Detailed information of FUN_028275-T1 in Siderastrea siderea

Genomic Location: contig_28:5068853...5070922
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
Protein
 Gene family
Family typeMembership / link
Ubiquitin familyE3|E3 activity|RBR · all ubiquitin genes in this species

 Pfam domain
No Pfam domain signature was detected for FUN_028275-T1. This gene does have a gene model — the search simply returned no hit.
 InterPro
InterPro termTypeDescriptionSource
IPR013083
all species →		Homologous_superfamilyZinc finger, RING/FYVE/PHD-typeInterproscan
IPR044066
all species →		DomainTRIAD supradomainInterproscan
IPR051628
all species →		FamilyLinear Ubiquitination-Associated E3 LigasesInterproscan
IPR047544
all species →		DomainE3 ubiquitin-protein ligase RNF216, RING finger, HC subclassInterproscan
IPR047546
all species →		DomainE3 ubiquitin-protein ligase RNF216, Rcat domainInterproscan
IPR047545
all species →		DomainE3 ubiquitin-protein ligase RNF216, BRcat domainInterproscan
IPR002867
all species →		DomainIBR domainInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR22770
all species →		UBIQUITIN CONJUGATING ENZYME 7 INTERACTING PROTEIN-RELATEDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0000151
all species →		Cellular Componentubiquitin ligase complexInterproscan
GO:0004842
all species →		Molecular Functionubiquitin-protein transferase activityInterproscan
GO:0043130
all species →		Molecular Functionubiquitin bindingInterproscan
GO:0043161
all species →		Biological Processproteasome-mediated ubiquitin-dependent protein catabolic processInterproscan
GO:0071797
all species →		Cellular ComponentLUBAC complexInterproscan
GO:0097039
all species →		Biological Processprotein linear polyubiquitinationInterproscan
GO:0008270
all species →		Molecular Functionzinc ion bindingInterproscan

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
KOEnzymeEnzyme IDPathwayMap IDSource
K11976RNF216, TRIAD3; E3 ubiquitin-protein ligase RNF216EC:2.3.2.31
Ubiquitin systemko04121deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of FUN_028275-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
10TPM > 0
7Conditions
64.4Max TPM
1.1Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
holobiont · low.pH_high.temp 20 2 0.61 7.51
holobiont · low.pH Control.temp 20 0 0.00 0.00
holobiont · control.pH_high.temp 20 0 0.00 0.00
holobiont · control.pH Control.temp 19 2 3.62 64.38
Whole organism 4 4 2.17 2.53
unannotated 1 1 1.83 1.83
live coral tissue/skeleton 1 1 1.46 1.46

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

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.

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