Gene detail

Detailed information of RMX59268.1 in Pocillopora damicornis

Genomic Location: SczhEnG_386:27064...36576
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_00005682

ATGGCGGAAACTCTGGAGGATTTGATTGAATTGAAATCTAAAATTAACTATTTCACAGATAAAGCCACGGATCCTTCTAAAACTAAGGACGGCGTGGACTACTCGACACCAGTATGCGACAGAATAAATGTGGACCTAGATGGACCAACAATTGGGATCCGTTACATGGCGACAAAGGTCAAAAGCGCGAGGGAAGACGAGGCTCTTTTAGGACTGGACTTAATTGAAACCTGTGTCAAAAACTGTGGTCAGAGATTCCACAGTGAAGTTGGAAAATATAGATTCTTGAATGAACTCATTAAATTGATATCTTCAAAGTACGATGGTGACTGGACAGCTGAACCAGTGAAGAAACGCATTATTCAGTGTATGTATAGCTGGAGTGTAGGTTTACCAAAGGAGACCAAAATTGCAGAGGCTTACAAGATGCTAAAAACACAAGGAATTGTTACCACAGACCCACAAGATCCTTATGCTCAAACTGCTGCTGAAAATCCTCCTGACAAACCAAAAGATACAATATTCCAGGATGAAGAAAAATCAAAGCTGCTGGCTCGTCTTCTGAAGAGTACTCATCCCGAAGATTTACAAGCTGCCAACAGACTGATCAAGACCATGGTTAGACAGGATGAAATGAAGATGGAGAGACTGGTGAAAAGAAATACAGAAATGGAAACTTGCTGTAATAATATCAAGCTTCTGACAGAGATGTTGAATCATTATGGTCCTTCTTCTCCAGCCCAGGATAAAGAACTCATGAAGGAACTGTATGACTCCTGTGATAAAATGAGACCACAATTGTTTAGACTGGCCAGTTCAGCCACAGAAGATGGCGATGAAGGATTAGCTGAAATCCTCAGAGTGAATGATGACTTATCAAGAGTATTAGAGTATTATAAAAGGATATTTGGATTGGCTCCAGCAGCAACCACTACACCAAGTAGTCCTGGGCCAATTTCTACAACCCAGACAACAAATTCTGAAGTCAGTTCTCCTACTGGTGCTTCCACTCTTATTGATCTGGGCTCTGGAGGCCAACAGGGAACGTCAATGGAAACTCCAGCATCCAGTGTTTTGGAAAATGAACTTAAAGCCTTAGGTCAGTCCTATTTGCAAGCCCCTCAGCAGCCTGGTGTTGCGGGACCGTGGGGTGCACCAGCCCAGAACTATGGTATTCTGCCACCACCTTCCACTACAGTAGGTGTGGTTAGACCCATGGGTCAGTCTCAGGTGGCTGGCATGATGCCCCCCATTTATATGGGTGCAGGGCAGATGAACCGAATGCCATTCCAAGCCATGTCTCCTGGCACAATGTCCATGGGGCCAAGGCCAGGACCACTGAGTATGGGTGTCAGTAGCTTTACCATGCCAACTGCTGGTTCATTACCTCGTGGGAATCTCCCTGCAGCAGGAGGTAGGAAGGCAGAAGAGCAGGCAAGGGCGCCAAGTGCGTTGGACTTACTTGGTCAAGAGTTACTACAGACCCAGAAGCAGCAGCAGAAGCAGAAACAAACTGTCGCTCCTCTGCAAGAGAAACCTGCACCTGAGCAGCAGCAGGCAGCAGCCCCTACAGCTGACAGTCTGTTGTCGTTAGGAATAGAGCCAAGCCCTTCAACCCTCCCTGTCAGTGTTGGTTCATCTTCATCTGCCGCTTTTCCTTCAGTACCTTCTCCACCAAAGCCAACCCCTCCGCCCTCTCTAGACAATGTCTTTGTTCCTTTAGATACTATTACACCAGGAAGCCATCCACCACTAACAGTTCTTGATAAAAACAGCATCAAATTAATTTTTCACTTTGCTAAGACGAGCGCAGAGTTGGCCAGGAAAGACTTACTGGTTGTTGTGATTTCCACTATGAGCTCACTATCATCTGCAGTTAAAAATTTCGTTTTCCAGGCAGCAGTACCAAAGACAATGAAGGTGAAGCTCCAACCTCCATCTGGCAGCGAGTTGCCAGCATATAATCCTATCCTTCCTCCGTCAGCCATTACACAAGTTATGTTGATTGCCAATCCAGCAAAGGAAAAGATCAGATTAAAGTACAAAGTAAGTTATCAAGTTGATGGCACTCCCATGACGGAAACTGGCGAGGTGGACAGCTTCCCTATTGATGTTCAAGGATAA

