Detailed information of FUN_054974-T1 in Siderastrea siderea

Genomic Location: contig_98:1384895...1442150
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
PF04054
all species →
Not1CCR4-Not complex component, Not1RepeatInterproscan
PF12842
all species →
DUF3819CCR4-Not complex, Not1 subunit, domain of unknown function DUF3819DomainInterproscan
PF16417
all species →
CNOT1_TTP_bindCCR4-NOT transcription complex subunit 1 TTP binding domainRepeatInterproscan
PF16415
all species →
CNOT1_CAF1_bindCCR4-NOT transcription complex subunit 1 CAF1-binding domainRepeatInterproscan
PF16418
all species →
CNOT1_HEATCCR4-NOT transcription complex subunit 1 HEAT repeatDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR007196
all species →
DomainCCR4-Not complex component, Not1, C-terminalInterproscan
IPR024557
all species →
DomainCCR4-NOT transcription complex subunit 1, domain 4Interproscan
IPR038535
all species →
Homologous_superfamilyCCR4-NOT subunit 1, TTP binding domain superfamilyInterproscan
IPR032193
all species →
DomainCCR4-NOT transcription complex subunit 1, TTP binding domainInterproscan
IPR032191
all species →
DomainCCR4-NOT transcription complex subunit 1, CAF1-binding domainInterproscan
IPR032194
all species →
DomainCCR4-NOT transcription complex subunit 1, HEAT repeatInterproscan
IPR040398
all species →
FamilyCCR4-NOT transcription complex subunit 1Interproscan

 PANTHER
PANTHER termDescriptionSource
PTHR13162
all species →
CCR4-NOT TRANSCRIPTION COMPLEXInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0000288
all species →
Biological Processnuclear-transcribed mRNA catabolic process, deadenylation-dependent decayInterproscan
GO:0000932
all species →
Cellular ComponentP-bodyInterproscan
GO:0017148
all species →
Biological Processnegative regulation of translationInterproscan
GO:0030015
all species →
Cellular ComponentCCR4-NOT core complexInterproscan
GO:0060090
all species →
Molecular Functionmolecular adaptor activityInterproscan

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
K12604CNOT1, NOT1; CCR4-NOT transcription complex subunit 1-Messenger RNA biogenesisko03019deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of FUN_054974-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
85TPM > 0
7Conditions
4,646.0Max TPM
966.1Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
holobiont · low.pH_high.temp 20 20 799.84 2,289.39
holobiont · low.pH Control.temp 20 20 1,322.48 2,690.27
holobiont · control.pH_high.temp 20 20 1,088.64 4,645.97
holobiont · control.pH Control.temp 19 19 927.38 3,010.66
Whole organism 4 4 48.69 59.13
unannotated 1 1 34.92 34.92
live coral tissue/skeleton 1 1 47.49 47.49

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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