Gene detail

Detailed information of FUN_054147-T1 in Siderastrea siderea

Genomic Location: contig_93:666220...681268
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_054147-T1

CAAAACTGGACATCGACGAAAATGTGGAGTTTCTGATTTACAGTTAAGTGACCCTATACTGCATAAACTCATTAACACCCACTGCAAAACTCTGGACTCCATGAAACACTTGAGACCTGTCATGACAAGTAATCTGATCATTCTGGCAAGCTGATGGCGGGCAGGCCTTTCGACTGGAACTGGGAAGGGTTTATGGTCTTGAATGTTTATACTGCTGACAAAAAGAAACTTACAGGGTCATAAAGTCAATGAAACTGAGCTGGCTCATGAAGTAATTAATCTTGTCAATCAATTTGGTTTTAGTCTCTTAGCTATCTCGTTCCCGATCTCATGGATCATTTTGCCCCCTTTAACCTTTTTAAGTTTTTAGTCCGGTCAGTGAAgggaaaatcgtgacaaatcgcgtaaaagcatcaaatttgggCTGCACAAGGGCTGCACACATATTGCAATCCGCGCCAAAAGGGAACTCGTTACCAGTGCCTGCGGTTTGGGCAAGGAAATAGTTACCAGTCCCTGTCGTCTGTGTTGAACAAAGATAAACAAGATGGCGCCGGATCGTTTGTGCCGTTGCGTGTGAACTTCTGTAGTCAGTTCACTCTACAAGAATAGCCGGTAGCTGTGAAGCTATGGCGGATCGTGGCAAAACGCGATCTAAAATTTACGAGAGGTTAAACAATCCTGAACTTCGCTGTAAAACTGGTTGTGGTTTCTATGGTAACCCTGCATGGAGAGGTTACTGTTCTGTTTGCTATCGGGAGGTGTATCTGAAGCAACAGAGAGCACGAGCTGCATCGCAAAGCAGAGAGGTTGCCCTTGCAGGAGGCTCTCAAAACTTACAAACTGAAGTTGGACATGAAGAGGAAGAAACAGGGGCCAAACTGAAGTTCAAcaagtttgaagaaaaaaagaagtttcAGTTGGAGTCTAAAAAGCAGAGTGTAAAGAACTTGTTCAAAAAGAGTCCTGGAAAATCTATGTTACCAGATGGGACCCCAGCTGCTAATGCTACACCATCACCAGTTGAACCTCAAAAGGCTGCTAGTGGTTTCCGTGAATTTTTGAAGACCCTTAAGAAGCCTGCTGCACAAGATGTCAATGAGAAATGCAGGCTGTTTGTCCAGAGGATGTTAAACAATCCATCACTAAGTGTTGAGCAACAGAGTCAAATGGTGCATGACTTTTATGGGgcaATGTCTGAGCATCTACAGTCCCACCCGTTGTTTCAAAACCAGCCGCAAGAAGTAATTGACAGGACGTTGGATGGTGTAGAAAAACATATTATGACCAAGCTGTACAGAGTTGTTTTCTGTCCGGCCTCCACTGATGATGAGACAAGGGACCTGGCAAATCAAAAACGTATTAGAAGCCTTAACTGGATATCTCCCCAGCATCTTGATGCTGCTATTAATCTGGACAGTGAAAAGGTTCAGCAATTAATTGAAGATTCCCAACAAGATCTTGTAGAAATAAACACCAGAAGAGCTCCTCAAGACAAGCTGGCATGTGTTGTTCGGTGCTGCAAGAATATATTTAAAATCATTCATTTGTCGACACCTGCTGGAGGAGCAGTAAGCGCTGATGATTTCCTTCCTTGTCTTATTTATGTTGTGTTAAAAGCAAATCCCACAATGTTGCATTCCAACGTGCAATACATTTCTAGATTTTGCAATCCAAATAAATTGATGATGGGAGAAGCTGGATATTACTTCACAAACTTGTGCTGTGCTTTGTCATTTATTGAGAAGCTTGATGCACAGGCATTATCCATGTCACAGGAAGAATTTAACAGAAACATGTATGGGGATGAAACTGATAGTGCAGAACAAACCAAACCTAAACCAGTAGAACCACTAGTGATGTGTAAAGGTCTGGAACTCATGAAGACTAATCTTGAAATGCTTGGGTCTCTAAGGGAGAGACAGTTAAAACTCAAAGAGGATGCTCTTGTGTTGCAAGAACAAATGACAGAATTTAGAAACAATATTGTCAAAGAGGTTGATGCTATCTTGGCTGGTACAAGTAAAGGCAATTTGTACCTCAAGCCCACATTAACAACAAGTGATCAACAAGAGGCTTCAGTGGTGGCAAGCTGATCAAGTAAAGGTGGCACATGCAGGAGACAGTTACTGTTCAACTGCTTGTTGATCAAATAAGACAATTAATACAAGCTACGCAAGTGAGTTATGAAAGCATGCTGACCAAGATAAACCAAGAGAAATTTGCCTTATAATAAGCCTATTGAACATCAACCGTGCCAGGTTTATCAGTCTCGTGGTAAAAACTCCAAAGCTTGTCAACGATGATAGGTGTCCAGTTGCAGTGGATTTTGGGGCTTTCCTGGAGTCATTAACTGCCATGCGGTAACACCCAGGTTCCTCCAAAAAAGTGAAGTTggttttaaagaaatttttgcTGAATGTGGACAAAGTATCATTTTATATTAATCTGAATCACATGTAAATTTGGGAATTTTATAGAAAAAATTTTGGACTTATTGAGGGTGAGGTTAGAATGCTATACCATAATTATTAATCATAACTGGGCAAAAGAAATATGTGAAGGAATATTAGCTTTTTATTTCATGGATTTCTGTGTAATGTTTACTTAAGTTATGCAATGCTTGTGAGTGCACAAGATTTGTGTGTAAATTTAAGAAAGTGATTCATTGTGCACTTTATCAAAGCTTGCAAAGAAAAACTGACTAAATGAATGCTTCTTTGATCAGAGGTGAAAAGCAATAATGCTACCACTTAAGTGGTATGTACCAAAGGGAAAtacattacaattttaaaagtTCATCCAAAAAGATATATACTCtataccaaaaaataaaatcattacattaatttttgagtAACACTATCACCAGTTTTCCATGAAATCCCTTATTAATGATAACCATGGAATACACAGGAATAGGATCCTGAATTTgtattgaaaaaaatatttacaagatAACATACACTGTAGGCTTTGAATAAAGTAGATTTTTTgcatttgatttgattttttaTAATTATCCAATTATAATTTTCCTGTATTTAAGATAACACTCGAGGTTAACAT

