Gene detail

Detailed information of XP_068698744.1 in Montipora foliosa

Genomic Location: chr3:18474378...18487444
NR annotation: XP_029193531.2, solute carrier family 28 member 3-like isoform X2 [Acropora millepora]
Species Montipora foliosa · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_068842643.1

GTATCTCTGTCACCATTATCATTTACATAACTAAACCTCGTTATCTCTTTACAAATCGATCAAGGAAACCGGTTGTCGACAGCCATAATCATCGATTACCTCAACAGACTCAAGCGCAAACTTTGAGGCAAAATATGATCTTTTTTGTCGGTACATTTTAGACTAACAACTGAACTGTCCTGTCACTCGAGCAAAACACATGTCAACAGCTTGTTCAACATTGCGAAATTTTTACACACAATGGATGGCAGTTACAACGCGGTGAATGCTCCTTCCAGCATAAACCCAACAAGTGTAAATATAGTGGAAATGGTGGAGAACGGACGACCACGCGCTGCCTCCGTTGAACAAAGCAGACGAAACGTAAGGTTGAGAACCCTTGAGGAACTATGGCTCAACTATTCATTTCAGATTGTTGTTGTCACGATTTCATTCGTCTTGCTCATTTACTCAATTGCAGCCATCGCTGTTTCCGGCTTCCATCAGGTCACTGGATTTTTCGCTGTAACTATGGTCTTCTGGTTTTGTGTGACGTATATGTTTCTTCGAGACTATTTTGGAGAAACCATTTACAAACTTTGTTGTCTACCTGTTATTTCACTTTTGCGAGAGAAATGGAGGTATCTGAGATGGATTGTTCTTCTAGTGGTGTTGACTTTGATAGGTTTATGGTTTGGTTTGGACACAGCAAAGGAACCCAAGAGATTTATATCACTGCTGGGAATGCTAGTTTATGTGGGAATCAGTTATGCGTTCTCAATTCATCGGAGGAAAataAAATGGCGCCCGGTCCTATGGGGTTTGGGATTGCAGCTGGTTTTCGCTCTTATTATTCTCAGGACGTCGCAAGGATACCAGGCCTTTAAATTTATCGGTGACACAGTAACGAGATTTCTCGAGTATACAGATGTCGGAtcagcttttgtttttggagaCAACTTCGCGACCCATTATATCGCATTTAAGATTCTCACGGTCATCATTTTCTTCAGTTCCTTTATCTCGGTTCTCTACTACTTAGGGGTAATGCCGCTGATCATCGCCAAGATCGCTTGGCTGATGCAGATTACTATGGGAACTTCTGCTGCCGAATCTCTCTCGGCCGCGGGAAATATTTTCGTCGGCCAGACTGAGGCACCTTTGCTAATACGACCATTTCTTGCGAATCTCACTCAATCCGAACTTCACGCGGTCATGACAGGAGGCCTGGCCACTGTGGCGGGAGGAATCCTTGCAGCGTTCGTGGGAGTAGGTATCCAGGCCTCGCACTTAATCGCTGCCTCCGTGATGTCGGCTCCTGCCGCCTTGGCTGTCTCGAAAATCATGTGTCCAGAAACAGAAGTACCAGAAACTATGTCACAAGAAACTATACATTTTGAGCCACCAGTAGAAAGAAATGTGATTGAAGCAGCAGCCAAAGGAGCAAGCACCGCTATTCCTCTCGTTGCGAACGTGCTCGCAATGCTTATAACATTTTTTGCTTTTATCGCCTTTTTCAATGGAGTTCTATCCTATTTGGGAAGCATGGTTGGATATTCCGAGCTAAGCTTTCAGGTAATCTGCTCTTACGTGTTTATGCCTTTCGCATTTCTCATGGGTGTGGACTGGGCAGACTGTCAAAACGTGGGCAGGTTCTTGGGCGTGAAAACATTCCTCAACGAGTTTATAGCATACATCGAGATGGGACCGTATATAAAAAATCGCAATGAAATGAATGGAGGACCAACTATATCGCGTCGTTCCGAGGTCATTGCCACTTACGCTTTGTGCGGCTTCACGAATTTTCTTGGCCTTGGGGTTCTTCTGGGAGGTCTGGGACCGATGGCTCCCAATCGGCGGGGGGACATGGCGAGGTTTGCTATAAGGAGCCTCTTTGCAGCCACCATCGCATGTTTCATGACTGCTAGTATTGCAGGATTTCTGTATGATGGATCGCTGGAAACCCCACCGGCAATTACAGAAACAATAACCACAACTTTGTCGCCTACAACATTGTCATGAATCATTGCAAATTTTATAGTCAAGGGTAACTCTCCTCGAGTGGTGGTTGCATTCGTAGGGTTATCAGTAATATCTGTCCTAAAGCAATCTGTGGACGCCAATCATAAGCGAAGGGACCAGTCAGATTGTTTCAGTGATGGATGTGCACACATCATCAAAATATAGTCTAATAAAATTCAGTGGCAGTGAAATTAAATAAAAGATTCTTTAGTGCAACGCGA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9UA35	Solute carrier family 28 member 3 OS=Eptatretus stoutii OX=7765 GN=SLC28A3 PE=2 SV=1
Q8VIH3	Solute carrier family 28 member 3 OS=Rattus norvegicus OX=10116 GN=Slc28a3 PE=2 SV=1
Q9ERH8	Solute carrier family 28 member 3 OS=Mus musculus OX=10090 GN=Slc28a3 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001083 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01773 all species →	Nucleos_tra2_N	Na+ dependent nucleoside transporter N-terminus	Family	Interproscan
PF07662 all species →	Nucleos_tra2_C	Na+ dependent nucleoside transporter C-terminus	Family	Interproscan
PF07670 all species →	Gate	Nucleoside recognition	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002668 all species →	Domain	Concentrative nucleoside transporter N-terminal domain	Interproscan
IPR011657 all species →	Domain	Concentrative nucleoside transporter C-terminal domain	Interproscan
IPR018270 all species →	Family	Concentrative nucleoside transporter, metazoan/bacterial	Interproscan
IPR011642 all species →	Domain	Nucleoside transporter/FeoB GTPase, Gate domain	Interproscan
IPR008276 all species →	Family	Concentrative nucleoside transporter	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10590 all species →	SODIUM/NUCLEOSIDE COTRANSPORTER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005337 all species →	Molecular Function	nucleoside transmembrane transporter activity	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:1901642 all species →	Biological Process	nucleoside transmembrane transport	Interproscan
GO:0005415 all species →	Molecular Function	nucleoside:sodium symporter activity	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0005887 all species →	Cellular Component	plasma membrane	Interproscan
GO:0015293 all species →	Molecular Function	symporter activity	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
K11536	SLC28A; pyrimidine nucleoside transport protein	-	Transporters	ko02000	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_068698744.1 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

