Gene detail

Detailed information of RMX42402.1 in Pocillopora damicornis

Genomic Location: SczhEnG_3381:91389...105024
NR annotation: no NCBI-NR hit recorded
Species Pocillopora damicornis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

pdam_00004865

TTTCTTGCCCTTGGAACTCACTATGGAGTTGTTCATATACTGGACCATCAAGGAAACCCAAGCAGTAGTAAAAAATATCCATCACACACTACAGCTATCAATCAAATCAGCATTGATCAGAGTGGAGACTATGTTGCCAGCTGCTCTGATGATGGACGAGTTGTAATAAATGGCCTTTATAGCTCTGAAAACAATGTCCAGGCCAGCTTTGACACTCCTGTTAAGTCAGTAGCTTTGGATCCTGAGTTCTCCAAGAAAAGAACCAAAATGTATGTTACAGGAGGAACAAAGTTGATTTTGACAGAGAGAGGCTGGTTCAGAAACAAGTCAAGTATCTTACATGAAGGAGAAGGAAACATTAGAACAATAAAATGGAAAGCATCCCTTATAGCATGGGCTGATGACACAGAGGTCAAGGTGTTTGACATGAATTCTCACAGAGTAATAACTCATATAAAGAGAGAAACCAGAAATTATAGACCTGAGTTATATCGCTGCTGTCTGTGTTGGAGGGATGATGTCACTCTTTTAATTGGCTGGGCAGACATGGTTCAGATTTGTGTGGTTAAAGAAAGGCTGGTTCCAAGGTCAGATCTCCCTCCTTTGGTTGTGGAAATAGTTGCAAGGTTCAAAACTGACTATTACATTTCTGGAATTGCATATCTTAAAGATGACTTGGGGACAGCATTGGATTTAGATTGTATAATGCTGCCTCTTGGTGCAAAAAATGTTGTGGAAGAGAATCTGTTTTACATTGTTAGCCCTAAAGATCTTGTCCTGGCTAAGCCCAGAAATATTGATGATCACATTAAATGGCTCATGGATCATGGAAAGTATGAGGAAGCTCTGAGTGTATCTGAAACAAACAGTAAAGAAGTCAAGAAACATAATCATCAAGATATTGGAAGAGCTTTTTTGAAATCTTTGATGGAGGAAGGAAAATATGAGACAGCTGCCAGATTGTGCATCAAAGTATTAAGTGATGACAAGAAACTCTGGGAAGATGAAGTGTACAAATTTGCTAGAAAACATCAGCTGGAGGCTATCGCCCCTTATATTCCTACCAAAGCAGTGAAGCTGAGCTCAGCAATTTATGAAATGGTTCTGTATGACTTCCTCAAGAAAGATGTCAAGAAATTCCAGGCACTGATCAAGGAATGGCCAGCAGATTTATACAATATGAAGCCCATCATTAATGCTATACAGGATCAGCTGGATAAGGACCCTAAGAACCGTGTTCTTTTGGAAACTCTTGGAGAACTTTACACGCGGCTGAAGAGATATGATAAAGGGCTCGCCATATACCTTAAACTTGGACATAGCGATGTGTTTAACTTGATCCATCAACACAACTTGTTTAGCTCTATTCAGGACAAGATTATTATGCTCATGGAATTTGACAAAGAGAAAGCCGTGAAGATGTTGATTGATAATACAGACAAAGTTCCTGTTGAAGAGGTTGTGCGCCAACTGAACAGGCGATCAGAACTTCTTCATGTGTATCTTGACTCGCTCTTCGTGAAAGATCCACAAGCCGGGATGGATTATCACGAACTACAGATTCCTCTTTATGCAGAATTTGAGCGATCAAAATTGCTTACTTTTCTGAGAAACAGCAATTATTATCCTCTGCAAAAGGCTCTAAACGAATGTGAACAGAGGCGCTTGGTTCCGGAGATGGTTTTTTTGCTCAGTCGCATGGGAAACAACAAGCAAGCTTTGCAGTTGATAATTCAGGAAGAAAATGATGTAGAGAAGGCAATTGAATTCGCCAAAGAACAAGACGACGAAGATTTATGGGATGATCTGATCAATTATTCTCTTGACAAACCAGAGTTTATCACGGGGCTCTTGCATAATATCGGGACTCATGTTGATCCGATCAAACTCATAAAGAGGATTCCTGAGGGAATGAAGATTCCTGGTTTGAGAGATTCATTGGTGAAAATTCTTCAAGACTTCAATTTGCAGATCTCTCTTCGTGAAGGTTGCAAAAAGATTCTCGTCAAAGACAGCGTGTCTTTGCTACAAAGGTTGAGCAAGGTTCAGCAAAGGGGAGTGTCAGTTGACGATGAAACAAAGTGTCCCGTTTGTCAAGGAGCAGTTATTGCTGAAGATACAAAACGAACCTCACATGTTGTGGTGTTTTTCTGTAAACATGTTTATCATGAAGATTGTTTACCAGCTCGTGACGTGGGTCCGTTTTGCCAGATTTGCACAGCGCATAGCCAAGTGAAGAGACTGCGTTCCCGTCACGTGCAGAGAAATGAAGCAAGGCCTTGA

