Gene detail

Detailed information of amic_s0112.g8.t1 in Acropora microphthalma

Genomic Location: sc0000112_pilon:74648...94185
NR annotation: XP_044173102.1, conserved oligomeric Golgi complex subunit 4-like [Acropora millepora]
Species Acropora microphthalma · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

amic_s0112.g8.t1

ATGGCGGCCCACGAAATTGATGTATTCAGTCTGACAGATATTACAGAAGTACAACAAGCTTATGCACAAATCCATCTTCATGAGCAAAAATTGAACAACGAACTGGATGCCATATTGGAAAACCAGCCCAGACTTGATGCAAAAATGAACTCGTTACAGAATGTCATTCCCAATCTACAGCTAGTTATGAGAGATGCCCAACATTTGCATGGTATGATTTCCAATACATCTGATTTAGCTGAAAAGGTTAGCAGCAAAGTCCGACTCCTGGATCAGGTTAAGAACAGAGTTCAAGAGACAATAAAGCGTGTGGATGACATTCTAGATTTAAAGGCCTGTGTGGATGGAGTTCAGATAGCTCTGAATACAGAGAATTATGAACAGGCGGCAGCACATATCCACAAATATCTAAATCTTGATGAAGACAAGCTGAAAGAGATCACAAGGGATTCTCAAGAAGGTTCTGACTTAGCAGGATCTTTTGCTTTACTTCATGAGGCAGAGGTAAAACTGAAAAGCATAGTTTGTGGCAAGTTTGAAGCAGCCATTTCCAATGGTGACAGAAATTCTGTTGAAAGGTTTTTCAAGATTTTTCCTCTGCTTGGCCAGCATCAACTTGGACTGGAAAAATATGCCGAGTATTTATGCTCACAGATTGCTGCTCATTGCCAGAGAAATCTTGACAATGCTGTTGCTATCAAAGAATCTGAGCGACAAGCTAATGTGGTATTTGCTAACACCCTGACATTGCTGTTTGAAAAGATTGCAAGAATGGTGGAAGAACATCAGCCTTCTGTAGAAACATATTATGGACCTGGAAAAATGTTTATTCTGCTACAAGCAATGCAGGTGGAGTGTGACAAGCAAGCAAGTCAAGTTGTGGACCAGTTTGTCATAAAACGTCAGTTTAAGGAAAAGTTCAAATCAGTTCAGAACAGTCAGACATTCAAGGGTTCTTCTGCGAACATGGAAAGATATGATCCAAGAGAACTTGATGTGGTTTTAAGAGAAGTTGTGGTAATGAATGCAAGAGCAGAGATGTATTTAAAGTTTATTGAGAAAAGGATAAAGGATGATATAGAAAACATACCAGAAGAGGAGAAAACTGAAGAAATCATGGTAATTCAAGAGAAGGTGATATCAAACTGTGAGTTGAGCAAAAAAATGCAGGAGCTGATCGGAAATTACATTTACATGGAAGAATATTTTATGAGAGAAACTGTCATGAAAGCTGTCAAAATGGATGCTTCAGAAGGAGGGGATGATGAAGCTGTTACGTCAAGTATGGTGGATGATGTGTTTTTCATTGTACAGAAGGCTGTCAGGCGTGCGCTGTCCAGCTCCAGTGTTGACGGAACTTGCGCGATGCTTAATCATGCATGTGCTCTCTTATCATCTGATTACCGCGATGTATTGACCTCAAGGCTGAAAGCAGGTTTTCCTTCGGGCAGTCTCGATTTTTCTGGAATGCTTCAAGGCAAGATTCAAGTGGGTTATTCTTCAACAGCGGAGAATACAGCCGCCAGAAAGGCGTTTCTTGTTACACTGAACAATCTCGAAGTTAGCAGCGATAATATTATTAAACTGAAGAAAGATTTGGAGGTCGAATGTGAAAGGATTCTTGCTTTTACAGAGCCTTCAAAACTGAAGTTAGAGAGCTGCCTTGCGGACTTAATGAACACGTCAAATATCTTCAAAGGGTTACTTCAAGAAGGAATTTATCAACTGTGTTCCACGGCTGTTATTCCAAGATTAAAACCTTTGATTGATGGATTTAACTCAACTAGCCACAACATATCAGAGGAGGAGTTCTCATTTTATGAAGTTAATGACCCCTTTGTTCAAAGCTTTATCACAAGTTTGGATTCAATGCTGACGTCATTCAAGGGTCCGCTGACTACTGCGAATTATGACTCGTTGGTCAGTATGGCAGCCACAGAGATAACGAACCAACTGGAGACTTCAGTCATGAAAGCTTCTTTCAATAGGTTAGGTGGCCTGCAGTTCGACAAGGAATTGCGTTCATTGGTTGGTTATTTAACAGCGGTTACGCAATGGACAATTAGAGACAAATTTGCCCGATTGACACAGATTGCTACCATTCTTAATCTAGAGAAGGTTGGTGAGATCATGGACTACTGGGGTCCCAATTCAGGACCAATGACTTGGCGGCTTACTCCGACAGAAGTCAGACAAGTGTTGTCTTTAAGGGTGGACTTTAGAAGTGAAGATATCAACCGCCTCAAACTTTAG

