Gene detail

Detailed information of XP_068690545.1 in Montipora foliosa

Genomic Location: scaffold_420:68805...151395
NR annotation: XP_044174791.1, recombining binding protein suppressor of hairless-like isoform X1 [Acropora millepora]
Species Montipora foliosa · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_068834444.1

CCTTCACGAAATGTAACACAGTTTTCTCTTCCGaacaaaaatggcggaaggAGGTCTATTTCGAAGCATTCCGGTACACAGCGAAGGAAGTGGCAACATGTGATTAATATACCTCGCTCCCAatcctgagccttagtctgttaaATTTAAGGAACGTAATGGTCGAGATCTCGCCAGCGACTCGAGTGCTATCGAGACAACCGATCAGTTCATTTAGGTGTAACACGCCTTGTTTAAATGACATATTAAGTGGACATTTATGGAAAGGAAGACACTGCGTAAAGTTACATTGGTGAGGGAAACTTTCCTCAACCGGAAGTTTAACACAGAAATATGATCGCAGAACAAGTTAATTACCAGGAACAGCTTGTAGACCCTTAAAGGTTCAAGGACTTTAGAACTGAAAAGTTTCAGAAAAAgaacagtgacagtgacagtgggCAACTGCATCTAATACAACAGAGTCTGATGGGATCCTCCTCCATGCGGAAAGCGAATCCGGTAACCCACCCAGCCTTAAAAGGAGAGTTTGACTTACCTCTGTTTTTGATTCTACTGGATCTTGGTGGACAGCGACTTGGGGTTTTGCTGGGGCCGAACTTGACCCAAGCCTGAGCCTAAAAAGGAATTTTCAGAGGATTTTCCCCTCAAGGAGCATTCTGGCTAAAGTGGCCACAGCGGTGCATACCTCTGGTCATTAACCAAGACAGAAATCTTCTTTGATATGTGGACAAGAATAGAGCTCTACCAAGGGAAGTGTAGCAGCATGGAGCTGTAGCTGCAGGTAGTTGAAAGGGCAAGCAAGCCTTATGCTAAGCTTTTCATTTGGCGAGTGTGGTAGGATGCCGAACAGTGCTTTGCCCAAATGCATTTTATAGAGTTAAGGAATGGAAGGGTACACAGTGGCAAGCGTAGCTAAGGTGAGTTGAGCAGTTTCCATTCTGCATTTTGaatcattttacatttttttgtaatgATCCTTTTTAGATGATTCCtgttttcaaacagtttcactCAGGTGCCTCGACTAGCTTCCTTTACCTTTGCTTAAGATTTGAACCAAAAACTTAACATGTAACCCAGCGCCCCCATTAAACCCCACGCATGACGGTTTTAAGTCACAGCTGGATATCTAcccggggaagggggggggggggactcccatatgaaacagacggggatgctcgtcgtctcgcttagtggattttggtctcgcttagggtgttccaggCAAAGCGCcgatattttaagccgccaagatctcgtttagggttccgcaaAGAAACAGAATTatgcgaagagaaacagaagacaaattttctttttaacttgtttttaggggtcaaaatttccttaagccatgcccagattagtctcctttaggggtcacaaaaagcttgagccacgcccagatggtctcctttaggggttaaattcaaaattttcaacgagcatccccgtctgttccatatgggagtcccccggggggggggggggtatctACTGGTATTCACTCAGTTTATACAATTGTAAATATCTTACCCAAGGAATCAAGTGACATCAATTTTTGCTTTAATTACAAAAGCCATTTCAGGTGCTTATCTTTACTTCGGAACTGGAGTTTTGGGGACATTTGCGATGTAAATTATCTGCACTCTTTTAAACgggtgatgttgaagttggagagAAGAGCAAGCCTGGGACACTTCGTGAAGTGATGTTTTACACAAATCCTACATTGAATCCAGCATTTGTGAAGTATGTTTCCTTTTGACTGTTTTATCTGGTGATGTGACAGCAATATTTTTGTATTCCCTGCAGAATTGTCTTTAAAAAGTCAGCGAGCATGACAAGAATGGAACAGGAAACGTTTAAACAAGGAAGGAAGCTCAGAAGAAGGACTCACCTCTACTTCACTTAGTTTTGATGGACATTTACTTAAGCAGTTACACGGCGTTTTGTGATGTGCGTACAGCCTTTGCTGAATGCAGCAGAAGGATACTATTATTGCTGTTCAATCAAGGTGCTGGAGCTGATTTGGCAAGGAGAGGCCCTTATCATAGGGTGGCTGGTGGTTACACTTCAACACCCAATCATGGGCATGAGGGTGTGAGAATGAGTGTGGATATGGCCAGTCTACCAGTGCAACTTAGTTCCCCTACTACGCCTTCGCCACCCCCGGAGGAAGAGGAAGATAAGGGAGAATATTACAAAGATCCAGCACATCCAAGGCTCTCCAAAGGTGCCATGAACAAATACCTCAATGATGTTGTCCCCAGAGATGGCCATCAGACTGTCATTATTTTTCATGCCAAGGTTGCACAGAAATCTTATGGCAATGAGAGAAGGTTCTTTTGTCCGCCACCTTGTGTTTATCTTGTGGGAGATGGTTGGCAGTATCGGCAGGCCATTATGCCACCACCCCAAGAGGAAGACGCAATGCAGCATCCTGTGGCATTTATTGGAATAGGAAGCAAAAATGAACAGGAAATGCAACAGCTCATCATTAAAGAAAAAGGGTATGGAGCTGCCAAAACCTTGTACATATCAGATTCAGACAAGCGAAAACACTTTGAATTATCACTTAAGTTATTATATCCCAGTGGAGATCATGTTGGAACTTTTAATTCCAAAAGGATAAAGGTTATTTCAAAACCTTCCAAGAAAAGGCGGTCACTTAAAAATGCAGATTTATGTATCCAGTCAGGCTCGACTGTAGCCCTCTTTAATCGCCTCAGATCACATACTGTGAACACGAAATATCTCCATGTTGAAAATGGAACATTTCATGCCAGCAGTCAGCAGTGGGGAGCCTTCACCATTCATCTCTTACATGATGATGAATCTGAGAGCGAGGAATTTTCTGTCAGAGAAGGGTACGTTCATTATGGCTCCACAGTGAAGCTGGTGTGCTCTGTAACGAAGATGGCTTTACCGCGACTGaTAATACGAAAAGTGGACAAGCAAACAGCTTTATTGGATGCTGATGATCCAGTGTCCCAGCTTCATAAGGTGGCGTTCTGTGTTAAAGAAACAGAACGTATGTACCTCTGTCTTTCACAAGAGAGAATTATCCAGTTTCAAtCAATGCCTTGTCCAAAAGATCAGAACAAAGAGATGATCAACGATAGAGCCTCATGGACAATAATAAGTACAGACAAATCAGAATACAGTTTTTTTGAGGGAAATGGTCCAGTCAGAACACCCATCACCCCTGTCCCTATAGTAAACAATTTACAGTTGAATAGTGGCGGTGATGTTGCCATTTTGGAGCTGACAGGAGAACATTTTACGGCTAATTTGAAAGTTTGGTTCGGAGATGTGGAAGCAAAAACAAGGTACAGATGTGGCGAAAGTCTCTTGTGTGTTGTCCCTGACATATCAGCGATACGTGGCGGTTGGAGATTCGTTCGTCAGCCTACCGAGGTCGCAGTCAGTCTTGTTCGTTCGGATGGCGTCATTTATCCAACAGGACTGACATTTACATACACTCCTGAACCAGTGGAGAGACCAACTTCGTGCTTTTCAGAAACCGTCCTAAGGGCCGATATTTGAAGGCGTTTTGAAAGAAACGGACTTCGAACGAAAGTGAACTATGCAAAGCCGAAGTTCAAGTTTGGCCCGACTTTTTCCGAACAATACACGGAAGGCAGACAAACGTTCTTTCGGCTTTGCGAAACTTTCAATGCATTTAAAAGTGACAttaatccaagaagacttgcTAAGGATCTTCTTGAATACGCTCTTGCAATTATACTACGTGTAAACACTGCTAGGAGATAGTACGTTTTTCTTACAATCGTGAGAATCGTTTTCGTACATTGTTAAGCTGTTGTGTAGTTTCCAGTTCAAATTTGATAGATATTAATCGTTAGCAATATATTGTTTGCATCGCTGCAACGTGATGAGATAAGTTGTAAGTAGCCGGAAGCTTTCCGTTCTTTTGAACCATGAAATGAAGTGATAAAGAAAAATTTTACGAATGCAAATAGAGGCAAAGCTTCGCGTTTACAGGGAGACGGGCCAAAAGTTGCTCTTTCCACAAACCCAATGAAACTTTTTTTGATTTCAGGTAGTTTGCCTGTTGGAAAATATACTGCgcaaatactaaaaaaaaaaaaaagctagaaTAAAAGgatttatcatatgacccgtacggccccgcgcgcgctttcattgcaaaactattgagaaaatccccgtatgagggccgcacgctatgg