Transcript

rna-pdam_00004865

TTTCTTGCCCTTGGAACTCACTATGGAGTTGTTCATATACTGGACCATCAAGGAAACCCAAGCAGTAGTAAAAAATATCCATCACACACTACAGCTATCAATCAAATCAGCATTGATCAGAGTGGAGACTATGTTGCCAGCTGCTCTGATGATGGACGAGTTGTAATAAATGGCCTTTATAGCTCTGAAAACAATGTCCAGGCCAGCTTTGACACTCCTGTTAAGTCAGTAGCTTTGGATCCTGAGTTCTCCAAGAAAAGAACCAAAATGTATGTTACAGGAGGAACAAAGTTGATTTTGACAGAGAGAGGCTGGTTCAGAAACAAGTCAAGTATCTTACATGAAGGAGAAGGAAACATTAGAACAATAAAATGGAAAGCATCCCTTATAGCATGGGCTGATGACACAGAGGTCAAGGTGTTTGACATGAATTCTCACAGAGTAATAACTCATATAAAGAGAGAAACCAGAAATTATAGACCTGAGTTATATCGCTGCTGTCTGTGTTGGAGGGATGATGTCACTCTTTTAATTGGCTGGGCAGACATGGTTCAGATTTGTGTGGTTAAAGAAAGGCTGGTTCCAAGGTCAGATCTCCCTCCTTTGGTTGTGGAAATAGTTGCAAGGTTCAAAACTGACTATTACATTTCTGGAATTGCATATCTTAAAGATGACTTGGGGACAGCATTGGATTTAGATTGTATAATGCTGCCTCTTGGTGCAAaaaATGTTGTGGAAGAGAATCTGTTTTACATTGTTAGCCCTAAAGATCTTGTCCTGGCTAAGCCCAGAAATATTGATGATCACATTAAATGGCTCATGGATCATGGAAAGTATGAGgaAGCTCTGAGTGTATCTGAAACAAACAGTAAAGAAGTCAAGAAACATAATCATCAAGATATTGGAAgagcttttttgaaatctttgatGGAGGAAGGAAAATATGAGACAGCTGCCAGATTGTGCATCAAAGTATTAAGTGATGACAAGAAACTCTGGGAAGATGAAGTGTACAAATTTGCTAGAAAACATCAGCTGGAGGCTATCGCCCCTTATATTCCTACCAAAGCAGTGAAGCTGAGCTCAGCAATTTATGAAATGGTTCTGTATGACTTCCTCAAGAAAGATGTCAAGAAATTCCAGGCACTGATCAAGGAATGGCCAGCAGATTTATACAATATGAAGCCCATCATTAATGCTATACAGGATCAGCTGGATAAGGACCCTAAGAACCGTGTTCTTTTGGAAACTCTTGGAGAACTtTACACGCGGCTGAAGAGATATGATAAAGGGCTCGCCATATACCTTAAactTGGACATAGCGATGTGTTTAACTTGATCCATCAACACAACTTGTTTAGCTCTATTCAGGACAAGATTATTATGCTCATGGAATTTGACAAAGAGAAAGCCGTGAAGATGTTGATTGATAATACAGACAAAGTTCCTGTTGAAGAGGTTGTGCGCCAACTGAACAGGCGATCAGAACTTCTTCATGTGtaTCTTGACTCGCTCTTCGTGAAAGATCCACAAGCCGGGATGGATTATCACGAACTACAGATTCCTCTTTATGCAGAATTTGAGCGATCAAAATTGCTTACTTTTCTGAGAAACAGCAATTATTATCCTCTGCAAAAGGCTCTAAACGAATGTGAACAGAGGCGCTTGGTTCCGGAGATGGTTTTTTTGCTCAgTCGCATGGGAAACAACAAGCAAGCTTTGCAGTTGATAATTCAGGAAGAAAATGATGTAGAGAAGGCAATTGAATTCGCCAAAGAACAAGACGACGAAGATTTATGGGATGATCTGATCAATTATTCTCTTGACAAACCAGagtTTATCACGGGGCTCTTGCATAATATCGGGACTCATGTTGATCCGATCAAACTCATAAAGAGGATTCCTGAGGGAATGAAGATTCCTGGTTTGAGAGATTCATTGGTGAAAATTCTTCAAGACTTCAATTTGCAGATCTCTCTTCGTGAAGGTTGCAAAAAGATTCTCGTCAAAGACAGCGTGTCTTTGCTACAAAGGTTGAGCAAGGTTCAGCAAAGGGGAGTGTCAGTTGACGATGAAACAAAGTGTCCCGTTTGTCAAGGAGCAGTTATTGCTGAAGataCAAAACGAACCTCACATGTTGTGGTGTTTTTCTGTAAACATGTTTATCATGAAGATTGTTTACCAGCTCGTGACGTGGGTCCGTTTTGCCAGATTTGCACAGCGCATAGCCAAGTGAAGAGACTGCGTTCCCGTCACGTGCAGAGAAATGAAGCAAGGCCTTGA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
E7F590	Vacuolar protein sorting-associated protein 41 homolog OS=Danio rerio OX=7955 GN=vps41 PE=1 SV=1
