Gene detail

Detailed information of FUN_047406-T1 in Siderastrea siderea

Genomic Location: contig_67:936095...957202
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_047406-T1

ATGAGCATTATATTTCATGGTATTTTGGCGCTGTATCTCAAAAATTATGAACAGCCACGTGAATGGAAAATGTGTTGTCTCTCCAGAGTTGTTGCACACTGCTATACTGATGAACTGGAACATTTTCCTCAAGAACTGATAGATGTTCTGCAAAGACACCACAATGTTATGGATGCTGAACTCAGAATGACACTTTGTAGGGCCCTTATACTTCTGAGAAACAAAACCTTGTTATCACCTACAAGCCTTCTAGAGCTGTTTTTTGCATTGTTCAGATGTAAGGATAAGCTACTGAGGCAGGTTTTATACAGTCATGTTGTAACAGATATCAAGAATataaatgcaaaacacaagaaCAATAAAGTTAACACTACACTGCagaattttatgtttacaatGCTCCGAGACAACAATGTCATAGCAGCCAAGAAATCCTTAGACGTGATGGTGGAGCTTTATAGGAGGAACATTTGGAATGATGCAAAAACAGTCAATGTTATTACCACAGCTTGCTTTTCACCTGTGACAAAGATTTTAGTTGCAGCTCTGACATTTTTTCTTGGCAAAGATGATGGCGATAAAGATAAAGAGGACAGTGATAGTGACGAGGAGGTAGACCAGTCTACGATTAGACGAATGCTCCATGCCAGCGGTGTAAGCAAGAAAACCTTGAAAAAGAAACATAAAATTGATAAGGCCATGGCAAGTTTCAAGaaacaaaagaaaaagcacCAAAACACGTCTGTTGTCAATTTTTCTGCTCTTCACCTTATTAATGACCCGCAAGGTTTTAGTGAAAGATTATTTAAGCAGCTTGAGTCATCAACAGAAAGATTTGAGGTGAAAGTGATGATGATGGACCTGATATCAAGACTTGTTGGCATTCACCAGCTCTTCTTGTTCAACTTTTATCCATTTATTCAAAGATACTTACAGCCACATCAGAGAGAGGTCACCAAACTGATGACGTATTTTGCTCAAGCCTGCCATGAACTTGTTCCTCCAGAgGTTATTGAATCGGGTCTAAAAGCGATTGTAAATAATTTTGTAACGGAGAGAAACTCTAACGAAGTGATGGCAGTTGGTCTTAACGCTGTCCGAGAGGTGTGTGCAAGATGCCCGCTTGTAATGACAGATGAGCTTTTACAAGATTTAGCGCAGTACAAGACATCTAAAGACAAAAGTGTGATGATGGCTGCTCGATCTCTCATTCAGTTATTCCGTGCCGTGAATCCAGCTCTTCTCCACAAGAAAGACAGGGGCAAGCCTACCGAGGAGAGTAAAAACTTTGCAGTGAAACAGTATGGTGAGCTGAAAACAACCGACTTCGTTCCTGGAACAGAGATACTTGATGATGAAcataatgttgaagatgaaaGTGATAAAGAAGATGCAAACCAAGGTGAATGGGAaagtgatgacgatgatgacgaggGTGAATGGGTGGATGTTTATCACTCTTCAGACGAGGAAGAACAGAACGAAGAAGATGATGACAACGACAACGAGGAGAATGAAACCGAAGAAGATTTGAAAGCTAAAGCAGCGAGAATAAGCCAGACACGGcttCTCACGGACGAGGATTTCAAAAAGATTCGGTTACGAGAAGCAGCGTGCCAGATTGATCCAAAAGCGGGCAAAAAGCGTAAAAGGAACGCCGATGACACAAGAACTACGGAAAGAGGCGAGTTAATTTCTGTAGGAGACATTGAGAACATCCAcaagaagagaaaacacgataaagAATCAAGATTAGAGACCGTGCTTGCTGGCAGACAAGGCAGAGAGAAGTTTGGCTCaaagaaagcaagaaagaagAGGTTGAATGAGTTTGCTAGTACATCGAATAAGgagaaaagaagaaagaagaattttatgATGATGCGCCACAACAGAGATGTGAGAGGGAAAACAAAGCGCTCGTTCCGAGACAAACAGGTGAGAGAGGCTCTGCGAAGCAAACAATTGGAATTATTACCTGTAGTCAAAATCATATGCAAGTGCCTGCACGTGGGATTTTACTGA

