Gene detail

Detailed information of aflo_s0018.g78.t1 in Acropora florida

Genomic Location: sc0000018_pilon:1355368...1372468
NR annotation: XP_029187696.2, sorting nexin-33-like [Acropora millepora]
Species Acropora florida · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

aflo_s0018.g78.t1

CGGAAAGTTTTGGAAAAATATTTGGCCGCGTTTATATTTGGTGGACAAGTACAACTTGCCCACAGCCTCAGCAACCGGTGGATACCTTACCCTTAAAAAATCATTCACGTGACATCTTGGAATCATGAAAGGGAGAGTAGATTGACTCGTAACATTTGCGTACTCAAATGGCTGTATCGCCTGGCTGTAAGGTCCGTGTGTTGTATGATTTTGAGGGCGATGCTCCCTCCGGTGAGCTTATCGTGTACACAGACGAAATCTTGACTGTGACTCGAACGGATGTTGGCGATGGCTGGTGGGAGGGGATCGGCCCTACAGGACATCGAGGCCTCTTTCCCGAAGCATACGTAGAGCTTGCTGAGGATTATTCGCATCCACCTGTGCATCAAAACAGTGCTCTTCCTCCAACTATAAACATCGGCCCTCTGAATAACCAAGGCTCCATTGATGGAGCAGATGGCTGGGACGATGATTGGGATGACGAGGAAAATGGGAGTTCTCACAATGGAGATCAAGAGACTGGGACAGTTGCATCTTTACCTCGGAGAAACACTGGCTCATCGGGGATAACAAGGACTGGTACCGTTCGGAAGAGCATGAACAGGTTTTCACATTTTGTCAAATCTGGTGGAGAAGCATTCATTATTGGTTCATCACAGTCAGAGATGGATATCCCTCCAGAGGAAAGGGTATCAGTCCAGGATTATCAAGGTAGAATCATTTGGAGAGGAGTTGCTGAGCCATTTAATTGTGTAATTGATGCACCTGAAAAGAAAAGCAAATTTAAAGGAATAAAAAGCTTCATTGCATACAACATAACCCCAAGTAATACAGGAGTGGCTGTCAGTAGACGTTACAAACATTTTGATTGGCTGTATGATCGTTTTCTTGAGAAGTTTACATTAATTTCCGTTCCTCCATTACCAGACAAACAAATCACAGGGAGATTTGGTGATGAGTTTATTGGGAAAAGAAAGGACAAATTACAGATGTGGATGAACAGAATATGTCTTCATCCTGTACTATCACAGAGTGTAGTGTTTCATCATTTTATTACCTGTGGAGATGATGAAAAAGAATGGAAGCAAGGGAAGAGAAAAGCTGAGTCTGATAAACTTGTTGGAGGATCTTTCTTTAGTTCAGTCGACTGTCCACAACAATCATTATCACTTGCTGCAAGTGCAATTACTAAGGTGAAAGAATGCGAGAAACTGAAAGATGAAGAAAAAATGGAGCATTTAGCATTTCAAGACATAAGCACTCGTGCAGATACAATAACCAATGTGTCTTTTGCGGAAATGAGTCATTTTCACGATCAGAAAGTAACAGACTTCAAGAATATGATGCAACATTTCCTTCGAGAACAAATAAGTTTTCACCAAAGAATTATTGAAAAGCTTGAAGACTCACTCAAGATGTATGATAAAATTCAATTAGGCAATTAATGAAGTCTGCTTTTTTGTTGCTGAATGACCCCAAATGTGACATCTTTCACGCAGATTAAAGGTTGGTTGCCATTATTCAGAATGACCAGTTGAAAAATGTAATGCTTCCCTTATCATTTCTCTCCGGTCTGCAAATTGATGCATTTATTATGCCATTACATTTTGTGCACTGGTTGAATTAGGCAACCGGTTCTGACAAATGGCAAGCACCCTTAATAATTACAACAAATTAGTAATCTAGTTTTCTATTTAAAACGAACACCTTGTCACTTTTGTACTTATAAAGTTTTATCACGTCCTATAGGCAAACAGTTCATTCAAGTGAAAACTTTTGCTATTTTTATCAGGTTGAAGtaatagtaataattattattaattattgttaatgttaatgttttaatattattaattattgttattgtttgttgatgttttaatgacattgtgattCAGTGAACAGCTTGCTATACATAATTTCTTAAAATGAACTCAAGGGTAAGATGAACCAAAAAGTGTACTTGCTCTCTTCTGCTGTGCAGAGGGAGCATAGAGATATACAAGGCTAAGGGTTTAGGGCTTTTTTTTGCTATGGGATGGCACTTCTTGTATTTGAATGCTGTAACAAGTCCATATAAAGTGTGAGAATGCAATCCCCATTCACTTAGCTTTAAAACTTGTACTTCATCAAGTTCCtgatgtagattgcagttgctgtttagttaggcaaggccttttcaataatatacaactatcccccgaaggggaggtgaatagtggtggatatatactgagacgcgaagcgtcgaggtatgtatccaccgctcttcaccgaccctgagggggatagttgttttagtatttaccaaatcagatggataacaaaacgcttcttcaatttcttcttctaaaactttcacgaaacgaccatttttctctcggttcacaaaacagtgaatatccaaggatattccgagttacgggagccaatcaaaatgcgcgaaaattgctatccactgatttggtaaatactaaATAGTATTATCAACTAACTGGGATTGTCACAAGCAGACAACAGATATGATGTAGTCAAAATATGTTGGCAGGTAAAAACAGATCATTGGTAAATGGTCATGTTCTTGTGATTGCTATAAATGCTCACCTAGTTGCCTATGAGAAAGACTTACTATAGATGAATTTGCTGACTTTTTGAGCAAGTGAAAAATAATAATAATTTATACTACCAGTGTTGCATAAAGGCAATAATTTAATTCATTAAGTTTAGGCAAAAATGTTTGGACAAGGACACTTGATGGTGAATGCAGCAAGCATTAGACTGCTTAGCAAGAGTTTCTGTGATATTTTTATAGCAAAGATGAGTCTTGGATGTGCAAAACAATAAGGCTAGACCAAAGCAAGAGAAAGAGGGGGATAATGGAATTATTGCATAACCTTAACACACATCACAAAATAGTTTCAGCCTGTCAAGGCATAGGCATAAGGGTATCTTCCAGCATACAATATTGAAGGACAACAATTTTTGTTGGGCATATTTTGAAATGTCTGAAGTACAATTATAATCAATGCAAGAATGCAGT

