Detailed information of FUN_61025-T1 in Siderastrea siderea

Genomic Location: contig_35:8211333...8215589
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
 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF09416
all species →		UPF1_Zn_bindRNA helicase (UPF2 interacting domain)DomainInterproscan
PF18141
all species →		UPF1_1B_domRNA helicase UPF1, 1B domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR040812
all species →		DomainRNA helicase UPF1, 1B domainInterproscan
IPR018999
all species →		DomainRNA helicase UPF1, Cys/His rich zinc-binding domainInterproscan

 PANTHER
No PANTHER signature was detected for FUN_61025-T1. This gene does have a gene model — the search simply returned no hit.
 Gene Ontology
GO termCategoryDescriptionSource
GO:0000184
all species →		Biological Processnuclear-transcribed mRNA catabolic process, nonsense-mediated decayInterproscan
GO:0003723
all species →		Molecular FunctionRNA bindingInterproscan
GO:0003724
all species →		Molecular FunctionRNA helicase activityInterproscan
GO:0005524
all species →		Molecular FunctionATP bindingInterproscan
GO:0005737
all species →		Cellular ComponentcytoplasmInterproscan
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
No KEGG orthology assignment for FUN_61025-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_61025-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
8TPM > 0
7Conditions
10.4Max TPM
0.6Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
holobiont · low.pH_high.temp 20 1 0.52 10.42
holobiont · low.pH Control.temp 20 0 0.00 0.00
holobiont · control.pH_high.temp 20 1 0.22 4.38
holobiont · control.pH Control.temp 19 0 0.00 0.00
Whole organism 4 4 6.27 7.39
unannotated 1 1 4.85 4.85
live coral tissue/skeleton 1 1 9.98 9.98

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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