Gene detail

Detailed information of FUN_011587-T1 in Siderastrea siderea

Genomic Location: contig_9:3492988...3511443
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_011587-T1

ATGGACCCCTTACAATTGAACGAACTTTTGGAGTGTTCGGTCTGTCTGGAACAGCTCGatcaaacttgcaaggttttACCGTGTCAACACACATTCTGTAGAAGGTGCCTGAAGGAAATCGTAGAGACAAGAAAGGAGCTGAGATGCCCTGAGTGTAGAATTCTCTGCAAAGAAGACGTGGACGATTTACCGGTTAATATCCTGCTTGTGAGGATTCTAGAAGGCTTGAACCGGCCGAAACAGAGAAAACATTCTTCCGACAGTTTAGATGAAGAAGCAAGGGACAAGTCTTCTGACCAGGTGCCTCTTCCATGTGCAAGAGCTTTGTATGATTATGAACCAAAAGAGGCAGGtgACTTAACATTGCATAAAGGAGAAATCGTAACCTTATTAAAACAAGTAGATGAAAACTGGTATGAGGGACTTAGTAATGGCTGCCAAGGATTCCTTCCAGCAAATTATGTAGAGGTTATCAACCCACTGCCCAGCCTAGATGATTCGTTTGACAGACCCATTGCTAAAGCATTGTTTGACTTTGAAGATGAACAAGAACAAGACCTGCTTTCCTTCAAACAGGGTGAAGTCATAGATGTATTACGTCGAGTTGATGAAAACTGGTGTGAAGGAAAGCTAAATGGCAAGCTGGGTATCTTCCCAATAACGTTTGTTGAGCTTAACATAGCAGCACGGAACCTCGTAGAAGGAAGTGAAAATGGCGAAGATCAAACTCGGGCTGTTGCAAAACCACAGAGAAAATCTCTGACAAGCGAAGCAAACAAAGGAGAACCCAAGCGGCATACCATGCATTTTGTTGGGCAGCGCAGTGAGGAGAGCCAACCTGCTGGACTTCAAAGGCGTTCTCTTGATATTTCTTCTTCAGAAAGGCTTGCAGATACACTTGATAGTTCAGCATCACCAGGATCGGGGACATCCCAGAACAGACAGGGTACACCTTCCCCCAGATCTTCCAATAACAGTCTTTCTAATCAGTCACACTGCACTGGGGGAGAATCAACTAACTTGCGGCGAGGATCTTCGCCACCTTCTGTCAGTCCATCTCAGTCAGTTTCAGGGAGGCAAGGGTCACCCGTGGACTCTAGTGCAGGAGCTGGGTCTCGCCCGGTGTCAGCAGAGATGGGCAAAGAATTGTATGTAGCACTTTACACATACAAGCCATCTAAAGATGACGAGCTGGAGCTCATAAGGAACGAGCATTACTGTGTGACAGAAAAGTGTAAAGACGGCTGGTTCAAAGGATATTCTGTGTCTACTCAGAAAAGAGGTGTCTTTCCAGGAAATTATGTTAGGCTGGCGAGCCTTCACAATTTACTTACAAGATCAAGAAGCAACAGTGCAGAGCAAGACAAAGTCTTACATTCGCTAACACAGAACAATGCTCTACCACAACCTCCACCACATCAAAGGCCACCACCACCGCGACACACCATCTCAGAGGGGGGTTCCAATCCGAGATTCCACCGGTCAGATTCTGCCCCACCCTACCCCCATCGACCAGGCATGCCTATGGAAAGCCTTGTGGTTAATTTAAGTCAAGGAAGAAGTTCAATGGAAAACAGAAATGTTGCTGAGGGACCCCCTGAGAGGAGCAGATTTGCCCCAACatcacccctccccccaccacCAGCACCTAAATCGAGTAGTTTCTGGAAAAAGCTGAAGGGCAAGAAGAAGGAGAGATCAAGAGCTTCCCCACCTCACCCTCCGCCTCCGCCGTATCAAAGGCATATTCCCGTGGGACACAGTGCATTATCACCGCCGCCTTATGATTTTGGAGCGTTGACATCCTCTTCCTCTCAGGTCCCGAGGGAAGAAAGTTCAAGGGGCCATAATAGAGTGGAGAACCCGCCAGTCAGAGAAAGgtACCGTGTTCTGGTAGCTTATCCACCTCAACACGAAGCCGAGCTTGAACTTCGAGTCGGCGACATTGTTTATGTAACGAAAAAGCGGCAAGATGGCTGGTATAAAGGGACGCTAgaacgaaatggaaaaacggGCTTATTTCCTGGAAGTTTTGTGGGCAGCTTTTAA