Transcript

FUN_047406-T1

Protein

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF08158 all species →	SDA1_HEAT	SDA1, HEAT repeat	Repeat	Interproscan
PF05285 all species →	SDA1_dom	SDA1, conserved domain	Domain	Interproscan
PF21638 all species →	SDA1_C	SDA1, C-terminal	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR027312 all species →	Family	Sda1	Interproscan
IPR012977 all species →	Domain	SDA1, N-terminal	Interproscan
IPR007949 all species →	Domain	SDA1, middle domain	Interproscan
IPR048292 all species →	Domain	SDA1, C-terminal domain	Interproscan
IPR016024 all species →	Homologous_superfamily	Armadillo-type fold	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12730 all species →	HSDA/SDA1-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000055 all species →	Biological Process	ribosomal large subunit export from nucleus	Interproscan
GO:0005730 all species →	Cellular Component	nucleolus	Interproscan
GO:0042273 all species →	Biological Process	ribosomal large subunit biogenesis	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
K14856	SDA1, SDAD1; protein SDA1	-	Ribosome biogenesis	ko03009	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_047406-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

53TPM > 0

7Conditions

480.0Max TPM

106.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
holobiont · low.pH_high.temp	20	11	117.93	417.91
holobiont · low.pH Control.temp	20	12	83.88	351.79
holobiont · control.pH_high.temp	20	14	118.84	463.15
holobiont · control.pH Control.temp	19	10	136.28	480.03
Whole organism	4	4	11.65	14.64
unannotated	1	1	7.98	7.98
live coral tissue/skeleton	1	1	12.77	12.77

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR22214410	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	417.91
SRR22214402	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	359.40
SRR22214412	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	341.98
SRR22214408	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	339.48
SRR22214407	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	262.91
SRR22214423	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	237.90
SRR22214404	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	150.85
SRR22214421	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	98.51
SRR22214413	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	61.71
SRR22214417	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	59.70
SRR22214418	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	28.31
SRR22214403	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
SRR22214409	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
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
SRR22214429	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	351.79
SRR22214431	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	256.67
SRR22214445	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	173.83
SRR22214436	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	173.41
SRR22214441	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	151.86
SRR22214424	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	116.63
SRR22214442	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	98.35
SRR22214430	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	95.24
SRR22214439	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	83.77
SRR22214425	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	81.60
SRR22214437	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	75.93
SRR22214434	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	18.45
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
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
SRR22214438	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
SRR22214443	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214453	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	463.15
SRR22214467	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	296.91
SRR22214461	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	223.14
SRR22214464	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	211.51
SRR22214463	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	187.44
SRR22214454	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	187.44
SRR22214446	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	174.85
SRR22214465	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	154.31
SRR22214459	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	125.89
SRR22214458	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	123.90
SRR22214462	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	83.26
SRR22214447	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	61.60
SRR22214457	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	52.84
SRR22214460	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	30.55
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
SRR22214456	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	480.03
SRR22214535	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	398.22
SRR22214466	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	383.84
SRR22214506	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	292.86
SRR22214548	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	269.44
SRR22214547	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	208.07
SRR22214411	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	189.84
SRR22214481	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	157.97
SRR22214468	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	142.09
SRR22214471	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	67.04
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
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
SRR22214492	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
SRR22214546	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	0.00
SRR14295603	Whole organism	Whole organism	not recorded	not recorded	SRP315757	14.64
SRR14295601	Whole organism	Whole organism	not recorded	not recorded	SRP315757	13.11
SRR14295604	Whole organism	Whole organism	not recorded	not recorded	SRP315757	9.63
SRR14295600	Whole organism	Whole organism	not recorded	not recorded	SRP315757	9.22
ERR12861049	unannotated	not recorded	not recorded	not recorded	ERP159209	7.98
SRR12454619	live coral tissue/skeleton	live coral tissue/skeleton	not recorded	not recorded	SRP277390	12.77

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.