Gene detail

Detailed information of FUN_007216-T1 in Siderastrea siderea

Genomic Location: contig_5:10622710...10631907
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_007216-T1

tcccttccccAATATAATACAGTGTAGGATTATATGCGGTTTCTTGTAACTAAACCTTTCTCTTTATGTTCACTTTCCACTCTTTAAGGTCCTTAAATAGTCAGCATATTCCTTAGAAATAATATCTTCTCCTTCAAGTATTTCATTCAGGTAAATCTCACTTGGTTTGAGTCCATCTTCAACAAACTCTTCATTTGCTTGGTAGGCCGTGGCCTCCACAACTTGAccgtttttcttttcaacttgTACGACCACACGGTGAAGCCGATTACCTTCGTCAATGTGTTCACGATCCATGTTAGCCAAGCTTCCTTTCTCACACACGTACAAAGCACCGTGAACCACGGAATCTTTATCTGGCGTGATATTAGCGTACCCAAACCCGTCATCTTTCCAGTTGGTGCTGAATTTGAATCGAAATCCTCGGAGAACTGCGCTTTCACGAGAAAGGAACTTCGCGCCGCgttctttcatctttctctGACTCAAGTTTGAGGCGAAGGCAAAATAAATCTCCTTCTCTTCCATGCTTCAACAAGTAAAAAGTACGGTTGTTAAGTACTTCTACTGCTGTAGTAGGAAGTATAAAGCTTGATATGGATTTCTATATTGCGTGACAAACGTAGCTGTCTTGGTCACGCACTCTCCTTGTTGATTGTCACAACACTGGAAGACTGGAAGTGTACATGTACGTGTTGGTTGGAGACTTTAAATTCCCTGTGTTTGACTTTGTTTATCTGTCTAACAAAcaagatttcttttttaaaagacTTCAAAGAAACTTTGGAAAACAAGTCCCCGTCGTCATTTTAGCGCTTTACTGAAAGCGGAGAGCAAGGttgagaaggccctggggagaAAGATGTGGAAACCTCTGTTCTAATGCAACGCAGGCTCATTCAAAAAATAGTCAACTCGCACAGCGGTACTAACCTAAAGAGCAGGACAATTCAAGATGGAGGACGATCTTGAACTGGAGCATGAAGGAGCAGCCCCAGGTTCAACGTCACAGCCAGTGAGAcgaaacatttctttaaaactGAAAGCAAAGAGCAAGTCAGCAAGCTCGCTGTCTTCAGGGAAGAGcaagaaaaaggaaggaaaaaccAGTGAAAGGTCCAGAACAGGATCAGATGGTGATAAAGAAAGTAAAAAGAAGCAGAAATCACCTGCATCCACTGGACCAACACCACAAGTGGTTGTCATGAGAGAACTCAAATGGGATCACCAAATTgtgctgattggccagaaagtACAAGATCCCCTTTTGCATTTGTGTGAGAAGTGTTCCCTTCCTATTTTGGTGTATGGTCGACTGAGTCCATGTAAACACTCTTTCTGCCTGACATGTGCGGAAAAAGGAAATGGAAAATGTCCAAGGTGCGGCGAAGGTGTTCAACGGATCGAGCGAGCACCGCTGGGCAGTGTATATGTGTGCTCAGTTGGAGGAAGTCGTTATGGAATCTCGGGATGCCGCCGTAGTTATTTCTCCCAGCGAGACTTGCAGTCGCACATCAAGAGACGTCACCAAAGAGAACAAGGAGGAGGTGAGAGTGACGGAGGAGAGGAAGCTGAGAACGAGATACAGCGCGCCATGTTTCCTCAAGCAGAACCCTTTTTCCCGGCCCCACTGCGCGAGGCCCTTCCTGCAGTACCTCCGCACCCCATACTGCCGGGTGAAAGGCCCTTTGGGAATGTGGGTACTGTCCCAGTCATAGACGGACGACATTTCCCTGGGGTTCCCACAATACCTCGCGAAACGTTTTTCATGGAAGGACCGCGCCAGCAACATCCAGTGGTCAGTGGTTTTCCGACTCAAGCTCCTGCCCCAGCCCCTATACCACATGTCCCTCAAGGCGGCTTTCCACGGCCTGAGCAAGGGCCTTCTCCGCGATTTGAGGAGATGAGAGTGTCAAGGCCAATGGCCCCAGCACCCATTGAAGAAGGCTTTGGACCTAGACCGGTAGCGCCCGGGTTCCCAGGAAGATTCCCTGGGCCACCGCGTTCCGAGGCTGACTGGATTCCAGCAGAACGAGGGCCTCCTGTTCGGGGAGAGAGAGACTGGATGCCACCTCCTGGACGAGGTGATAGGGACTGGATTCCACCGCGAAGTGTGGGAAACATGGTCCCCCCTGGGGCACCTCCGCCGGGTAGACCCCCACCAGGAGACCCTCATTTCCGCCCTATGTTTTGAAGCCCTCGGGGCTTACTGTTTTAGAATAATGAAGTTCTGCCTGCAATCAGTGATCAAACATTCTTAGAATACCCATTTCAAGTCGGCCAAACGAGAACGAGACTCGACGAGAGTTTAAGTTCTTCGAGAGTAAGAGAGTCAGTGAGAGTTCGCGAAAGCTGGAGACAAAACAAGAGCGAGAGTTTTGAACCTCCGCGGATTCTAATTGATTTAGCAGATGCAAAATTCTTCTTGAGCTCATAAGCGTTCAGGCCATACGAGTGCGAGAGATTGTACTCTCGGAAACTCTCGATCCCGTTTAGCTCGGGCGTAACGACGTCGAATTTCATGGCACGTTTTTAACAATATtcattagggagcttaagcagtCCCGAAGACGACGGCAACGAAAACGTCAATTTCAAACATAAATACATGACTTAAGCTACTTCGTGATTTTTCCATCATTTACAATGTAACCGAATTTTCCCGGAATTGAACTGGTAGGgactgagaaaaaaaatcacatcACTTTCGTGTGTTTACGTTCTCAATAAAGCTCAGTATTTATTCAATTCGCggcgttttttttgttttttgttttttttttggcagaggACGATATGTAATGTACCAAAATGTATAGCCAACGTGTATTTTCATTGGTTTGTTAATTAAACCTCTTGTTTAGTGCCGCTGTCGATGCCGTCGTTGCCTTGTGAAACAAAACGTCGCTTGGTTCCTAGTCCTGTCAGAGGATCTCGCCTGATAAGAGTCCCGCATGAACAGCGCATGTAAGTTTAGTATAAATGAATGGTTGTCAATATTAAAAACTTTATTTCATACgccaaataaaaacaaacaaaac