Transcript

rna-pdam_00005682

CTCAATTAAGAGGCCGTCATGGCGGAAACTCTGGAGGATTTGATTGAAttgaaatctaaaattaaCTATTTCACAGATAAAGCCACGGATCCTTCTAAAACTAAGGACGGCGTGGACTACTCGACACCAGTATGCGACAGAATAAATGTGGACCTAGATGGACCAACAATTGGGATCCGTTACATGGCGACAAAGGTCAAAAGCGCGAGGGAAGACGAGGCTCTTTTAGGACTGGACttaattGAAACCTGTGTCAAAAACTGTGGTCAGAGATTCCACAGTGAAGTTGGAAAATATAGATTCTTGAATGAACTCATTAAATTGATATCTTCAAAGTACGATGGTGACTGGACAGCTGAACCAGTGAAGAAACGCATTATTCAGTGTATGTATAGCTGGAGTGTAGGTTTACCAAAGGAGACCAAAATTGCAGAGGCTTACAAGATGCTAAAAACACAAGgAATTGTTACCACAGACCCACAAGATCCTTATGCTCAAACTGCTGCTGAAAATCCTCCTGACAAACCAAAAGATACAATATTCCaggatgaagaaaaatcaaagCTGCTGGCTCGTCTTCTGAAGAGTACTCATCCCGAAGATTTACAAGCTGCCAACAGACTGATCAAGACCATGGTTAGACAGGATGAAATGAAGATGGAGAGACTggtgaaaagaaatacagaaatgGAAACTTGCTGTAATAATATCAAGCTTCTGACAGAGATGTTGAATCATTATGGTCCTTCTTCTCCAGCCCAGGATAAAGAACTCATGAAGGAACTGTATGACTCCTGTGATAAAATGAGACCACAATTGTTTAGACTGGCCAGTTCAGCCACAGAAGATGGCGATGAAGGATTAGCTGAAATCCTCAGAGTGAATGATGACTTATCAAGAGTATTAGAGTATTATAAAAGGATATTTGGATTGGCTCCAGCAGCAACCACTACACCAAGTAGTCCTGGGCCAATTTCTACAACCCAGACAACAAATTCTGAAGTCAGTTCTCCTACTGGTGCTTCCACTCTTATTGATCTGGGCTCTGGAGGCCAACAGGGAACGTCAATGGAAACTCCAGCATCCAgtgttttggaaaatgaactTAAAGCCTTAGGTCAGTCCTATTTGCAAGCCCCTCAGCAGCCTGGTGTTGCGGGACCGTGGGGTGCACCAGCCCAGAACTATGGTATTCTGCCACCACCTTCCACTACAGTAGGTGTGGTTAGACCCATGGGTCAGTCTCAGGTGGCTGGCATGATGCCCCCCATTTATATGGGTGCAGGGCAGATGAACCGAATGCCATTCCAAGCCATGTCTCCTGGCACAATGTCCATGGGGCCAAGGCCAGGACCACTGAGTATGGGTGTCAGTAGCTTTACCATGCCAACTGCTGGTTCATTACCTCGTGGGAATCTCCCTGCAGCAGGAGGTAGGAAGGCAGAAGAGCAGGCAAGGGCGCCAAGTGCGTTGGACTTACTTGGTCAAGAGTTACTACAGACCCAGAAGCAGCAGCAGAAGCAGAAACAAACTGTCGCTCCTCTGCAAGAGAAACCTGCACCTGAGCAGCAGCAGGCAGCAGCCCCTACAGCTGACAGTCTGTTGTCGTTAGGAATAGAGCCAAGCCCTTCAACCCTCCCTGTCAGTGTTGGTTCATCTTCATCTGCCGCTTTTCCTTCAGTACCTTCTCCACCAAAGCCAACCCCTCCGCCCTCTCTAGACAATGTCTTTGTTCCTTTAGATACTATTACACCAGGAAGCCATCCACCACTAACAGTTCTTGATAAAAACAgcatcaaattaatttttcactttgctaAGACGAGCGCAGAGTTGGCCAGGAAAGACTTACTGGTTGTTGTGATTTCCACTATGAGCTCACTATCATCTGCAGttaaaaatttcgttttccaGGCAGCAGTACCAAAGACAATGAAGGTGAAGCTCCAACCTCCATCTGGCAGCGAGTTGCCAGCATATAATCCTATCCTTCCTCCGTCAGCCATTACACAAGTTATGTTGATTGCCAATCCAGCAAAGGAAAAGATCAGATTAAAGTACAAAGTAAGTTATCAAGTTGATGGCACTCCCATGACGGAAACTGGCGAGGTGGACAGCTTCCCTATTGATGTTCAAGGATAAATCGAATGATGATTTCAAGCCTCTGCTTGCGATGAGTATTGATAATAGGACGGGATGGCGTCCAGTTCTGTCTGTAATTATTAGAGTAACTTgcgggagtccgatttttCCAAaacgagtatgattacagacagaattggactaCAAGTAGTCCTGTTACCAAtgaatcaaaactatgacaaaatttgagaaacatACCAG

