Gene detail

Detailed information of g10226.t1 in Montipora capitata

Genomic Location: Sc0000283:181374...183596
NR annotation: CAH3171816.1, unnamed protein product [Porites evermanni]
Species Montipora capitata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q7KWX9	Putative exosome complex component rrp40 OS=Dictyostelium discoideum OX=44689 GN=exosc3 PE=3 SV=1
Q9NQT5	Exosome complex component RRP40 OS=Homo sapiens OX=9606 GN=EXOSC3 PE=1 SV=3
Q7TQK4	Exosome complex component RRP40 OS=Mus musculus OX=10090 GN=Exosc3 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006819 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF18311 all species →	Rrp40_N	Exosome complex exonuclease Rrp40 N-terminal domain	Domain	Interproscan
PF21262 all species →	RRP40_S1	Exosome complex component RRP40, S1 domain	Domain	Interproscan
PF15985 all species →	KH_6	KH domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR041054 all species →	Domain	Exosome complex exonuclease Rrp40, N-terminal domain, eukaryotes	Interproscan
IPR037319 all species →	Domain	Rrp40, S1 domain	Interproscan
IPR012340 all species →	Homologous_superfamily	Nucleic acid-binding, OB-fold	Interproscan
IPR036612 all species →	Homologous_superfamily	K Homology domain, type 1 superfamily	Interproscan
IPR004088 all species →	Domain	K Homology domain, type 1	Interproscan
IPR049469 all species →	Domain	Exosome complex component RRP40, type I KH domain	Interproscan
IPR026699 all species →	Family	Exosome complex RNA-binding protein 1/RRP40/RRP4	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR21321 all species →	PNAS-3 RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0000176 all species →	Cellular Component	nuclear exosome (RNase complex)	Interproscan
GO:0000177 all species →	Cellular Component	cytoplasmic exosome (RNase complex)	Interproscan
GO:0000178 all species →	Cellular Component	exosome (RNase complex)	Interproscan
GO:0000467 all species →	Biological Process	exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	Interproscan
GO:0034427 all species →	Biological Process	obsolete nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5'	Interproscan
GO:0034475 all species →	Biological Process	U4 snRNA 3'-end processing	Interproscan
GO:0043928 all species →	Biological Process	obsolete exonucleolytic catabolism of deadenylated mRNA	Interproscan
GO:0071034 all species →	Biological Process	CUT catabolic process	Interproscan
GO:0071035 all species →	Biological Process	nuclear polyadenylation-dependent rRNA catabolic process	Interproscan
GO:0071038 all species →	Biological Process	TRAMP-dependent tRNA surveillance pathway	Interproscan
GO:0071051 all species →	Biological Process	poly(A)-dependent snoRNA 3'-end processing	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
K03681	RRP40, EXOSC3; exosome complex component RRP40	-	Messenger RNA biogenesis	ko03019	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g10226.t1 across 48 RNA-seq samples of Montipora capitata. 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.

48Samples

48TPM > 0

3Conditions

122.1Max TPM

52.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole organisms · ambient pH treatment	21	21	53.86	107.18
whole organisms · low pH treatment	15	15	50.51	104.64
whole organisms · extra low pH treatment pH treatment	12	12	53.47	122.08

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11452262	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	107.18
SRR11452263	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	105.81
SRR11452251	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	103.76
SRR11452217	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	95.02
SRR11452260	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	72.13
SRR11452234	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	63.97
SRR11452259	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	58.59
SRR11452240	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	58.18
SRR11452243	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	56.77
SRR11452242	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	56.56
SRR11452237	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	54.50
SRR11452233	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	53.96
SRR11452254	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	52.74
SRR11452232	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	37.30
SRR11452250	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	33.40
SRR11452231	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	31.72
SRR11452252	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	25.67
SRR11452246	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	23.12
SRR11452230	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	15.02
SRR11452222	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	13.00
SRR11452228	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	12.62
SRR11452218	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	104.64
SRR11452229	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	101.30
SRR11452216	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	83.75
SRR11452255	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	63.23
SRR11452238	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	59.74
SRR11452241	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	58.00
SRR11452258	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	56.41
SRR11452253	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	55.79
SRR11452236	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	50.88
SRR11452249	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	32.91
SRR11452247	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	21.11
SRR11452245	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	18.91
SRR11452221	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	17.54
SRR11452223	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	16.83
SRR11452224	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	16.56
SRR11452220	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	122.08
SRR11452219	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	117.07
SRR11452261	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	84.24
SRR11452257	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	74.07
SRR11452239	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	60.91
SRR11452256	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	51.25
SRR11452235	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	50.11
SRR11452244	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	26.31
SRR11452248	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	17.39
SRR11452227	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	15.26
SRR11452226	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	11.97
SRR11452225	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	10.94

Source: CnidoSite RNA-seq expression matrices (MCAPI_TPM, StringTie quantification over 48 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.