Transcript

amic_s0112.g8.t1

TGTATGACCAAATAAAGTGTAACGTTAATAATGGCGGCCCACGAAATTGATGTATTCAGTCTGACAGATATTACAGAAGTACAACAAGCTTATGCACAAATCCATCTTCATGAGCAAAAATTGAACAACGAACTGGATGCCATATTGGAAAACCAGCCCAGACTTGATGCAAAAATGAACTCGTTACAGAATGTCATTCCCAATCTACAGCTAGTTATGAGAGATGCCCAACATTTGCATGGTATGATTTCCAATACATCTGATTTAGCTGAAAAGGTTAGCAGCAAAGTCCGACTCCTGGATCAGGTTAAGAACAGAGTTCAAGAGACAATAAAGCGTGTGGATGACATTCTAGATTTAAAGGCCTGTGTGGATGGAGTTCAGATAGCTCTGAATACAGAGAATTATGAACAGGCGGCAGCACATATCCACAAATATCTAAATCTTGATGAAGACAAGCTGAAAGAGATCACAAGGGATTCTCAAGAAGGTTCTGACTTAGCAGGATCTTTTGCTTTACTTCATGAGGCAGAGGTAAAACTGAAAAGCATAGTTTGTGGCAAGTTTGAAGCAGCCATTTCCAATGGTGACAGAAATTCTGTTGAAAGGTTTTTCAAGATTTTTCCTCTGCTTGGCCAGCATCAACTTGGACTGGAAAAATATGCCGAGTATTTATGCTCACAGATTGCTGCTCATTGCCAGAGAAATCTTGACAATGCTGTTGCTATCAAAGAATCTGAGCGACAAGCTAATGTGGTATTTGCTAACACCCTGACATTGCTGTTTGAAAAGATTGCAAGAATGGTGGAAGAACATCAGCCTTCTGTAGAAACATATTATGGACCTGGAAAAATGTTTATTCTGCTACAAGCAATGCAGGTGGAGTGTGACAAGCAAGCAAGTCAAGTTGTGGACCAGTTTGTCATAAAACGTCAGTTTAAGGAAAAGTTCAAATCAGTTCAGAACAGTCAGACATTCAAGGGTTCTTCTGCGAACATGGAAAGATATGATCCAAGAGAACTTGATGTGGTTTTAAGAGAAGTTGTGGTAATGAATGCAAGAGCAGAGATGTATTTAAAGTTTATTGAGAAAAGGATAAAGGATGATATAGAAAACATACCAGAAGAGGAGAAAACTGAAGAAATCATGGTAATTCAAGAGAAGGTGATATCAAACTGTGAGTTGAGCAAAAAAATGCAGGAGCTGATCGGAAATTACATTTACATGGAAGAATATTTTATGAGAGAAACTGTCATGAAAGCTGTCAAAATGGATGCTTCAGAAGGAGGGGATGATGAAGCTGTTACGTCAAGTATGGTGGATGATGTGTTTTTCATTGTACAGAAGGCTGTCAGGCGTGCGCTGTCCAGCTCCAGTGTTGACGGAACTTGCGCGATGCTTAATCATGCATGTGCTCTCTTATCATCTGATTACCGCGATGTATTGACCTCAAGGCTGAAAGCAGGTTTTCCTTCGGGCAGTCTCGATTTTTCTGGAATGCTTCAAGGCAAGATTCAAGTGGGTTATTCTTCAACAGCGGAGAATACAGCCGCCAGAAAGGCGTTTCTTGTTACACTGAACAATCTCGAAGTTAGCAGCGATAATATTATTAAACTGAAGAAAGATTTGGAGGTCGAATGTGAAAGGATTCTTGCTTTTACAGAGCCTTCAAAACTGAAGTTAGAGAGCTGCCTTGCGGACTTAATGAACACGTCAAATATCTTCAAAGGGTTACTTCAAGAAGGAATTTATCAACTGTGTTCCACGGCTGTTATTCCAAGATTAAAACCTTTGATTGATGGATTTAACTCAACTAGCCACAACATATCAGAGGAGGAGTTCTCATTTTATGAAGTTAATGACCCCTTTGTTCAAAGCTTTATCACAAGTTTGGATTCAATGCTGACGTCATTCAAGGGTCCGCTGACTACTGCGAATTATGACTCGTTGGTCAGTATGGCAGCCACAGAGATAACGAACCAACTGGAGACTTCAGTCATGAAAGCTTCTTTCAATAGGTTAGGTGGCCTGCAGTTCGACAAGGAATTGCGTTCATTGGTTGGTTATTTAACAGCGGTTACGCAATGGACAATTAGAGACAAATTTGCCCGATTGACACAGATTGCTACCATTCTTAATCTAGAGAAGGTTGGTGAGATCATGGACTACTGGGGTCCCAATTCAGGACCAATGACTTGGCGGCTTACTCCGACAGAAGTCAGACAAGTGTTGTCTTTAAGGGTGGACTTTAGAAGTGAAGATATCAACCGCCTCAAACTTTAGAGGATTAGACCTTGTAGATAATGGAATTGTTCAATAAATTCTGTGGTCAATATATCACTGTTAAAAGCTACTTACAGTTGCCTTTCTTCCATTTTTATGGAGTTGATGAGGACATAAtagggagctttagcaaggaagacgacagcgccacaaattaagaatttgattggtcgagtgagggaaaataagcgtactgcatctgcggcacgcttttatgaaaaagtccgtgccgtcctctgaaatgtaaaattaccacgattaccgttttgataacaacttgagcatacaaccgtaaatctttcattctccgtatttattacgacggcgcccacactaatccacttgcagctttctttaccaacattatagaatgcgagcaagatggggcaatcgcaaatagtcacaatagaccattttcgaattctcacggctggactggatctagcatgaaatggaggctaatgcgggcaaatcttttcaaatgcaaattaatttgccggcattagtctccatttcatgctagatccagtccaaccgttagaatacgaaactggcctattgagcaagtatttattttcaagtgacgttttcctcgccgcagcagtcgtcattgctaaagctcgctGATGAATGATCTCTTTTCTGTTGTATGTCGATAAGCGTGTCGAAAGTAAATGGTATTTCTGTCAATGTAGCGAAGCGGAATACACAGATATGGTCATTTTGCCAGCACGGACAGAAGGTCTAGGTTGGTGTTGGAAGGATTATTAGTATACTTGTAAGGTATTTAAAGTGGAACGTTGTGAATTTAAACCAGTCGAGGACCGCACTCACTCATCTTCTCGGTTTTTTTTGTTTTCGATGTGAATGTATAGTTTTCTGCATGATTCATCATTGTAATTCAGCCCCTAGAGTTAGCTGCGCCGCAGCAGATGTGGTATACGTTCCCTTTTTTCCAAGCAGTGGTTTTAGGTTTTTTCCTATCTGGCGGTGTCGCAATCTTTTCGCTGCTATTAAATTGCGAGACAGAAATCCTGTATTGTAACCCAGCGTTATCTGATTGTCCAATGGTTGTGTAAATAAATGGTCGTTTGAGGT