Protein

Gene family

Family type	Membership / link
Ubiquitin family	UBD\|ZnF\|ZnF_A20 · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01754 all species →	zf-A20	A20-like zinc finger	Family	Interproscan
PF02204 all species →	VPS9	Vacuolar sorting protein 9 (VPS9) domain	Family	Interproscan
PF18151 all species →	DUF5601	Domain of unknown function (DUF5601)	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002653 all species →	Domain	Zinc finger, A20-type	Interproscan
IPR003123 all species →	Domain	VPS9 domain	Interproscan
IPR037191 all species →	Homologous_superfamily	VPS9 domain superfamily	Interproscan
IPR045046 all species →	Family	Vacuolar protein sorting-associated protein 9-like	Interproscan
IPR041545 all species →	Domain	RABX5, catalytic core helical domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23101 all species →	RAB GDP/GTP EXCHANGE FACTOR	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0005085 all species →	Molecular Function	guanyl-nucleotide exchange factor activity	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0016192 all species →	Biological Process	vesicle-mediated transport	Interproscan
GO:0030139 all species →	Cellular Component	endocytic vesicle	Interproscan
GO:0031267 all species →	Molecular Function	small GTPase binding	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
K20131	RABGEF1; Rab5 GDP/GTP exchange factor	-	Membrane trafficking	ko04131	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_054147-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

24TPM > 0

7Conditions

272.8Max TPM

20.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
holobiont · low.pH_high.temp	20	6	25.52	251.76
holobiont · low.pH Control.temp	20	3	12.70	186.00
holobiont · control.pH_high.temp	20	4	21.31	272.84
holobiont · control.pH Control.temp	19	5	19.18	91.20
Whole organism	4	4	24.19	26.64
unannotated	1	1	29.97	29.97
live coral tissue/skeleton	1	1	33.36	33.36

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	251.76
SRR22214423	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	72.63
SRR22214410	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	71.84
SRR22214415	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	48.95
SRR22214407	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	46.73
SRR22214408	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	18.55
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
SRR22214409	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
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
SRR22214438	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	186.00
SRR22214436	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	44.30
SRR22214442	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	23.73
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
SRR22214437	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
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
SRR22214460	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	272.84
SRR22214459	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	74.84
SRR22214463	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	40.13
SRR22214454	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	38.45
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
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
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
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	91.20
SRR22214506	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	90.21
SRR22214422	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	67.03
SRR22214411	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	62.63
SRR22214468	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	53.42
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
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	26.64
SRR14295600	Whole organism	Whole organism	not recorded	not recorded	SRP315757	24.07
SRR14295604	Whole organism	Whole organism	not recorded	not recorded	SRP315757	23.74
SRR14295603	Whole organism	Whole organism	not recorded	not recorded	SRP315757	22.30
ERR12861049	unannotated	not recorded	not recorded	not recorded	ERP159209	29.97
SRR12454619	live coral tissue/skeleton	live coral tissue/skeleton	not recorded	not recorded	SRP277390	33.36

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.