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P31266	Recombining binding protein suppressor of hairless OS=Mus musculus OX=10090 GN=Rbpj PE=1 SV=1
Q5RFK6	Recombining binding protein suppressor of hairless OS=Pongo abelii OX=9601 GN=RBPJ PE=2 SV=1
Q3SZ41	Recombining binding protein suppressor of hairless OS=Bos taurus OX=9913 GN=RBPJ PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002748 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF09270 all species →	BTD	Beta-trefoil DNA-binding domain	Domain	Interproscan
PF20144 all species →	TIG_SUH	TIG domain	Domain	Interproscan
PF09271 all species →	LAG1-DNAbind	LAG1, DNA binding	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR038007 all species →	Domain	RBP-Jkappa, IPT domain	Interproscan
IPR013783 all species →	Homologous_superfamily	Immunoglobulin-like fold	Interproscan
IPR015351 all species →	Domain	RBP-J/Cbf11/Cbf12, DNA binding	Interproscan
IPR036358 all species →	Homologous_superfamily	Beta-trefoil domain superfamily	Interproscan
IPR008967 all species →	Homologous_superfamily	p53-like transcription factor, DNA-binding domain superfamily	Interproscan
IPR015350 all species →	Domain	Beta-trefoil DNA-binding domain	Interproscan
IPR014756 all species →	Homologous_superfamily	Immunoglobulin E-set	Interproscan
IPR040159 all species →	Family	Suppressor of hairless-like	Interproscan
IPR037095 all species →	Homologous_superfamily	RBP-J/Cbf11, DNA binding domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10665 all species →	RECOMBINING BINDING PROTEIN SUPPRESSOR OF HAIRLESS	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0003700 all species →	Molecular Function	DNA-binding transcription factor activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0000978 all species →	Molecular Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:0000981 all species →	Molecular Function	DNA-binding transcription factor activity, RNA polymerase II-specific	Interproscan
GO:0001228 all species →	Molecular Function	DNA-binding transcription activator activity, RNA polymerase II-specific	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
K06053	RBPSUH, RBPJK; recombining binding protein suppressor of hairless	-	Transcription factors	ko03000	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_068690545.1 across 36 RNA-seq samples of Montipora foliosa. 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
SRR12710845	Polyps	Polyps	OA4 day3	not recorded	SRP199550
SRR12710852	Polyps	Polyps	OA4 day9	not recorded	SRP199550
SRR12710853	Polyps	Polyps	OA4 day9	not recorded	SRP199550
SRR12710854	Polyps	Polyps	OA4 day9	not recorded	SRP199550
SRR12710865	Polyps	Polyps	OA4 day3	not recorded	SRP199550
SRR12710866	Polyps	Polyps	OA4 day3	not recorded	SRP199550
SRR12786895	Polyps	Polyps	OA4 day0	not recorded	SRP199550
SRR12786903	Polyps	Polyps	OA4 day0	not recorded	SRP199550
SRR12786904	Polyps	Polyps	OA4 day0	not recorded	SRP199550
SRR12807380	Polyps	Polyps	OA4 day0	not recorded	SRP199550
SRR12849112	Polyps	Polyps	OA4 day0	not recorded	SRP199550
SRR12904780	Polyps	Polyps	not recorded	not recorded	SRP199550
SRR12904791	Polyps	Polyps	not recorded	not recorded	SRP199550
SRR12904792	Polyps	Polyps	not recorded	not recorded	SRP199550
SRR12927879	Polyps	Polyps	E4 day0	not recorded	SRP199550
SRR12959181	Polyps	Polyps	E4 day0	not recorded	SRP199550
SRR12959185	Polyps	Polyps	E4 day21	not recorded	SRP199550
SRR12959186	Polyps	Polyps	E4 day21	not recorded	SRP199550
SRR12959187	Polyps	Polyps	E4 day21	not recorded	SRP199550
SRR12959198	Polyps	Polyps	E4 day15	not recorded	SRP199550
SRR12959199	Polyps	Polyps	E4 day15	not recorded	SRP199550
SRR12959200	Polyps	Polyps	E4 day15	not recorded	SRP199550
SRR12959211	Polyps	Polyps	E4 day9	not recorded	SRP199550
SRR12959212	Polyps	Polyps	E4 day9	not recorded	SRP199550
SRR12959213	Polyps	Polyps	E4 day9	not recorded	SRP199550
SRR12959224	Polyps	Polyps	E4 day3	not recorded	SRP199550
SRR12959225	Polyps	Polyps	E4 day3	not recorded	SRP199550
SRR12959226	Polyps	Polyps	E4 day3	not recorded	SRP199550
SRR12959237	Polyps	Polyps	E4 day0	not recorded	SRP199550
SRR12959238	Polyps	Polyps	E4 day0	not recorded	SRP199550
SRR12963483	Polyps	Polyps	E4 day0	not recorded	SRP199550
SRR27940177	Polyps	Polyps	not recorded	not recorded	SRP199550
SRR27940179	Polyps	Polyps	not recorded	not recorded	SRP199550
SRR27940180	Polyps	Polyps	not recorded	not recorded	SRP199550
SRR9129315	Polyps	Polyps	not recorded	not recorded	SRP199550
SRR9613518	Polyps	Polyps	not recorded	not recorded	SRP199550

Source: CnidoSite RNA-seq expression matrices (MFOLI_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 foliosa 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 foliosa 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 foliosa, 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 →