Gene detail

Detailed information of XP_068673902.1 in Montipora foliosa

Genomic Location: chr9:6505009...6519089
NR annotation: XP_015753825.1, PREDICTED: histone-lysine N-methyltransferase SMYD3-like isoform X2 [Acropora digitifera]
Species Montipora foliosa · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_068817801.1

ATTTTCATCATGGCGGCTTCAGAAGCGTTGGGAAAGGTTGTTGAAATATTCAAGTGTTCGGAGTCTAAGGGGTATGGTTTGCGAGCTTTAAAACCATTGAAACctggtgaaaatgttttgcaatcAACTCCATCAGTGTTTGTTTTAGGCAGTAATATGCGAAGCCACTGCTGCGACTTTTGTTTCGCGAAAAGAGATGAAATTCAGCGTTGTTCAAAGTGCAAGTTTGCGCGGTATTGTAACAGAGAATGTCAAAAGAAGGCTTGGAAGGAGCATAACATAGAATGTGAACGCATACGCGAGGTTTCACCCAATACGCCTACAGATCTTGTGCTCCTCATTTCAAGAATCATTTATAAAAAGCAAATGGATAAAACGTTTAGCGCTGAATTGGCTCGTTTAGTGTCACATCGGGAGCAGTTTGGGAAAGCGAAGAAAGACGTCTTCTCTGCCATTCTAGCAGTTTTAGTAAAGTTCATAGGAGAAAAGAAGTTTCGGGAGACTTCACCATCGGAATTGTTTGAACTGTTTGGAAAAATATGTTGCAACAGTTTCACTATTTGTGATAACGAGTTGCAACCTCTCGGCGTTGGTGTCTACACTACAGCCTCTTATCTGAACCACTCATGTTGTCCAAACTGTGCAGCAGTATTTAATGGTACAACACTAATCATTCATGCAACAGAACAGGTCAAGGAAGGGGATGAGCTGACAATAAGCTACACTGAATTGCTTTGCCCTAGTTATGAGAGAAAGGAAGACCTGATGAGCCGTTACTGTTTTGAGTGTAAATGCATTAAGTGCACCTCACCTTTGGAAGAAGATGGACTTATGCTAAGTGCACAGTGCTTTGATCCTGGCTGCAAGGGAGCAGTCCCAAGATATAGTGAAGGGGGTAATTTGGCTTCTTGTAATACTTGTGGAAAAAGCCTTATTGACAGAAGTGATGTGGTGAAGGCAGAATCCCTAATGGTGAAGTCTAAAAAGGCTTTGAAGGAAATTGAAGTGTTGGATAAACTAGGGGATCATAAAGCTGTTTTTGAACTTGTTGAGGAATTATTAGCGCAACAGAATGGACTTTTTCACAAGCTTCACTATGTCAAGATCAGTTTACTTGATAAAGCTATGGATGCATGTATTTATCTTGAGATGTGGGACACTGCATTAGCCTACGGGCTGCAAACAATGGATGGCTATAAGCTATATTATCCAAGAAACCACCCAGTTgttggaattcagttgtttagAATTGgcAAACTGCAAGTGTATCTTGACAAATTACTTGAAGGGTTCAAGTCTTTGCAGCAGGCAGAAGCTATTCTTGACGTTACCCATGGAATAAACCATCCACTGGTGACGGAGCTTAAGGAAATGATAGCAAGGACTGTGGAAGAAGTCAGAGCAAAAGGGAAGCAAACACATTTTAACAGAAATTTGGACCTGGTTCTTTTGAAAAGTCCGTAAACCAGATCCATTTGTTAATTAAGAGAAACAACTGTAACCATTTTTGTTGTGACATGAACTGTAACTTATTCAAGCGTATTGCTTTGTTGATTCACTTTACTACCTGAATTTCTGAAAGATTACAGGCAATGGAGATGTTTTCGCCAACATTACCCTCTCCTTTCAGTTCATTGAGAATCTGACCGAAATTTACCGAATGACCGAGACTCGCAGTAAAAACCAACATGTAAAAAACTAGCTTCTTTTGCTTTACTATGCATGCACGATTGTTGCTGTATCAGAGAGGACTCGTTCATTACACACAAAACCTAACTCTTACATGATATGTGCGAACGAACGCGCTCCCTCTCCAAAACCAATACAAGGACGCACCAAATTATACATGGtagaaatttgcatacattggcTGTTGTCAGGACAATACGTATACCAGAggttataatccatcaaatattttcgctcgcgcgcgattggtctaaacgcgtcacgtgggcgaatattccccagctaaaactggggaatatccgaggatattccccaatgatattccccaatttttaaaaccgacttcaaggattcaagtctcacattaaaattaatgttaggatggcagaacggtttgctttcgtaacagaagaagagataaacctgctggtcgatagagcggtaccagaaaacaccaaaaaatccacttcatacgctgttaacttttttgacggtaagctgtttgtaaatcgtatccgccaatTGTATCCACAcgattaaaaaagtatgttttcctttcactgaaatgttccAAGCATAtgaactgaagcgaagtctgttcgaaattctggaaatgaatattgaatgacacggttttggaagccaattgacaaactttgacgtgttgacatatgacggactggcagatcccgcttgttgcgaaaactgttcgcttctcggaacagataatgtccgcggacaaatatccgagcatattttcgcgccaaatgaaggctattgtttatatatcgAATATGCATGTAAATATCAGTTTATGTACTGACAGGAAAACTGAAAACGTTTTCTTAATcatttcttcttttcaattCCGGGCTGTTTCTTTCACTACAGTTCCTTTTCCAGTCCTCCTCTTCTTCGACACATTGTTCTCAAACTCTGCCTCTCTGAACATCTGGATTACATGATTGAGCTATCATGATAAGATGCTTAGTCATACCTTAAAAATTTCACATATATAGGACTTGACAATTTGTATGAGTCAATGAGCGGCGTTTGCGTTATGACTGGTGCATGGAAAAGGGCTCATTGTAACCAATAATCGGACCTGGCGTGACTATGGAGAAAGATGATTTGGGTATATTTGACATGGCTGGAAGAAACCAAGCAAAagaattctcggttttcagctgacgtcataaccttatgcaaattaggtttccgccattctggtgcccctgattatagggaaatgtatgacattttgagcgctcactttcgaagtcttcaaataattcatctttccaatggatatttcccaagaaagcgacccaaaatcactcgacgaggtaccagtactttcatcctacccaaaaaaaacctcgaaagccacgttcgagagcgctatttgaagaagattttctgTCGTTTGCGTAGACCCAGCGGCCATACGGAACGATCAGTTTGGCTCCTCTCGAAGTTTCAGACTTGCTTTCCTAGTTAGTTTTAGAGACAAGCTACTatacaaacaagcagtttaaggccttcaaatttttgaaagcgtacaaccagatgatttctggtttcgttgcgtccgtttaaggaagggaaggaaatcgcgggcaagattgttgttgtttgtggccaAGGTGACTCGGAAGTTTGACACTCGGCGTCGACCTTATCTGTATCTATTCAGTTTCCCGttggatttcttttaataccttcgctaactgctatggccgccagatgagaagaaaaggcctcctcattccctttgttacgatgatttccctcttcttctgtcaaagtacttggtcgattagagtctcagtccttcaccttgagaaggtgagaagcttttttccttcgaaattcgtccgatttccttcaaactcagtcaatttgggcgctccatccctcgcattcgcctgtcgaatttcagcgaaatcgaataaaacgcctccgagttagacatttgctaacctgagtatcacaaacgcctgatactcaggttaaattcacctcattaaatattcaaaatcggagcacctcatttgcatcgggcatatttaatgagatgaATTTTCGAAGATGAATTTCTCGGCGACGTTGTGGTTTAATCGGTCGAAATTGAGCACACTTGTTTGAGGGGTTCAAGCGCTTCGGTGGTGTGAATTGGGAAGACATCGGTGGAAACCCGACCGAGAAACGCTTTATCGAAAAAAAGCCAACTTTCGACAAATTCTGACTCGCTCGCCTTTTACCCTAAAACCCTGAACCAACGCGTGctaaatcgctgcgaaagctttacaggataaaacacaaccgttcacagcaaaagccgttactggcaatcaccgcaaaagctttaattgctaaacctgtaaagacaatttcagcaaaataagtccaaccccacacttaaagttaaaatctaacattaaaccgtgagtcaatcgctgcgaaagcttttaaattgtcctttgttcgttttatctgtcccagagtaaggcaggcttcccagaaacaaagtctttcgatttcgtGTCGTCTCGGCTTATCTGTGAAATCCACCCGTTTCGGCGATCTTCTGTTAGCTGTTTTTAACTTTCAccgttcttatcaacaacgataggtatacggaatagactaataccttccttgtttccagattttactccacagccaggtattatacagagaaccatcgcactacaactcactcacatctctctctacgcgtctctgtttacgattcgaggggctccacaatggcggttaacgacggttgtcaaggactaaggtcacgtgggtgaaaaccaagaataagaGGAAGACGGATACCTGGAAC

