Gene detail

Detailed information of XP_068747872.1 in Montipora capricornis

Genomic Location: chr4:5156172...5163888
NR annotation: XP_015754331.1, PREDICTED: ribonucleases P/MRP protein subunit POP1-like [Acropora digitifera]
Species Montipora capricornis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

LOC138045324

ATGAAAAACACAGGCAACAAAACTCAGAAAACTGGGGAAGGAGCAAAGAAGAAAAGCAGACGCTGGCGTCGCAAGCCCAAAAACCTGCTTGAAGAGTATGCCCGCCGACAGCGGAAGCATGCCTGGTTAGAGACGCATATTTGGCATGCAAAGAGAATGAGAATGATTGATACTTGGGGTTACAGGCTGGCAGATCACCCAAATGACAAAGGCTTTAGAGCATGTTACAGAGCTGTGAAGAATCATAGCTTGTTACAGGACATTTCCTTTCATGGTTGTATCGAAGTAATTGGAGTTCAGAGTAAAATTATACAAGCCATGAGCCACTTAACCAGCCAAGATGCAGGGTTGACAATGGGCGCAAAGTGGTACAAAAATGGTTCGCGTCAGGGTAATGTTATCTTGTACAAGTTTGATAAATATCCTTATGGAGCTCTTGGCCCAGTCTCTTTTCTCTGGAGACAAAAGCAAGAAACAGAAAGTTGCACTCCTGGCGACACGGAAATGAAAGAAGAAAATGTCGACGAAAGTAAAGCCCCAAAGAGAAACATTGCAAACGTGAACGGTGAAATTTCTGAAAGAGGGAGAGATAGTCAGCTGTGGATCTGGGCCCATCCTGCAAGCTTCCAGTTAGTGTTTGATGCAATTACTGAAGCTTGCTGTTATGTTGGAAAGACTTCGGTGAAAAGGGATTGTAAACTTGCTGTGGAATGTCAAAGGGATGGGGTTGACAAACCAGAGGAATCTGTTGCTGAGGAAAGCTTGGCAAATGACGGTGAACATGCTGAGTTATCAGTTGCCTCCCGTCGCTTCGATTTAGTGAAATTTCGTCTCACGGGACCGCGATCGCATGCTCTACTTGCAAGCACTTTGACACTGTTACAGGCAAATCCTTCAGGGAAAATACACAAGGAATCCTCACGATGTGATCGGGATGACAGGGTCAAGAACACTTTGTTCTCCAATTGGTGTTGTGATACGGAGGGTGTTGCAAAGACTTTGGCATCAAATGTATTATGGGAAAGTTTGAAGCAGGCCAGTTCTGCCGCAGTCCTTCCCCCTGGGTGTGTAATCGGCCTCACTGTGAGGGATCCACGTTTGGATTTGCCTGTCATGAAGTTGAGCATTTCTGATGCCACTGAAGAAATCAATTCAGAAGAGGCATTCAGCAATGTGGATGAAGCTGAGAATACGCTTGACACCAAAAACAAGAAGCCGTGTTTTGAAGATATCCTGACTCACTGGCCAACAGATGTTGCTGGTTCGCACATCTGGGATGAGCAAGTCCGCGCTGAAGTGAAAGAAGCGAAAATCTCAGAACACGAGTTAAACCAAAAGAGATCTGAGCTCCTAGTGCCAGGTTCCCGGCTGGCGTTGAGTGAGGAGGAGATATCCCATATTCCGTTGTTGCTTGTACAGCTGCCAGGTTGTCGTGAGGATCACCATGGATATGCTGACTTTATCTCTGGATATGGGAGTGGTTGGGACATCATATTGCCGGCAGGATGGGCCATGCCTTTCTGGATAGCTCTCGTCTACCGAGGGGCGAGAGCGGGGGGTCTTCAGGAGGCTCATGCGCTAGCCCTTGAGCAAGGAGTTCCTTTCTTTCCCAATGACTTTCCAGACACTCCGGCCGGCGAGGCGTTCAATTCTAAACTGAACGATGATGGAGAGGCCCGGCACAATAGATGTCCGCCAGCGAAGAGGCCAAACTATGATAAATTAGGCATGAAATGTCCGTACGGTCCACCATGGAGAGAGCTTGTTGACGAGTGGAGTTGTTGTGTGGATAAGTCCAGTAGTGAGAGACGTGAAGCACTAAAAAGCGCTGAAGCCACTTCCGTTGTAGCTTCTAAAATTGGGGACTCTTCTGACCAGCTTTGTTCTTTAGGAGGCACCTCCAAAGAAACTACTTCTCAATCAGCCGAAGCCGATGTTAATAAGGGTGGTCCTCAGATAGGTGGGCCTTCGGTCCAGCCTCTGTATGCCATGAGGTCGCAATCAAAGCTGTCCACCTTGCGTAATTTTGCTGCGCGTTGCCAACAAAGGCAGCTAAGCGGCGTAAATCGGCATAAGCTAGCGTTGGACGATTCCACTTTAACCTGCATCGTCAATAGTCACCAAAATGCTCTTGTGGGCGTGTTTTTGCGAATGACCAATCGAAGTGTCCCCGAACCCAATTCGTCGGTAGCGATTCCTGCCCAAAAGGACACCTCGAGTCTTGCGGCATGCAAGTCTTATGCCGGACCGGTTGAACCGCTGCGAAAAGGTTCGAGGGTTCAGTCTGACCAAAAGACTTTAAGGAACTCTTGTTCTAGGGAAATCATCGGGTTTGTCTCCTCGGGTCATTACTGCTTTTCCCGTGGGTGTGGGTGTGGGGTAGCGTTCTGTGCTCTTCCGGGTCTGGCGAAATTATTGATGTCTTCACGTTCCTCTGGGGGTCCTCTTGTGTTGGTGCGAGGACCTGGTACTCAACAATACCGATTTGCGCATTTTACGATATTGTAG