Protein

UniProt (Swiss-Prot top hit)

No Swiss-Prot hit above the reporting threshold for this gene.

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004762 (this species only) · gene tree & orthology
Ubiquitin family	UBD\|Alpha-Helix\|GAT · all ubiquitin genes in this species
Ubiquitin family	UBD\|Alpha-Helix\|VHS · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02883 all species →	Alpha_adaptinC2	Adaptin C-terminal domain	Domain	Interproscan
PF03127 all species →	GAT	GAT domain	Domain	Interproscan
PF18308 all species →	GGA_N-GAT	N-terminal extension of GAT domain	Family	Interproscan
PF00790 all species →	VHS	VHS domain	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR004152 all species →	Domain	GAT domain	Interproscan
IPR008152 all species →	Domain	Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain	Interproscan
IPR008942 all species →	Homologous_superfamily	ENTH/VHS	Interproscan
IPR008153 all species →	Domain	Gamma-adaptin ear (GAE) domain	Interproscan
IPR027422 all species →	Family	ADP-ribosylation factor-binding protein GGA1-3	Interproscan
IPR013041 all species →	Homologous_superfamily	Clathrin adaptor, appendage, Ig-like subdomain superfamily	Interproscan
IPR038425 all species →	Homologous_superfamily	GAT domain superfamily	Interproscan
IPR002014 all species →	Domain	VHS domain	Interproscan
IPR041198 all species →	Domain	N-terminal extension of GAT domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45905 all species →	GOLGI-LOCALIZED, GAMMA-ADAPTIN EAR CONTAINING, ARF BINDING PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0035091 all species →	Molecular Function	phosphatidylinositol binding	Interproscan
GO:0043130 all species →	Molecular Function	ubiquitin binding	Interproscan
GO:0006886 all species →	Biological Process	intracellular protein transport	Interproscan
GO:0016192 all species →	Biological Process	vesicle-mediated transport	Interproscan
GO:0005802 all species →	Cellular Component	trans-Golgi network	Interproscan
GO:0006893 all species →	Biological Process	Golgi to plasma membrane transport	Interproscan
GO:0031267 all species →	Molecular Function	small GTPase binding	Interproscan
GO:0034394 all species →	Biological Process	protein localization to cell surface	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
K12404	GGA; ADP-ribosylation factor-binding protein GGA	-	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 →