Gene detail

Detailed information of XP_068758767.1 in Montipora capricornis

Genomic Location: chr7:28501636...28525054
NR annotation: XP_015780142.1, PREDICTED: synaptophysin-like [Acropora digitifera]
Species Montipora capricornis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_068902666.1

GCGCGCGGGAAAGCGGGAAGGAGCGGTCGAGCAGGACGAAGTGAATTGATGCACTTGTCCTGTCGTTGATTGCTGAAACTGCATTACCTCAAAATGAATCAGAAACCCAACATAGCCATCTTCAAGGAGCCTAAAGGACTGATAAAAGTCATCGAGCTTGGCATCACTATCTTTGCATTTGCCACAGTGGCAGGCTTTATTGGTCGATTTACATTCAACGTCAAATGTGTGGAAGGCGGAAACATTCGTACAGTTAAAGGGGTTATCTACTATCCATTCAATGAACCAAAACTCTATGCTACAAATCCTTGCAAAAATGAAACTGCTGATGATTTGGAAAAATTTACATCAGAGATTGACTACCGATCAGAGGCTGAATATTTTGTGTTTACTGGAGTGACGTCAATGTTATTTGTGCTTGTGGCCGCTGGTTATTATGTGTTTTTTGAAGACAGAGCCAAAGATGCAACTTCCACTGATGTTGGActattttcttttcctgttgtgGACTTTGTATTCACCATTGTCTTGGTGATCTTTTGGTTCACAAGCTCCATAGCATGGGCTGCTGGATTCAGTGGCCTCAAGAAGGCAACAAGTCAAGAGAATGTGTTTAAAAGCTATCCTGCATGCGCAGATCAAAGTGTCATCACCAAATGTGATCCTGGTACCTTTCAGGGTGCTGTTTATGGAGCACCTCTTATCGCTGTGATTTTGGGTTTTCTGAACTTCTTTGTGTGGGGCGGAAATTTGTGGTTTCTTTTCAAGGAAACTCCTTGGCACAGTCCGAGAAGCTCTGGAATGAAAGGAGGAGAGATTCCCCAGCAGGAACCACCTCATCAGGAGATTCCTCCTTCAGCAATTTAATTACCAACAAGGCCATGTAAATGAATCTTACTTTTAGGGTTgacccttttttattgcttgaTATTATCCAGCTCTGTAAGTTGTGAACAGAAAACCCATTAGACAAGTTCAAAGTAAATATTCCATGAAGATGGCATACAGAAGTTGACTGTAGTCATCTCACTTTTGGCTTGCTTAATAGAATATTACTCTGGTACAagtatctttttttgtttttgctgcaACAGTTTACAGAACTAGAAAACCACAATTCACTAATTCACTGCAAGATTGCAATTAGGCAACCAGTGAATCTGTAACATGTGGTTATAATTAGCATGATTACACTGTATAGCAACAAGTCAGATcatggggggggggaggggcatTCTTGTGGCTGGGGCTTGTGCTTGCCTTTGATTCAGAAAATATTGAAAAGGGAAGCTACTATAACAGAAATTAAAGCTGCAAAGAAATGCAAAATTGGGGACTTTGAATCAATTAAGTGCTGAGCATTGGTTTTCTAGACACAAGTAACTTAAAGGAAGTGTGAATGACTTCAATATTACATTGGTTAGTCAGcccaaaaagatacaaaaaattaGGACTTAGATTGCTAGATTAGTAACTGGCAGTGAGAAGTTAAGTTTGGAACTGTACATTGGCAGTAGCCAGCTTCTATTTATTTCCCTGTCATAGAAAATGTTGTTCCACCTCGTCAACTATCATTGAAAACTTTGTCACCTTTTTTGTTGCCCTAAAATAGAAATCAACAAAAGACTTTGTTGTAAACTTAGCTACAAAGGGATTTATGCCAATAGCCATACTTGATTTCTTGGTCAAATTTCACCATATGCAGTTTGCCTTTATCTGGGTGAAGTCACCTTGAGTGACCAAATCTGGGTTACCAGATGTATTGTGCATGGCATTATAGCTCCTACACAATGATGCTATAGAATTACATTTTCTGATGACAAAGTCTTAAATGAAAGTGGATACATGTATCATTTAACTAGTAGTACTGTTGTTAAGTTTGTGTATGATTGATTATTTTATTGCCGTGTTGATTCTCACCTGTGGTAtttattttcattgaagaattaCATGTCTGCAGCTGGGATGATGGCAACTAATATATTAAGAACCATTTTAATAATGGATCTTATCAAAGTGAAACTCTGAAAATGTTAAGGCTTTTGTATCTTCAGAAAGGTCTGATGTGTAATACTTGAAACCTCTGTGCTTGTATGCTTAGAACATAAAAATTTAATGTCAATCTgatatttggaaaaaatgtttaaatagcaaataattatttaatctcTCTAGTTCATAATTCAAGCCTTTAtcagagggaaaaaaataagatcCATTCTGTAAGTTTGCGATTTAACACCTTTCTGCCTCCCAGTCCTAAATGAAAGTTTCAGACGATCTGAAAGAATTATTTTCTCTTCCTGTGTGATGATTCCGGAACAGAATTCAGAGGTGTGGTCAATGCACCAAGAGGAGAAGAACGAACTAAAGCAAGTTTGTCTATCCAACTTTTATGTTAGGATAGAGCATAGTTAGTCGACTAACTATGGATAGAGTAAGTCTTTTTTTTGAGGAATGTCTAAGGGATATTTTTGGAGAAGCCGTCCCCAAAGCTGAAGTCAATATTTGCACGAGTGTAATTCTGGAAAAACACATTGGTAAGAAGTGGAAAATACTTgttcccaaaaaaaaattttacaatactttAATTAATGCTGATGACAACACGTTCAataatttctcaattttcttttgaaatatttatCTAGAACTACGAAAATCCAATTACCGGTACATAGCAACCTTTTCCCCAAATAATTAAGAGGTACTGGAATACTCAGGTTTTTTCATAGTCATTATTAGGTAATGGTAGGAAAATGGTTGAGGAAACATTAAAATATTGCTTTAACCGATTTGACAACATTCTTTGGCTTAACATTGACTTTTTTCCAACTCTACTGCAAAACTAATTTAGTTTAAGTTCTACATTACGTTGCTGCTAGCAATATTACTACAGTTTCTACAATAACTAGCTGTAAAATCAACTTGCTGTGGTAGTGTGATTAAAGAGTTATCGCTTTTCGTCTAAA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q16563	Synaptophysin-like protein 1 OS=Homo sapiens OX=9606 GN=SYPL1 PE=1 SV=1
O09117	Synaptophysin-like protein 1 OS=Mus musculus OX=10090 GN=Sypl1 PE=1 SV=2
O62646	Synaptophysin-like protein 2 OS=Oryctolagus cuniculus OX=9986 GN=SYPL2 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006936 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01284 all species →	MARVEL	Membrane-associating domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR008253 all species →	Domain	Marvel domain	Interproscan
IPR001285 all species →	Family	Synaptophysin/synaptoporin	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10306 all species →	SYNAPTOPHYSIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0008021 all species →	Cellular Component	synaptic vesicle	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