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q5R7R6	Conserved oligomeric Golgi complex subunit 4 OS=Pongo abelii OX=9601 GN=COG4 PE=2 SV=1
Q9H9E3	Conserved oligomeric Golgi complex subunit 4 OS=Homo sapiens OX=9606 GN=COG4 PE=1 SV=3
Q3MHG0	Conserved oligomeric Golgi complex subunit 4 OS=Bos taurus OX=9913 GN=COG4 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003268 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF08318 all species →	COG4_m	COG4 transport protein, middle alpha-helical bundle	Repeat	Interproscan
PF20662 all species →	COG4_C	Conserved oligomeric Golgi complex subunit 4, C-terminal	Repeat	Interproscan
PF20663 all species →	COG4_N	Conserved oligomeric Golgi complex subunit 4, N-terminal	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR048682 all species →	Family	Conserved oligomeric Golgi complex subunit 4	Interproscan
IPR013167 all species →	Domain	COG4 transport protein, middle alpha-helical bundle	Interproscan
IPR048684 all species →	Domain	Conserved oligomeric Golgi complex subunit 4, C-terminal	Interproscan
IPR048680 all species →	Domain	Conserved oligomeric Golgi complex subunit 4, N-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR24016 all species →	CONSERVED OLIGOMERIC GOLGI COMPLEX SUBUNIT 4	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006890 all species →	Biological Process	retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	Interproscan
GO:0007030 all species →	Biological Process	Golgi organization	Interproscan
GO:0017119 all species →	Cellular Component	Golgi transport complex	Interproscan
GO:0048213 all species →	Biological Process	obsolete Golgi vesicle prefusion complex stabilization	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
K20291	COG4, COD1; conserved oligomeric Golgi complex subunit 4	-	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 Acropora microphthalma 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 microphthalma, 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 →