Transcript

FUN_011587-T1

Protein

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006413 (this species only) · gene tree & orthology
Ubiquitin family	E3\|E3 activity RING\|RING · all ubiquitin genes in this species
Ubiquitin family	UBD\|Other\|SH3 · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00018 all species →	SH3_1	SH3 domain	Domain	Interproscan
PF00097 all species →	zf-C3HC4	Zinc finger, C3HC4 type (RING finger)	Domain	Interproscan
PF14604 all species →	SH3_9	Variant SH3 domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR017907 all species →	Conserved_site	Zinc finger, RING-type, conserved site	Interproscan
IPR001452 all species →	Domain	SH3 domain	Interproscan
IPR050384 all species →	Family	Endophilin/SH3RF	Interproscan
IPR036028 all species →	Homologous_superfamily	SH3-like domain superfamily	Interproscan
IPR035816 all species →	Domain	SH3RF1/SH3RF3, fourth SH3 domain	Interproscan
IPR001841 all species →	Domain	Zinc finger, RING-type	Interproscan
IPR018957 all species →	Domain	Zinc finger, C3HC4 RING-type	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR028502 all species →	Domain	E3 ubiquitin-protein ligase SH3RF3, RING finger, HC subclass	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR14167 all species →	SH3 DOMAIN-CONTAINING	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0016567 all species →	Biological Process	protein ubiquitination	Interproscan
GO:0032436 all species →	Biological Process	positive regulation of proteasomal ubiquitin-dependent protein catabolic process	Interproscan
GO:0046330 all species →	Biological Process	positive regulation of JNK cascade	Interproscan
GO:0061630 all species →	Molecular Function	ubiquitin protein ligase activity	Interproscan
GO:0046872 all species →	Molecular Function	metal ion 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
K12171	SH3RF, POSH; E3 ubiquitin-protein ligase SH3RF	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_011587-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

81TPM > 0

7Conditions

210.4Max TPM

55.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
holobiont · low.pH_high.temp	20	19	58.50	150.15
holobiont · low.pH Control.temp	20	19	39.37	159.46
holobiont · control.pH_high.temp	20	19	60.80	207.21
holobiont · control.pH Control.temp	19	18	73.69	210.42
Whole organism	4	4	28.14	30.70
unannotated	1	1	21.86	21.86
live coral tissue/skeleton	1	1	21.04	21.04

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	150.15
SRR22214420	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	102.02
SRR22214421	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	93.69
SRR22214414	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	92.86
SRR22214407	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	91.66
SRR22214417	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	73.70
SRR22214408	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	69.67
SRR22214416	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	68.33
SRR22214406	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	63.02
SRR22214418	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	61.54
SRR22214413	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	59.12
SRR22214404	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	49.74
SRR22214423	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	49.48
SRR22214419	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	46.46
SRR22214405	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	28.87
SRR22214402	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	25.15
SRR22214409	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	24.89
SRR22214410	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	16.04
SRR22214412	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	3.56
SRR22214415	holobiont · low.pH_high.temp	holobiont	not recorded	low.pH_high.temp	SRP406607	0.00
SRR22214445	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	159.46
SRR22214437	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	96.10
SRR22214442	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	82.26
SRR22214441	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	51.28
SRR22214436	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	48.49
SRR22214430	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	44.46
SRR22214438	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	41.10
SRR22214425	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	36.36
SRR22214427	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	34.25
SRR22214432	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	32.71
SRR22214424	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	31.92
SRR22214426	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	30.91
SRR22214439	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	25.30
SRR22214428	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	21.18
SRR22214440	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	17.37
SRR22214431	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	16.93
SRR22214429	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	10.96
SRR22214443	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	5.10
SRR22214434	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	1.33
SRR22214435	holobiont · low.pH Control.temp	holobiont	not recorded	low.pH Control.temp	SRP406607	0.00
SRR22214464	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	207.21
SRR22214463	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	123.23
SRR22214459	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	102.75
SRR22214447	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	96.18
SRR22214448	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	87.89
SRR22214458	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	84.55
SRR22214462	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	71.49
SRR22214454	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	70.51
SRR22214467	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	58.79
SRR22214460	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	52.78
SRR22214451	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	51.35
SRR22214452	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	44.65
SRR22214465	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	38.97
SRR22214461	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	36.04
SRR22214457	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	34.99
SRR22214453	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	20.47
SRR22214449	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	11.94
SRR22214446	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	11.44
SRR22214450	holobiont · control.pH_high.temp	holobiont	not recorded	control.pH_high.temp	SRP406607	10.85
SRR22214456	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	210.42
SRR22214471	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	142.23
SRR22214481	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	139.56
SRR22214506	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	133.32
SRR22214547	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	115.47
SRR22214466	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	91.88
SRR22214468	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	84.69
SRR22214400	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	76.81
SRR22214535	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	71.22
SRR22214470	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	64.31
SRR22214411	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	61.39
SRR22214469	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	52.22
SRR22214433	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	44.75
SRR22214548	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	42.10
SRR22214455	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	24.28
SRR22214422	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	23.09
SRR22214524	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	14.38
SRR22214492	holobiont · control.pH Control.temp	holobiont	not recorded	control.pH Control.temp	SRP406607	7.96
SRR22214546	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	30.70
SRR14295603	Whole organism	Whole organism	not recorded	not recorded	SRP315757	28.88
SRR14295604	Whole organism	Whole organism	not recorded	not recorded	SRP315757	27.56
SRR14295600	Whole organism	Whole organism	not recorded	not recorded	SRP315757	25.43
ERR12861049	unannotated	not recorded	not recorded	not recorded	ERP159209	21.86
SRR12454619	live coral tissue/skeleton	live coral tissue/skeleton	not recorded	not recorded	SRP277390	21.04

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.