No KEGG orthology assignment for XP_068758767.1.

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

Expression pattern (RNA-seq)

Transcript abundance of XP_068758767.1 across 36 RNA-seq samples of Montipora capricornis. 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

30TPM > 0

1Conditions

128.3Max TPM

79.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
Polyps	36	30	79.34	128.34

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
SRR12786896	Polyps	Polyps	OA3 day0	not recorded	SRP199550	128.34
SRR12786898	Polyps	Polyps	OA3 day0	not recorded	SRP199550	125.11
SRR12786897	Polyps	Polyps	OA3 day0	not recorded	SRP199550	120.17
SRR12959202	Polyps	Polyps	E3 day15	not recorded	SRP199550	116.12
SRR27940191	Polyps	Polyps	not recorded	not recorded	SRP199550	110.60
SRR12904783	Polyps	Polyps	not recorded	not recorded	SRP199550	110.04
SRR12959201	Polyps	Polyps	E3 day15	not recorded	SRP199550	110.04
SRR12904781	Polyps	Polyps	not recorded	not recorded	SRP199550	106.31
SRR12959203	Polyps	Polyps	E3 day15	not recorded	SRP199550	106.25
SRR12710855	Polyps	Polyps	OA3 day9	not recorded	SRP199550	105.62
SRR27940193	Polyps	Polyps	not recorded	not recorded	SRP199550	103.85
SRR12959189	Polyps	Polyps	E3 day21	not recorded	SRP199550	102.71
SRR12959190	Polyps	Polyps	E3 day21	not recorded	SRP199550	102.37
SRR12959188	Polyps	Polyps	E3 day21	not recorded	SRP199550	101.72
SRR12710848	Polyps	Polyps	OA3 day3	not recorded	SRP199550	101.45
SRR12904782	Polyps	Polyps	not recorded	not recorded	SRP199550	101.14
SRR12710857	Polyps	Polyps	OA3 day9	not recorded	SRP199550	100.05
SRR12710858	Polyps	Polyps	OA3 day9	not recorded	SRP199550	97.50
SRR12710846	Polyps	Polyps	OA3 day3	not recorded	SRP199550	95.42
SRR12710847	Polyps	Polyps	OA3 day3	not recorded	SRP199550	91.68
SRR12959183	Polyps	Polyps	E3 day0	not recorded	SRP199550	86.18
SRR12959184	Polyps	Polyps	E3 day0	not recorded	SRP199550	85.49
SRR12959229	Polyps	Polyps	E3 day3	not recorded	SRP199550	83.76
SRR12959182	Polyps	Polyps	E3 day0	not recorded	SRP199550	78.35
SRR27940192	Polyps	Polyps	not recorded	not recorded	SRP199550	77.22
SRR12959227	Polyps	Polyps	E3 day3	not recorded	SRP199550	69.50
SRR12959214	Polyps	Polyps	E3 day9	not recorded	SRP199550	63.92
SRR12959216	Polyps	Polyps	E3 day9	not recorded	SRP199550	63.04
SRR12959215	Polyps	Polyps	E3 day9	not recorded	SRP199550	56.95
SRR12959230	Polyps	Polyps	E3 day3	not recorded	SRP199550	55.49
SRR12807381	Polyps	Polyps	OA3 day0	not recorded	SRP199550	0.00
SRR12849113	Polyps	Polyps	OA3 day0	not recorded	SRP199550	0.00
SRR12927880	Polyps	Polyps	E3 day0	not recorded	SRP199550	0.00
SRR12963484	Polyps	Polyps	E3 day0	not recorded	SRP199550	0.00
SRR9129316	Polyps	Polyps	not recorded	not recorded	SRP199550	0.00
SRR9613519	Polyps	Polyps	not recorded	not recorded	SRP199550	0.00

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	22	XP_068721559.1	0.934377460250331
Negatively correlated	4	XP_068724527.1	-0.599883818162523

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.	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 →