Transcript

rna-XM_068891771.1

AAAGAGTCGGCCTCTTTTAGTCCACTCCCCAGAGCCAAACGAGCAAGCAAATTATAGGAGTGAAGTGTGAAAATCCGACCACCATTGTCTCTTTAAAGGCGtatcgtttgaagaacgagATGAAAAACACAGGCAACAAAACTCAGAAAACTGGGGAAGGAGCAAAGAAGAAAAGCAGACGCTGGCGTCGCAAGCCCAAAAACCTGCTTGAAGAGTATGCCCGCCGACAGCGGAAGCATGCCTGGTTAGAGACGCATATTTGGCATGCAAAGAGAATGAGAATGATTGATACTTGGGGTTACAGGCTGGCAGATCACCCAAATGACAAAGGCTTTAGAGCATGTTACAGAGCTGTGAAGAATCATAGCTTGTTACAGGACATTTCCTTTCATGGTTGTATCGAAGTAATTGGAGTTCAGAGTAAAATTATACAAGCCATGAGCCACTTAACCAGCCAAGATGCAGGGTTGACAATGGGCGCAAAGTGGTACAAAAATGGTTCGCGTCAGGGTAATGTTATCTTGTACAAGTTTGATAAATATCCTTATGGAGCTCTTGGCCCAGTCTCTTTTCTCTGGAGACAAAAGCAAGAAACAGAAAGTTGCACTCCTGGCGACAcggaaatgaaagaagaaaatgtcGACGAAAGTAAAGCCCCAAAGAGAAACATTGCAAACGTGAACGGTGAAATTTCTGAAAGAGGGAGAGATAGTCAGCTGTGGATCTGGGCCCATCCTGCAAGCTTCCAGTTAGTGTTTGATGCAATTACTGAAGCTTGCTGTTATGTTGGAAAGACTTCGGTGAAAAGGGATTGTAAACTTGCTGTGGAATGTCAAAGGGATGGGGTTGACAAACCAGAGGAATCTGTTGCTGAGGAAAGCTTGGCAAATGACGGTGAACATGCTGAGTTATCAGTTGCCTCCCGTCGCTTCGATTTAGTGAAATTTCGTCTCACGGGACCGCGATCGCATGCTCTACTTGCAAGCACTTTGACACTGTTACAGGCAAATCCTTCAGGGAAAATACACAAGGAATCCTCACGATGTGATCGGGATGACAGGGTCAAGAACACTTTGTTCTCCAATTGGTGTTGTGATACGGAGGGTGTTGCAAAGACTTTGGCATCAAATGTATTATGGGAAAGTTTGAAGCAGGCCAGTTCTGCCGCAGTCCTTCCCCCTGGGTGTGTAATCGGCCTCACTGTGAGGGATCCACGTTTGGATTTGCCTGTCATGAAGTTGAGCATTTCTGATGCCACTGAAGAAATCAATTCAGAAGAGGCATTCAGCAATGTGGATGAAGCTGAGAATACGCTTGACACCAAAAACAAGAAGCCGTGTTTTGAAGATATCCTGACTCACTGGCCAACAGATGTTGCTGGTTCGCACATCTGGGATGAGCAAGTCCGCGCTGAAGTGAAAGAAGCGAAAATCTCAGAACACGAGTTAAACCAAAAGAGATCTGAGCTCCTAGTGCCAGGTTCCCGGCTGGCGTTGAGTGAGGAGGAGATATCCCATATTCCGTTGTTGCTTGTACAGCTGCCAGGTTGTCGTGAGGATCACCATGGATATGCTGACTTTATCTCTGGATATGGGAGTGGTTGGGACATCATATTGCCGGCAGGATGGGCCATGCCTTTCTGGATAGCTCTCGTCTACCGAGGGGCGAGAGCGGGGGGTCTTCAGGAGGCTCATGCGCTAGCCCTTGAGCAAGGAGTTCCTTTCTTTCCCAATGACTTTCCAGACACTCCGGCCGGCGAGGCGTTCAATTCTAAACTGAACGATGATGGAGAGGCCCGGCACAATAGATGTCCGCCAGCGAAGAGGCCAAACTATGATAAATTAGGCATGAAATGTCCGTACGGTCCACCATGGAGAGAGCTTGTTGACGAGTGGAGTTGTTGTGTGGATAAGTCCAGTAGTGAGAGACGTGAAGCACTAAAAAGCGCTGAAGCCACTTCCGTTGTAGCTTCTAAAATTGGGGACTCTTCTGACCAGCTTTGTTCTTTAGGAGGCACCTCCAAAGAAACTACTTCTCAATCAGCCGAAGCCGATGTTAATAAGGGTGGTCCTCAGATAGGTGGGCCTTCGGTCCAGCCTCTGTATGCCATGAGGTCGCAATCAAAGCTGTCCACCTTGCGTAATTTTGCTGCGCGTTGCCAACAAAGGCAGCTAAGCGGCGTAAATCGGCATAAGCTAGCGTTGGACGATTCCACTTTAACCTGCATCGTCAATAGTCACCAAAATGCTCTTGTGGGCGTGTTTTTGCGAATGACCAATCGAAGTGTCCCCGAACCCAATTCGTCGGTAGCGATTCCTGCCCAAAAGGACACCTCGAGTCTTGCGGCATGCAAGTCTTATGCCGGACCGGTTGAACCGCTGCGAAAAGGTTCGAGGGTTCAGTCTGACCAAAAGACTTTAAGGAACTCTTGTTCTAGGGAAATCATCGGGTTTGTCTCCTCGGGTCATTACTGCTTTTCCCGTGGGTGTGGGTGTGGGGTAGCGTTCTGTGCTCTTCCGGGTCTGGCGAAATTATTGATGTCTTCACGTTCCTCTGGGGGTCCTCTTGTGTTGGTGCGAGGACCTGGTACTCAACAATACCGATTTGCGCATTTTACGATATTGTAGTGCCCCTTGCAAGTTGCCCAGAGACATGTACTTGGTAATATTGTAGGTGAATCGTCGTCGTTTCAGTTTGGTACTTTACTTTTCCatttgatgtttttaaaggGAACTTCTAGCCCAGCAAAAGGAAACCCTTAACGCACACAGGAAATAACCTCTACAGtcaaatttatttaataatttttcaaagaaagcgtttgtatccgaaataaacaAGTTAAGAAACG