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q8I4E2	Sorting nexin lst-4 OS=Caenorhabditis elegans OX=6239 GN=lst-4 PE=1 SV=1
Q28GP7	Sorting nexin-33 OS=Xenopus tropicalis OX=8364 GN=snx33 PE=2 SV=1
Q6NRL2	Sorting nexin-33 OS=Xenopus laevis OX=8355 GN=snx33 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005065 (this species only) · gene tree & orthology
Ubiquitin family	UBD\|Other\|SH3 · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF10456 all species →	BAR_3_WASP_bdg	WASP-binding domain of Sorting nexin protein	Domain	Interproscan
PF00787 all species →	PX	PX domain	Domain	Interproscan
PF14604 all species →	SH3_9	Variant SH3 domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR019497 all species →	Domain	Sorting nexin protein, WASP-binding domain	Interproscan
IPR001683 all species →	Domain	Phox homology	Interproscan
IPR027267 all species →	Homologous_superfamily	AH/BAR domain superfamily	Interproscan
IPR001452 all species →	Domain	SH3 domain	Interproscan
IPR036871 all species →	Homologous_superfamily	PX domain superfamily	Interproscan
IPR036028 all species →	Homologous_superfamily	SH3-like domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45827 all species →	SORTING NEXIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0035091 all species →	Molecular Function	phosphatidylinositol binding	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0006897 all species →	Biological Process	endocytosis	Interproscan
GO:0016197 all species →	Biological Process	endosomal transport	Interproscan
GO:0031410 all species →	Cellular Component	cytoplasmic vesicle	Interproscan
GO:0097320 all species →	Biological Process	plasma membrane tubulation	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
K17923	SNX9_18_33; sorting nexin-9/18/33	-	Domain-containing proteins not elsewhere classified	ko04990	deepkoala

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

Co-expression network

Genes whose expression across the transcriptome samples of Acropora florida 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.

No co-expression network has been built for this species, so this gene has no partners to show. Networks are available for the species listed on the Network Analysis page.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Acropora florida, 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 →