29TPM > 0

1Conditions

75.1Max TPM

27.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
Polyps	36	29	27.06	75.07

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
SRR12959211	Polyps	Polyps	E4 day9	not recorded	SRP199550	75.07
SRR12710854	Polyps	Polyps	OA4 day9	not recorded	SRP199550	72.54
SRR12959199	Polyps	Polyps	E4 day15	not recorded	SRP199550	54.94
SRR12959200	Polyps	Polyps	E4 day15	not recorded	SRP199550	53.07
SRR12959198	Polyps	Polyps	E4 day15	not recorded	SRP199550	50.55
SRR12710853	Polyps	Polyps	OA4 day9	not recorded	SRP199550	48.89
SRR12710852	Polyps	Polyps	OA4 day9	not recorded	SRP199550	47.19
SRR12959212	Polyps	Polyps	E4 day9	not recorded	SRP199550	44.29
SRR12959213	Polyps	Polyps	E4 day9	not recorded	SRP199550	43.64
SRR12959185	Polyps	Polyps	E4 day21	not recorded	SRP199550	35.75
SRR27940180	Polyps	Polyps	not recorded	not recorded	SRP199550	28.80
SRR12904780	Polyps	Polyps	not recorded	not recorded	SRP199550	28.61
SRR12959226	Polyps	Polyps	E4 day3	not recorded	SRP199550	26.32
SRR12959238	Polyps	Polyps	E4 day0	not recorded	SRP199550	25.54
SRR12959225	Polyps	Polyps	E4 day3	not recorded	SRP199550	25.52
SRR12959187	Polyps	Polyps	E4 day21	not recorded	SRP199550	25.40
SRR12959224	Polyps	Polyps	E4 day3	not recorded	SRP199550	24.70
SRR12786903	Polyps	Polyps	OA4 day0	not recorded	SRP199550	24.34
SRR12959181	Polyps	Polyps	E4 day0	not recorded	SRP199550	24.12
SRR27940177	Polyps	Polyps	not recorded	not recorded	SRP199550	23.92
SRR12904791	Polyps	Polyps	not recorded	not recorded	SRP199550	23.89
SRR12904792	Polyps	Polyps	not recorded	not recorded	SRP199550	23.56
SRR27940179	Polyps	Polyps	not recorded	not recorded	SRP199550	23.55
SRR12959237	Polyps	Polyps	E4 day0	not recorded	SRP199550	22.57
SRR12786895	Polyps	Polyps	OA4 day0	not recorded	SRP199550	20.85
SRR12786904	Polyps	Polyps	OA4 day0	not recorded	SRP199550	20.51
SRR12710865	Polyps	Polyps	OA4 day3	not recorded	SRP199550	19.67
SRR12959186	Polyps	Polyps	E4 day21	not recorded	SRP199550	19.09
SRR12710866	Polyps	Polyps	OA4 day3	not recorded	SRP199550	17.11
SRR12710845	Polyps	Polyps	OA4 day3	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
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	14	XP_068676601.1	0.938150680693336
Negatively correlated	6	XP_068681185.1	-0.391893060708803

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 →