGGTGGTATGACTGTTCTGCAGACCGGCGATTTCGATATTATTGGTGTCCAAGTGAAGGATGGGTATGTGGACGGAAACGTTGCAGATGGCCGTTACACATCCGACACTGAGGCCGGTCCAGGATTCGATGATGACGAGTTGCTTCACGATCTGACGGAGGATAGGCGCGAAAAGGCCATCCAAGCGCTGAAAGAAATACGACAGAAGTACCCAGATGCCGACCGAGAGACCGTCGAACGTTTGCTGGAGCAGGAAAACCTCAAGCTTCAACCCAAGAGTCGTGCGTTTTATCGCATCGAAGCCACTCGCAAGATGGTGGGCAGTGGAAACGTGCTGAAGATGAAGCATGACAAACTGGAGAAGGCCAGTAGTTCAATAGCAGATGCAAGACTCGAGATGCACGAAGTCGAGTACGAAGACCCACAGGTCGTTCGGGTTTATTTTGATCCCGTCCACTACATTGTCAAGGAAAACTGTGGCAGTGTGTTTATGAACATTTCACGCACCGGCGGTGATCCGAATAACACTGTTTTTGTGGACTTCAGAACGGAAGATGGGACCGCAGAGGCCGGCCAGGATTACGAGAAAACCGAGGGTACGATCTGCTTCAGACCAGGAGAAACCACCAAGACTTTCTCCGTTGTGGTAATCGACGATGACATCTTTGAAGAAGACGAGCATTTCTACGTGCACCTGGGCAATGTTCGAGTAGCCGGCGCTGATGGCGATCTGTTGCGAAACAAGTACCGAGGACCAGCCGGAAAAGTAGGCAAAGACGGTGTAGCTACTATCACAATCCTGGATGATGACTATCCCGGTATCTTCACGTTTGAGGAGGAAAAGCATTCGGTGACTGAAGCAGATGGAACGATTAAACTGAAGGTGATTCGCCACACGGGGGCTCGAGGCACTGTTCGTGTTCCGTACCATACCGTGGAGGGAACTGCTAAAGGCGGTGGCACAGACTACGAGGATGCTGTTGGCGAGTTGGAGTTCGAGAACGACGAAACCTGGAAAAACATTGAAATCAATGTCATAGATGATGAAGAATATGAGAAGAATGAGACCTTCTATGTTGTTCTTGGTGAaccaaaagttgtcaaaaatgaTGAGGATCAGGGTAGTGAAGCTGCTACTGACGAGGTTTATGATGCTGAGAAAGAACGCCTTGAAGAGCTGGGGAAGCCTAGACTAGGTGATTTCCCTAAGGCAGAGGTAACTATTATAGAAAGCAAAGAATTCAAGAACACAGTGGACAAATTGCTTGTTAAAGCCAATTTGGCACTGGTTGTTGGGACCTCTTCTTGGAAAGAGCAGTTTACTGATGCTCTTACAGTAAGTGGCAGTGGTGATGATGACGACAGTGAACAACCTAGCACGCCAACTTACGGAGACTACATGATGCACTACCTGACTGTGTTCTGGAAGCTTTTGTTTGCAGTTGTTCCACCTACTGACATCTGGGGTGGCTGGGCATGCTTTGTGGTATCCATCATCTTTATTGGCTTGTTAACAATGGTGATAGGAGATTTAGCCTCTCACTTTGGCTGTACTATTGGTTTGGCAGACAGTGTGGTTGCCATCACTTTTGTTGCTCTTGGAACAAGTCTCCCAGATACCTTTGCCAGTAAAGTTGCAGCTGTTGGTGATGAATATGCAGATTCATCCATTGGTAACGTCACTGGAAGCAACTCTGTGAACGTCTTCCTTGGACTTGGAGTCGCATGGTCTATAGCAGCAATAGCAAAAGCAGCCAAGGGACAACAATTTAAAGTTGAAGCGGGTTCTCTTGGCTTTTCTGTGGTAGTTTTCTGTTGTACAGCTGTCACTGCTATCACAGTAATGATGCTACGTAGAAATAAAAAGGTTGGGGGAGAGCTTGGTGGGGCTAAGGCCTTCAAACTTCCCACATCATTCTTTTTTACCTTCCTTTGGATACTATATATTGTACTATCTTCTTTACAAACATATTGCCACATCAAGGTAAACTTTTAG