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q99575	Ribonucleases P/MRP protein subunit POP1 OS=Homo sapiens OX=9606 GN=POP1 PE=1 SV=2
F4IL30	Ribonucleases P/MRP protein subunit POP1 OS=Arabidopsis thaliana OX=3702 GN=POP1 PE=1 SV=1
Q11188	Ribonucleases P/MRP protein subunit popl-1 OS=Caenorhabditis elegans OX=6239 GN=popl-1 PE=3 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005352 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF06978 all species →	POP1_N	Ribonucleases P/MRP protein subunit POP1, N-terminal	Domain	Interproscan
PF08170 all species →	POPLD	POPLD (NUC188) domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR009723 all species →	Domain	Pop1, N-terminal	Interproscan
IPR039182 all species →	Family	Ribonucleases P/MRP protein subunit Pop1	Interproscan
IPR012590 all species →	Domain	POPLD domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR22731 all species →	RIBONUCLEASES P/MRP PROTEIN SUBUNIT POP1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000172 all species →	Cellular Component	ribonuclease MRP complex	Interproscan
GO:0001682 all species →	Biological Process	tRNA 5'-leader removal	Interproscan
GO:0005655 all species →	Cellular Component	nucleolar ribonuclease P complex	Interproscan
GO:0008033 all species →	Biological Process	tRNA 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
K01164	POP1; ribonuclease P/MRP protein subunit POP1	EC:3.1.26.5	Mitochondrial biogenesis	ko03029	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of XP_068747872.1 across 36 RNA-seq samples of Montipora capricornis. This gene has no row in the species' RNA-seq expression matrix, so every value below is shown as zero — the matrix simply does not cover this transcript. 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.

