Gene detail

Detailed information of g14113.t1 in Montipora capitata

Genomic Location: Sc0000508:119722...131529
NR annotation: CAH3026055.1, 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
Q921I9	Exosome complex component RRP41 OS=Mus musculus OX=10090 GN=Exosc4 PE=1 SV=3
Q7YRA3	Exosome complex component RRP41 OS=Bos taurus OX=9913 GN=EXOSC4 PE=2 SV=3
Q9NPD3	Exosome complex component RRP41 OS=Homo sapiens OX=9606 GN=EXOSC4 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001803 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03725 all species →	RNase_PH_C	3' exoribonuclease family, domain 2	Domain	Interproscan
PF01138 all species →	RNase_PH	3' exoribonuclease family, domain 1	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR020568 all species →	Homologous_superfamily	Ribosomal protein uS5 domain 2-type superfamily	Interproscan
IPR015847 all species →	Domain	Exoribonuclease, phosphorolytic domain 2	Interproscan
IPR001247 all species →	Domain	Exoribonuclease, phosphorolytic domain 1	Interproscan
IPR050080 all species →	Family	Ribonuclease PH	Interproscan
IPR027408 all species →	Homologous_superfamily	PNPase/RNase PH domain superfamily	Interproscan
IPR036345 all species →	Homologous_superfamily	Exoribonuclease, PH domain 2 superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11953 all species →	EXOSOME COMPLEX COMPONENT	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000176 all species →	Cellular Component	nuclear exosome (RNase complex)	Interproscan
GO:0000177 all species →	Cellular Component	cytoplasmic exosome (RNase complex)	Interproscan
GO:0005730 all species →	Cellular Component	nucleolus	Interproscan
GO:0016075 all species →	Biological Process	rRNA catabolic process	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:0071028 all species →	Biological Process	nuclear mRNA surveillance	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
K11600	RRP41, EXOSC4, SKI6; exosome complex component RRP41	-	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 g14113.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

52.7Max TPM

24.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole organisms · ambient pH treatment	21	21	26.97	52.67
whole organisms · low pH treatment	15	15	21.01	40.06
whole organisms · extra low pH treatment pH treatment	12	12	24.10	41.10

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11452232	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	52.67
SRR11452234	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	47.84
SRR11452231	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	45.02
SRR11452228	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	40.14
SRR11452230	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	35.60
SRR11452233	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	35.52
SRR11452222	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	34.82
SRR11452254	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	25.13
SRR11452250	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	24.23
SRR11452251	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	24.16
SRR11452252	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	23.65
SRR11452263	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	22.98
SRR11452217	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	21.61
SRR11452259	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	21.54
SRR11452246	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	20.50
SRR11452260	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	17.43
SRR11452237	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	16.94
SRR11452243	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	15.85
SRR11452242	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	15.25
SRR11452240	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	12.85
SRR11452262	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	12.56
SRR11452224	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	40.06
SRR11452223	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	36.74
SRR11452247	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	29.10
SRR11452221	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	29.10
SRR11452258	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	26.05
SRR11452253	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	23.81
SRR11452236	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	20.80
SRR11452249	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	20.73
SRR11452229	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	16.48
SRR11452216	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	15.01
SRR11452241	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	14.56
SRR11452238	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	13.03
SRR11452245	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	10.29
SRR11452218	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	10.07
SRR11452255	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	9.32
SRR11452226	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	41.10
SRR11452225	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	32.06
SRR11452227	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	30.99
SRR11452244	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	29.65
SRR11452257	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	26.04
SRR11452248	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	23.74
SRR11452256	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	23.69
SRR11452235	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	21.12
SRR11452219	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	16.05
SRR11452239	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	15.82
SRR11452261	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	15.58
SRR11452220	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	13.40

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.