Gene detail

Detailed information of FUN_005820-T1 in Siderastrea siderea

Genomic Location: contig_4:11563039...11579888
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_005820-T1

ATGTCGGACCCTATTCCACCAAGGTCTCTACCCAGCAGGCTGGCAAGTTTGTCTGTTAGCAGGATTCCATCTAGCCTACCAGGGGCTTGGAGATGCACAGGACGAAATAACGAGGAAATGGTCGATAAGTTTGTTCACATGGGAGTGATAACAACGAAGGAGGTTGAAGAGGCTTTTAGAACTGTCCCTCGAGGAGCCTTCGTTCCCCATGATCTACAGCTTGAAGCTTACATAGATTCCCCTCTTCGCGGCGATCCACACGTTCATTTGTCGGCTCCTCATATGTACGCAACTGTTCTTGAAGCTCTAAAGCTTTCGCCAGGTTTGTCGTTCCTCAATATTGGCAGTGGCACTGGCTATTTTTCATGCCTAGCTGGTTACATTCTTGAAGCTCATGGTATAAATCATGGCATTGAACTTCATGACGATCTGGTGCAGTTTGCCAAGGAAAGAGTTGAGGAGTACCTACAGTTCTGCCCTGCTGTTGCTCATGAGATATGTGTGCCCAAGTTTGTGGCTGGAAACTGTTTTCGATTGGATCCGTCAAGTGGAAGCTATGACAGAGTTTACTGCGGTGCTTCTTGTCCCCCAAGTAAAGTTCCTTTCATCCTAGCATTAACCAAAATTGGAGGCTTTGCCATCATTCCTTGTAGGAACAAGCTGCTGAAGATTGAACGTATTTCAGCATCTGGAGTGAAACAGTCCTGTATCAGTGATGTGTGTTTTGCATCACTTGTTGCTCTGCCTGAGTCTGATTCAAGTCTTCCCAAACTCTCCTTTCCTAAGGAAAgcccaagaaaaaaagaaaagGCTATTCACGTTTACCCTCCAAACAATATCCTGGTTAGTCGTGGGCAGGCCAGAACACTATTAGCAAAACTGAGAGCTCTACAAGAAGCAAGTGAATGCTTACACATGTCTCAGCCTCTACCTATGGCCTTCTGTTACGTACCATCTCAACAACAGATCCAACAACACTTCAACAAGAAGACAAAGACAAAGAAACAATCAAGCACAGTGGTTACTTCACCTGTGGACCGAAAGATTTTGTTCTTTGGTTCTCAACGTACATGTGGGGAGGGTCAGGTTTTTGATGCAGGCAAGAGTGGTCCCGAGAGCATGTGGGGTCATATGCAGCAGGACAAGTTATGGCAAACTGTGCTGGAGTATTACTATGGCCTGTGCAATGTGTCCCAAGAGAAAAGGAGTCAAGCAATGAATGTTTACATCAGAAGAAGAGTAAAGCACAAGAATGAAAAGAGGGAGAGTCAAAAGTGTTTCTCTTATGCCGAAATTGCACATAAGCTTGGTATTCTTAGTGTAAAGACGCATATGGAGGTCTCAAAACGAGAATCTGAGAACTCAGAAGAACTCAAAAGGAATGATTCAGATGGAGCATTATGTACAACATCTACAGAATCTACCAGTCACTGTAGTAGCACAACAGGTTGTAATTCAACTGAAGAGCCAAGTTCTAATGTCTTTCCTGTTAACGTTTCATGCAGTACACTCACAAGTTCTTCAAATGATTCGATAAGAACAGATTCTGATCAAACTCACAAAGCAAAGCTGACAAATAAAACTGGTAAATGTCAATCATTAGAAAACTCTTTGCAGAAATCTTCAGATTCAGATGTACTTAGTCAAGGAAGTGTGTCTGATGAATGTAGAACTACATGCACGACAACAGGATCAAATGGTGCAAAATATACTAATGTACTTATTGACATGGAAAGAGAGGTTATGGAGCAATTATGCATGTCGCCATCAGGCAGTTGGAGTATTAATGATGACATTGTTCTTGTGCACTTTTTGTGTGACATTTGTGAAAAATCTGACAACCGTGGGAGATCCAAGGGTTGGTTCAATGCAGAATATGCTGTAACAGAGCTGTTATCCAAGACAAGCATTATGACTCACCCACGTTTGTCCTGTTATTCTCAAGAGAGCTTAGCTTACCGATCTATTGCCTTGTGCAGGATTGCTCAAATTCTTGATTCATTACTTTACCTTGTGAGCGGTCCCTCAGTTTTGGCAGAGCAGAGTTTTTCTCCAAGCAGATATCAGCTTGAATCCTTCACAGAGTCTTCTTTCACCTCATCACGGCTGTATCTGGAGGCTGGAGTCACTCAAAGCCCAATTCCCAAGAGAAAGGAAAAAGTTTTGGAGAGTGAAAGGAAGGGAATAGTTGAGGATGATTTTGCCAAAGAAGGAAACAACCACCTGATTGAAGCCAATCTGAAGAGGTTAAAGCCTTCACCAGCTTCAATTGAAAAGTGTGAGGAACAACTCAAGGCTGTCAAAAGAAAGATTTGTTTTATAGAAGAACAGAAACAGCTGGTTCATCACAGCAATAAAGAGCAGGAGTTATCCCCTCCTGAGTTAATGCTGGATATAGATGTCGCTGATGTGAAGCTCCAGCGAAGTGAAATGTTGGTGAAACAACAGAAGCAAGAGCATTACAAGAGTCACTTACTTGCCTTACTAAAGAAACTCAAAGAAGATGAGAGGATGCTATCAAAGTTACTTTTACATTACCAGTCATATAATTTGGAAACAACAACAGAAGTGTCAAAGCTTCCACAAATAGGCTCCTCCACTCAGGATAACACTCCCACACCGCAGCCAGCTGCGTCATCTCACAAATGGAGTATGCGCCCCACAAGTAGCCAAGAGTATAACAGTAACTCTGTGCGTTATAACCTCTCATCGCTACTGCCGCAAATACGCTTTCTGCTGCCTCTGTGCAGTCAGCGGTGGCGCTTTGTACACGAGTTGTTGCACAGCACTGAGCTCTCAGCTCCTGATTACATGCCTGTCATTACAGTCGACAGACGAGTGCCTTTGGCGGAGCGTCATAGTGGGTCACGGAGCAGTGTCTTCTTACAGGTCTACCATGAACTAAAAAGAGAGAAACTTCATTTTCGCTGGAACAAATGGAAGTATGATCAGTGGTGGGAAGTAAAATTTGTTGGGGAAGGCATCATTGATCAGGGCGGAGGTTTCCGTGACTCTTTGGCCGAGATAGCTGATGAACTGTGTCCTCTTGATGAACACATACCAGAGATCCTGCCATACTTTATCAAAACGCCTAATCATAAGGAGAAAACAGGTGATTTTCTGGACTGTTTCATTCCCAATCCTGGTTGTAATGATCTGAACATGTTCCAGTGGCTGGGTGTGCTTATGGGAGGTGTGTTTCGCAGCGATGAGAGCCTCACTCTCGCGTTCCCTCCTTTTGTTTGGAAACTTCTTGTTGGAGAACACGTCATGTGGGCTAAGGACTATGTCGCCATTGATGAAGCCACCGTTCATATCACAGATGAACTGGAAGTCCTAGATGAAGATTCATATCAAAGTAACTATGGCAACGAGTGCACCTTCTCCACTGTGCTGAGTGATGGCCGCCGTGTGGAGTTACTCCCAGGAGGGGAGGGTAGGGTAGTGAAACCTGAAGAAAGGCAGGAATATGCATCACTGGTCAGAAGAACCCGGATGACCGAGTTTACAAAACAGGTTCAAGCAATGAGACAGGGCTTGATTTCAGTTGTTCCTGAATCAGTGCTCGCTCTTCTAACCTGGGGTAACTTGGAGCGTGGAGTTTGTGGAGATCGAGATATTTCTCTTGCTCATCTTAAGACAGCCTGTAAATACGGTGATGACTTAACCGAGTCGTCCGAGTCAGTGAAACATATGTGGACAGTTCTGACCCAGTTCACTTCAGATGAACGCAGTCGATTCCTGAGGTTTGTGACTGGACGCAAGAGGCCGCCCGCACCCTTCACTGTAGCCAAGGCTGGAGGAGATAAGGACAGTCTGCCTCATGCCTCCACCTGCGCCAGCACGCTGTTCCTACCTGACTACTCATCTGCAGCCGTGGCTAAGGAGAAGCTTAGctATGCAATTCTAAACTGTGTGGCGATTGATACCGATACAAGTCCTTGGTGA