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9CWR2	Histone-lysine N-methyltransferase SMYD3 OS=Mus musculus OX=10090 GN=Smyd3 PE=2 SV=1
Q9H7B4	Histone-lysine N-methyltransferase SMYD3 OS=Homo sapiens OX=9606 GN=SMYD3 PE=1 SV=4
C3RZA1	N-lysine methyltransferase SMYD2 OS=Sus scrofa OX=9823 GN=SMYD2 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005582 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00856 all species →	SET	SET domain	Family	Interproscan
PF01753 all species →	zf-MYND	MYND finger	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001214 all species →	Domain	SET domain	Interproscan
IPR013383 all species →	Conserved_site	CRISPR-associated protein DxTHG, conserved site	Interproscan
IPR050869 all species →	Family	Histone-lysine N-methyltransferase	Interproscan
IPR002893 all species →	Domain	Zinc finger, MYND-type	Interproscan
IPR046341 all species →	Homologous_superfamily	SET domain superfamily	Interproscan
IPR011990 all species →	Homologous_superfamily	Tetratricopeptide-like helical domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12197 all species →	HISTONE-LYSINE N-METHYLTRANSFERASE SMYD	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0018024 all species →	Molecular Function	obsolete histone lysine N-methyltransferase activity	Interproscan
GO:0034968 all species →	Biological Process	obsolete histone lysine methylation	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
K11426	SMYD; [histone H3]-lysine4/36 N-trimethyltransferase SMYD	EC:2.1.1.354 EC:2.1.1.357	Chromosome and associated proteins	ko03036	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_068673902.1 across 36 RNA-seq samples of Montipora foliosa. 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