Protein

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF18408 all species →	zf_Hakai	C2H2 Hakai zinc finger domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001841 all species →	Domain	Zinc finger, RING-type	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR041042 all species →	Domain	Hakai, C2H2 zinc finger domain	Interproscan
IPR040380 all species →	Domain	HAKAI-like, RING finger, HC subclass	Interproscan
IPR017907 all species →	Conserved_site	Zinc finger, RING-type, conserved site	Interproscan
IPR040383 all species →	Family	E3 ubiquitin-protein ligase HAKAI/CBLL2	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13480 all species →	E3 UBIQUITIN-PROTEIN LIGASE HAKAI-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0016567 all species →	Biological Process	protein ubiquitination	Interproscan
GO:0030155 all species →	Biological Process	regulation of cell adhesion	Interproscan
GO:0061630 all species →	Molecular Function	ubiquitin protein ligase activity	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
K15685	CBLL1; E3 ubiquitin-protein ligase Hakai	EC:2.3.2.27	Ubiquitin system	ko04121	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_007216-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

49TPM > 0

7Conditions

445.6Max TPM

108.9Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
holobiont · low.pH_high.temp	20	14	135.43	445.56
holobiont · low.pH Control.temp	20	7	73.39	327.63
holobiont · control.pH_high.temp	20	12	131.01	439.24
holobiont · control.pH Control.temp	19	10	122.90	344.16
Whole organism	4	4	21.09	25.52
unannotated	1	1	20.63	20.63
live coral tissue/skeleton	1	1	16.48	16.48

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR22214416	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	445.56
SRR22214418	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	378.81
SRR22214403	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	343.64
SRR22214412	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	276.68
SRR22214413	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	160.54
SRR22214410	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	149.01
SRR22214415	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	148.59
SRR22214420	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	146.56
SRR22214423	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	144.33
SRR22214404	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	136.85
SRR22214402	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	99.88
SRR22214408	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	97.16
SRR22214407	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	95.00
SRR22214409	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	86.00
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
SRR22214414	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
SRR22214419	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	327.63
SRR22214425	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	237.56
SRR22214436	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	237.01
SRR22214426	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	194.13
SRR22214439	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	189.04
SRR22214432	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	146.22
SRR22214428	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	136.17
SRR22214424	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
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
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
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
SRR22214460	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	439.24
SRR22214462	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	335.39
SRR22214456	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	249.38
SRR22214467	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	237.49
SRR22214459	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	232.01
SRR22214458	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	220.40
SRR22214447	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	204.37
SRR22214454	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	172.07
SRR22214446	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	164.19
SRR22214464	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	138.94
SRR22214461	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	119.53
SRR22214465	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	107.25
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
SRR22214457	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
SRR22214422	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	344.16
SRR22214411	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	267.95
SRR22214469	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	255.07
SRR22214471	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	245.29
SRR22214444	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	243.64
SRR22214506	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	228.37
SRR22214400	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	208.81
SRR22214524	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	200.61
SRR22214535	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	177.28
SRR22214546	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	163.89
SRR22214433	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
SRR22214470	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
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
SRR14295603	Whole organism	Whole organism	not recorded	not recorded	SRP315757	25.52
SRR14295601	Whole organism	Whole organism	not recorded	not recorded	SRP315757	21.87
SRR14295604	Whole organism	Whole organism	not recorded	not recorded	SRP315757	21.61
SRR14295600	Whole organism	Whole organism	not recorded	not recorded	SRP315757	15.36
ERR12861049	unannotated	not recorded	not recorded	not recorded	ERP159209	20.63
SRR12454619	live coral tissue/skeleton	live coral tissue/skeleton	not recorded	not recorded	SRP277390	16.48

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.