P49754	Vacuolar protein sorting-associated protein 41 homolog OS=Homo sapiens OX=9606 GN=VPS41 PE=1 SV=3
Q5KU39	Vacuolar protein sorting-associated protein 41 homolog OS=Mus musculus OX=10090 GN=Vps41 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004194 (this species only) · gene tree & orthology
Ubiquitin family	UBD\|Other\|Beta-prp · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00637 all species →	Clathrin	Region in Clathrin and VPS	Repeat	Interproscan
PF10367 all species →	Vps39_2	Vacuolar sorting protein 39 domain 2	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001841 all species →	Domain	Zinc finger, RING-type	Interproscan
IPR000547 all species →	Repeat	Clathrin, heavy chain/VPS, 7-fold repeat	Interproscan
IPR011990 all species →	Homologous_superfamily	Tetratricopeptide-like helical domain superfamily	Interproscan
IPR045111 all species →	Family	Vacuolar protein sorting-associated protein Vps41/Vps8	Interproscan
IPR016024 all species →	Homologous_superfamily	Armadillo-type fold	Interproscan
IPR036322 all species →	Homologous_superfamily	WD40-repeat-containing domain superfamily	Interproscan
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	Interproscan
IPR019453 all species →	Domain	Vacuolar sorting protein 39/Transforming growth factor beta receptor-associated domain 2	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12616 all species →	VACUOLAR PROTEIN SORTING VPS41	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006886 all species →	Biological Process	intracellular protein transport	Interproscan
GO:0016192 all species →	Biological Process	vesicle-mediated transport	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005770 all species →	Cellular Component	late endosome	Interproscan
GO:0006623 all species →	Biological Process	protein targeting to vacuole	Interproscan
GO:0009267 all species →	Biological Process	cellular response to starvation	Interproscan
GO:0016236 all species →	Biological Process	macroautophagy	Interproscan
GO:0030897 all species →	Cellular Component	HOPS complex	Interproscan
GO:0034058 all species →	Biological Process	endosomal vesicle fusion	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
K20184	VPS41; vacuolar protein sorting-associated protein 41	-	Membrane trafficking	ko04131	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 Pocillopora damicornis 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 Pocillopora damicornis, 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 →