26TPM > 0

1Conditions

3.9Max TPM

1.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
Polyps	36	26	1.72	3.92

Per sample · hover a bar for the full sample record

Show the sample table (36 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR12959187	Polyps	Polyps	E4 day21	not recorded	SRP199550	3.92
SRR12959224	Polyps	Polyps	E4 day3	not recorded	SRP199550	3.62
SRR12959237	Polyps	Polyps	E4 day0	not recorded	SRP199550	3.31
SRR12959225	Polyps	Polyps	E4 day3	not recorded	SRP199550	2.95
SRR12959181	Polyps	Polyps	E4 day0	not recorded	SRP199550	2.92
SRR27940177	Polyps	Polyps	not recorded	not recorded	SRP199550	2.83
SRR12904791	Polyps	Polyps	not recorded	not recorded	SRP199550	2.78
SRR12959238	Polyps	Polyps	E4 day0	not recorded	SRP199550	2.77
SRR12904780	Polyps	Polyps	not recorded	not recorded	SRP199550	2.72
SRR27940180	Polyps	Polyps	not recorded	not recorded	SRP199550	2.67
SRR12959226	Polyps	Polyps	E4 day3	not recorded	SRP199550	2.66
SRR12959199	Polyps	Polyps	E4 day15	not recorded	SRP199550	2.66
SRR12786895	Polyps	Polyps	OA4 day0	not recorded	SRP199550	2.65
SRR12959212	Polyps	Polyps	E4 day9	not recorded	SRP199550	2.44
SRR12959186	Polyps	Polyps	E4 day21	not recorded	SRP199550	2.27
SRR12904792	Polyps	Polyps	not recorded	not recorded	SRP199550	2.23
SRR12786904	Polyps	Polyps	OA4 day0	not recorded	SRP199550	2.23
SRR27940179	Polyps	Polyps	not recorded	not recorded	SRP199550	2.23
SRR12959213	Polyps	Polyps	E4 day9	not recorded	SRP199550	2.18
SRR12959198	Polyps	Polyps	E4 day15	not recorded	SRP199550	2.15
SRR12710865	Polyps	Polyps	OA4 day3	not recorded	SRP199550	2.07
SRR12710866	Polyps	Polyps	OA4 day3	not recorded	SRP199550	1.60
SRR12959200	Polyps	Polyps	E4 day15	not recorded	SRP199550	1.55
SRR12710852	Polyps	Polyps	OA4 day9	not recorded	SRP199550	1.21
SRR12710853	Polyps	Polyps	OA4 day9	not recorded	SRP199550	1.06
SRR12959185	Polyps	Polyps	E4 day21	not recorded	SRP199550	0.41
SRR12710845	Polyps	Polyps	OA4 day3	not recorded	SRP199550	0.00
SRR12710854	Polyps	Polyps	OA4 day9	not recorded	SRP199550	0.00
SRR12786903	Polyps	Polyps	OA4 day0	not recorded	SRP199550	0.00
SRR12807380	Polyps	Polyps	OA4 day0	not recorded	SRP199550	0.00
SRR12849112	Polyps	Polyps	OA4 day0	not recorded	SRP199550	0.00
SRR12927879	Polyps	Polyps	E4 day0	not recorded	SRP199550	0.00
SRR12959211	Polyps	Polyps	E4 day9	not recorded	SRP199550	0.00
SRR12963483	Polyps	Polyps	E4 day0	not recorded	SRP199550	0.00
SRR9129315	Polyps	Polyps	not recorded	not recorded	SRP199550	0.00
SRR9613518	Polyps	Polyps	not recorded	not recorded	SRP199550	0.00

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	25	XP_068686672.1	0.954591952730303
Negatively correlated	3	XP_068681185.1	-0.384347300557411

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.	ready	open →
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 →