Transcript

FUN_005820-T1

Protein

Gene family

Family type	Membership / link
Ubiquitin family	E3\|E3 activity\|HECT · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01135 all species →	PCMT	Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)	Family	Interproscan
PF00632 all species →	HECT	HECT-domain (ubiquitin-transferase)	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000569 all species →	Domain	HECT domain	Interproscan
IPR029063 all species →	Homologous_superfamily	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Interproscan
IPR035983 all species →	Homologous_superfamily	HECT, E3 ligase catalytic domain	Interproscan
IPR042469 all species →	Family	E3 ubiquitin-protein ligase HECTD3	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46654 all species →	E3 UBIQUITIN-PROTEIN LIGASE HECTD3	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004842 all species →	Molecular Function	ubiquitin-protein transferase 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

No KEGG orthology assignment for FUN_005820-T1.

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of FUN_005820-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

52TPM > 0

7Conditions

233.3Max TPM

54.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
holobiont · low.pH_high.temp	20	13	56.13	161.11
holobiont · low.pH Control.temp	20	8	33.83	150.85
holobiont · control.pH_high.temp	20	13	70.27	199.32
holobiont · control.pH Control.temp	19	12	69.89	233.34
Whole organism	4	4	12.71	17.63
unannotated	1	1	9.60	9.60
live coral tissue/skeleton	1	1	12.38	12.38

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR22214403	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	161.11
SRR22214406	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	143.54
SRR22214420	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	127.40
SRR22214407	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	116.06
SRR22214404	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	114.32
SRR22214418	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	96.29
SRR22214423	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	74.79
SRR22214408	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	64.79
SRR22214413	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	58.36
SRR22214412	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	57.76
SRR22214421	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	50.88
SRR22214410	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	39.10
SRR22214402	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	18.13
SRR22214405	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
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
SRR22214436	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	150.85
SRR22214438	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	125.40
SRR22214426	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	93.57
SRR22214441	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	82.10
SRR22214442	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	77.86
SRR22214424	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	49.94
SRR22214437	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	48.69
SRR22214430	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	48.13
SRR22214425	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
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
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
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
SRR22214463	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	199.32
SRR22214448	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	155.07
SRR22214462	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	147.01
SRR22214458	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	144.85
SRR22214459	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	114.61
SRR22214464	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	111.69
SRR22214450	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	111.43
SRR22214461	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	98.03
SRR22214456	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	91.95
SRR22214465	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	74.95
SRR22214447	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	74.90
SRR22214460	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	45.26
SRR22214446	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	36.38
SRR22214449	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
SRR22214457	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
SRR22214444	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	233.34
SRR22214469	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	181.30
SRR22214481	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	166.61
SRR22214547	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	146.11
SRR22214468	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	123.56
SRR22214506	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	90.67
SRR22214548	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	89.43
SRR22214422	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	88.82
SRR22214411	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	61.68
SRR22214471	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	54.39
SRR22214400	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	54.21
SRR22214535	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	37.78
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
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	17.63
SRR14295600	Whole organism	Whole organism	not recorded	not recorded	SRP315757	11.69
SRR14295604	Whole organism	Whole organism	not recorded	not recorded	SRP315757	11.14
SRR14295601	Whole organism	Whole organism	not recorded	not recorded	SRP315757	10.39
ERR12861049	unannotated	not recorded	not recorded	not recorded	ERP159209	9.60
SRR12454619	live coral tissue/skeleton	live coral tissue/skeleton	not recorded	not recorded	SRP277390	12.38

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.