Transcript

FUN_057216-T1

Protein

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01699 all species →	Na_Ca_ex	Sodium/calcium exchanger protein	Family	Interproscan
PF03160 all species →	Calx-beta	Calx-beta domain	Domain	Interproscan
PF16494 all species →	Na_Ca_ex_C	C-terminal extension of sodium/calcium exchanger domain	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR038081 all species →	Homologous_superfamily	CalX-like domain superfamily	Interproscan
IPR051171 all species →	Family	Calcium/Cation Antiporter	Interproscan
IPR003644 all species →	Domain	Na-Ca exchanger/integrin-beta4	Interproscan
IPR004837 all species →	Domain	Sodium/calcium exchanger membrane region	Interproscan
IPR032452 all species →	Domain	Sodium/calcium exchanger domain, C-terminal extension	Interproscan
IPR044880 all species →	Homologous_superfamily	NCX, central ion-binding domain superfamily	Interproscan
IPR004836 all species →	Family	Sodium/calcium exchanger protein	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11878 all species →	SODIUM/CALCIUM EXCHANGER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005432 all species →	Molecular Function	calcium:sodium antiporter activity	Interproscan
GO:0005887 all species →	Cellular Component	plasma membrane	Interproscan
GO:0015491 all species →	Molecular Function	obsolete cation:cation antiporter activity	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0030001 all species →	Biological Process	metal ion transport	Interproscan
GO:0030424 all species →	Cellular Component	axon	Interproscan
GO:0035725 all species →	Biological Process	sodium ion transmembrane transport	Interproscan
GO:0042383 all species →	Cellular Component	sarcolemma	Interproscan
GO:0098703 all species →	Biological Process	calcium ion import across plasma membrane	Interproscan
GO:0098794 all species →	Cellular Component	postsynapse	Interproscan
GO:0007154 all species →	Biological Process	cell communication	Interproscan
GO:0055085 all species →	Biological Process	transmembrane transport	Interproscan
GO:0006816 all species →	Biological Process	calcium ion transport	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
K05849	SLC8A, NCX; solute carrier family 8 (sodium/calcium exchanger)	-	Glycosaminoglycan binding proteins	ko00536	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_057216-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

6TPM > 0

7Conditions

74.6Max TPM

4.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
holobiont · low.pH_high.temp	20	0	0.00	0.00
holobiont · low.pH Control.temp	20	0	0.00	0.00
holobiont · control.pH_high.temp	20	0	0.00	0.00
holobiont · control.pH Control.temp	19	0	0.00	0.00
Whole organism	4	4	65.45	72.48
unannotated	1	1	11.65	11.65
live coral tissue/skeleton	1	1	74.58	74.58

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	0.00
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
SRR22214410	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214412	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
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
SRR22214429	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
SRR22214446	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	0.00
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
SRR22214459	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
SRR22214462	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
SRR22214464	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
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
SRR22214468	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
SRR14295601	Whole organism	Whole organism	not recorded	not recorded	SRP315757	72.48
SRR14295604	Whole organism	Whole organism	not recorded	not recorded	SRP315757	67.93
SRR14295600	Whole organism	Whole organism	not recorded	not recorded	SRP315757	64.05
SRR14295603	Whole organism	Whole organism	not recorded	not recorded	SRP315757	57.36
ERR12861049	unannotated	not recorded	not recorded	not recorded	ERP159209	11.65
SRR12454619	live coral tissue/skeleton	live coral tissue/skeleton	not recorded	not recorded	SRP277390	74.58

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.