Detailed information of FUN_023939-T1 in Siderastrea siderea

Genomic Location: contig_22:5142786...5187274
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
PF12624
all species →
Chorein_NVPS13-like, N-terminalDomainInterproscan
PF16908
all species →
VPS13_ext_choreinVacuolar sorting-associated protein 13, extended-choreinRepeatInterproscan
PF16909
all species →
VPS13_DH-likeVacuolar-sorting-associated 13 protein, DH-like domainFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR026854
all species →
DomainVacuolar protein sorting-associated protein 13-like, N-terminal domainInterproscan
IPR031646
all species →
DomainVacuolar protein sorting-associated protein 13, extended choreinInterproscan
IPR031645
all species →
DomainVacuolar protein sorting-associated protein 13, DH-like domainInterproscan
IPR039782
all species →
FamilyIntermembrane lipid transfer protein VPS13BInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR12517
all species →
VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 13BInterproscan

 Gene Ontology
No Gene Ontology signature was detected for FUN_023939-T1. This gene does have a gene model — the search simply returned no hit.
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
K19526VPS13B; vacuolar protein sorting-associated protein 13B-Membrane traffickingko04131deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of FUN_023939-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
6TPM > 0
7Conditions
17.2Max TPM
0.7Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
holobiont · low.pH_high.temp 20 0 0.00 0.00
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 0 0.00 0.00
Whole organism 4 4 12.27 17.17
unannotated 1 1 2.49 2.49
live coral tissue/skeleton 1 1 5.78 5.78

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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