36Samples

0TPM > 0

1Conditions

0.0Max TPM

0.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
Polyps	36	0	0.00	0.00

Per sample · hover a bar for the full sample record

Show the sample table (36 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study
SRR12710846	Polyps	Polyps	OA3 day3	not recorded	SRP199550
SRR12710847	Polyps	Polyps	OA3 day3	not recorded	SRP199550
SRR12710848	Polyps	Polyps	OA3 day3	not recorded	SRP199550
SRR12710855	Polyps	Polyps	OA3 day9	not recorded	SRP199550
SRR12710857	Polyps	Polyps	OA3 day9	not recorded	SRP199550
SRR12710858	Polyps	Polyps	OA3 day9	not recorded	SRP199550
SRR12786896	Polyps	Polyps	OA3 day0	not recorded	SRP199550
SRR12786897	Polyps	Polyps	OA3 day0	not recorded	SRP199550
SRR12786898	Polyps	Polyps	OA3 day0	not recorded	SRP199550
SRR12807381	Polyps	Polyps	OA3 day0	not recorded	SRP199550
SRR12849113	Polyps	Polyps	OA3 day0	not recorded	SRP199550
SRR12904781	Polyps	Polyps	not recorded	not recorded	SRP199550
SRR12904782	Polyps	Polyps	not recorded	not recorded	SRP199550
SRR12904783	Polyps	Polyps	not recorded	not recorded	SRP199550
SRR12927880	Polyps	Polyps	E3 day0	not recorded	SRP199550
SRR12959182	Polyps	Polyps	E3 day0	not recorded	SRP199550
SRR12959183	Polyps	Polyps	E3 day0	not recorded	SRP199550
SRR12959184	Polyps	Polyps	E3 day0	not recorded	SRP199550
SRR12959188	Polyps	Polyps	E3 day21	not recorded	SRP199550
SRR12959189	Polyps	Polyps	E3 day21	not recorded	SRP199550
SRR12959190	Polyps	Polyps	E3 day21	not recorded	SRP199550
SRR12959201	Polyps	Polyps	E3 day15	not recorded	SRP199550
SRR12959202	Polyps	Polyps	E3 day15	not recorded	SRP199550
SRR12959203	Polyps	Polyps	E3 day15	not recorded	SRP199550
SRR12959214	Polyps	Polyps	E3 day9	not recorded	SRP199550
SRR12959215	Polyps	Polyps	E3 day9	not recorded	SRP199550
SRR12959216	Polyps	Polyps	E3 day9	not recorded	SRP199550
SRR12959227	Polyps	Polyps	E3 day3	not recorded	SRP199550
SRR12959229	Polyps	Polyps	E3 day3	not recorded	SRP199550
SRR12959230	Polyps	Polyps	E3 day3	not recorded	SRP199550
SRR12963484	Polyps	Polyps	E3 day0	not recorded	SRP199550
SRR27940191	Polyps	Polyps	not recorded	not recorded	SRP199550
SRR27940192	Polyps	Polyps	not recorded	not recorded	SRP199550
SRR27940193	Polyps	Polyps	not recorded	not recorded	SRP199550
SRR9129316	Polyps	Polyps	not recorded	not recorded	SRP199550
SRR9613519	Polyps	Polyps	not recorded	not recorded	SRP199550

Source: CnidoSite RNA-seq expression matrices (MCAPR_TPM, StringTie quantification over 36 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.

Co-expression network

Genes whose expression across the transcriptome samples of Montipora capricornis tracks this one. Counts are over the whole network; the network view itself draws at most 100 partners per query gene (CNIDO_NET_TOP_K), so a hub gene can show fewer edges than the number below.

Direction	Partners	Most correlated partner	PCC
Positively correlated	0	not in this network	-
Negatively correlated	0	not in this network	-

This gene has no edge at all in the Montipora capricornis network, in either direction — it is not one of the genes the network was built from (the network covers genes with enough expression variation across the transcriptome samples). The counts above are a property of the network, not a failed lookup.

Open this gene in Network Analysis → The network opens with the gene already entered and both directions selected. There you can add up to 9 more genes, switch between the positive and negative network, and export the edge list.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Montipora capricornis, and in which cell types it is a marker. Expression is stored per cell, so the violin plot and the cell-type means are computed in the viewer — open a dataset to see them.

No single-cell dataset has been published for this species. The atlases that do exist are listed in the Cell Atlas.

Epigenetic marks

Chromatin and DNA-methylation data covering this gene. Peak calls are listed per sample with the genomic region the peak falls in; DNA methylation is listed as sample availability only, because those tables are queried by the DNA Methylation page itself.

No epigenomic data has been deposited for this species. The assays that exist across the site are described in the Epigenomic Data module.

What you can do with this gene

Every tool below opens with this gene already entered, so you land on the analysis rather than on an empty form. Links open in a new tab.

Analysis	What it does	Status
Primer design	Design PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.	template found	open →
BLAST	Search this gene’s sequence against the CnidoSite BLAST databases. The query is filled in and the species’ database is preselected — press Run to start.	template found	open →
Expression heatmap	Draw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it.	no expression matrix	–
Gene family / orthogroup	Look this gene up in the single-copy orthogroups built from the high-quality cnidarian genomes, and see which other species carry an orthologue.		open →
Gene set analysis	Start a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.		open →