Gene detail

Detailed information of amic_s0256.g18.t1 in Acropora microphthalma

Genomic Location: sc0000256_pilon:309563...329545
NR annotation: XP_029207712.2, DNA excision repair protein ERCC-5-like isoform X2 [Acropora millepora]
Species Acropora microphthalma · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

amic_s0256.g18.t1

ATGGGGGTTAAAGGTCTGTGGCAGCTTTTGGAATGCGTGGGACGACCAATTACACTGGAATCATTAGAGAAAAAAGTACTGGGAGTTGATGCCAGTCTGATTCTTAACCAATCGGTGAAGGGACTGCGTGATAAGAATGGGAATCCTGTTTACAATGCGCATCTTGTTGGTTTGTTCAATCGATTGTGCAAGTTGTTGTATTACAGGATAAAACCTGTTTTTGTTTTCGATGGTGGAGTCCCAAATCTGAAGAAAAAGACTTTGGCAGCAAGAAAGGAGAGGAGGTTCAAAGCAATTCATGGATCCAGCAAAGCTGCAGAGAAAATCATCAAGAACTACTTAAAGGCAAAGGCTCTTGAAACTGTCACGGGGAGAAAAAGTGCTGTTGTTCCAAGGAGCAAAAGTCCAAGAGAACCTGATGTGTTCGAGCTTCCTCCATTACCTTCAACTTCTTCTGCTGCAAACGAAGGCTTTTCAGAAGAAGATGATATTCCAATACTGGATCATTTTCGCAGTCAACAGATGGAGCAAACGTACCAGGACCCTGCAACAATTAATATTGACTCACAAGATTTCAAGTCCTTGCCCGCAGAGATACAGCATGAACTTATCAAAGAGGTGAAAGAGGAAAGAAAGTGGAGAAACAAACATGACATGCCGCAGCAATCAAGAGATTTTTCGTGCTTTCAACTGGATAGAGTCTTGAAGCGAGGCAAAATGAATCAACGACTGGATGAACTTTGTAAGGAAATGAACAGCAAGAATTCAGGAGATCTTGTAGAAATGACTTCACAGGATTCATTGGGAGAAAACTCTGATGTTAAATCGCAAAAGATTTTGTCTGAAGATTCAGCTCATTACATCCTGATTAAGAGTACTGGAAACAGCCAAGGCAATGAGAAAGATCAGGAGGAAGAAGGATTGTCTTCAAACACAGATTTTTCTAGAGAGGGAGGATTTTTTCGTGATGGCGAAGACTGTAAAATAATCAGTTGGACCAATCCTCTCCCTAAAACAACAGTAACAGTGAAGCCTCCATGCTTTGACATTCCTGATCTTTCTACCAGCGATTCAGAGATGTTGTCCCCTCTGGTAGATAAACCATCAAAAGACATTTTCATGAAAAGTCCTACTCAAACAAACACAACTGCTTTTGATTTCTCCTCCATAAAGGAGGATGAGACTATTAATAAAATTGGTTTAAATGAGGATGAGAAAGTTGGAAGAGAAAGTGATGCACGAAAACTACAAAAACAAAACACTGACAATAATGAAATGTTGAATAGGAAAGAGTTGGAAGAGTTGAAAATGGATAATATTTGTAATCAGCAAGAAGGGACAAGTCAGGAAGGAAATAAGAATGATAGTCTCCTTACTGAGATTATAAACAAAAAGAAGGAACTTGAAGACCTCATCAAGAAGTGGGAGGTCTCTAATAAATCGAAAACACCAATTAGTTTGATGGCTTCTACTGTTGATGAGGATGTTGGCAAAGAAGAGAGCGTAATAACACCCCTTCACAGTTCACAGGACAGACAACAGGAGATCAAGATTGAAGGGGAAGAAACTAATCCAATAGTGTTGATTATTGGGGATGACAATGTTGATGAAGAAAAATCTGAGAGCTATGTTTGTGTCTTGGAGAATGACTCTGACGAAGGAAGCTCTGTGGAGGAAATTGGTGCTTCTCTTGAACCTTCAAAAAGTGTTCTTGGTTCTAAACATGAAGTGAGTGAAATTGGAATTCAGCAGACTGTTTCAAGATCACAAGAAGAATCCATGTTGATTTATGATGAAGAAAATGCAGCCATAGAGACGACAGAAATCAAACTGGTCTCTTCTAGTGTTGTCATGAATACTGAGCTTACAGACCATGCTACCGTGGCTAGCACAGAACAAGACATCAGCCCTTCCTGTTCGCATGAAATTATTGATAGTATAGAGATTCAAGATTCTTCAGATGAGAGTGGCATTGGCACAACTGTGGATGAACAAGAGGCTGGCCCCTCTGGGGTCCCTGTGGAATGGCAGGAAGCTACCACAGTGGAGAACTTGGAGGAAATCCAGAGGAACATTGAGACTGAACAAAAAAGCCTGGCGACTGAAAAAGCACGACAGAACCGTATAGCAGCTACAGTATCCAATGAAATGTTCACTGAATGCCAGGAGCTCCTACAGTTGTTTGGTGTCCCATTCCTTGTGAGCCCAATGGAGGCAGAAGCGCAATGTGCAGCATTGGATGCACTCGGCTTAACAGATGGTTCCATCACGGATGACAGTGATATTTTCCTATTTGGAGGAACGAGAATTTACAAGAACATCTTTAATCAGAACAAACACGCTGAGTTGTATCGCAGCGATGCAGTGCAACGAGATCTTGCTTTGGATCGATCAAGTCTTATTTGCATTGCTTTTGTAACCGGCAGCGACTACACTGAAGGAATACAAGGGGTTGGTCCTGTTGGCGCAATGGAGATATTGCAGGAATTTCCTGGTGAAGGTCTAGAAGGGCTGAAAAAATTCAAAAGCTGGCATAAGGAAACTCAAGAACAAACAAAGATTCCTAAAGAAACTAAAGTTAAAAGGAAGATGCGATCTGTTGTGTTACCAAGAGATTTTCCCTCGGAAGAAGTGTTTGAAGCTTATTTGCATCCTGTTGTCGATGAATCAACGGAGCAGTTTGAATGGGGAAAACCAGATTTGCATTCTCTTAGATTGTTTGCTTCCGACAAACTGGGCTGGTCAACAGCAAGAACCGATGAGATTTTGTTGCCAGTTTTAAAACAACTTAATAAGGATGAGGCACAAATGAAGATCGATAGTTATTTCCAAGTGGCTTTTGATGAGAAAAGAAGCATAAAAAGTAAGCGAATTCGTCAAGTGCTGAATCGTACGTTCAACCCGATTGAaaaggaaagcagtgaaaatcaaagcaaagAAGAAACCAGCAATCAAGACGAAGCGTCAAAGAGGGCGACGCGTCAGAGAAAACGACCACTGGCAACAGAAAAGGAGGCAGAGAAATCACAAGAAAAGAACGATAGTGTGAAGAAAGCAAAACTATTGGAGAAGGAAGAAGGTGATGGTGCGCGAGCGCACTTGAAGGGAAAAGAATTGATGGTTGAAATTACTCCTTTACAGCTTCCTTGTTCGTCAGGAAAAGGGCTTAATTCGTCTCAAAAAGGTGCTGAAAGCAAATTCGTTGCAGCAAGGAAGACGAGGGCAACAAGAAAGCTTGATTTGACTTCTCAAATTGCGGTTAACAAGAGAAAGGATTATTCTACTAGTGATAGCAGCGACAGTGATGGTTGCGATGACGTCATTTACGAACGATATGAGCGGCCTGTGCAGGGATTTCGCTCGATAAGGACACCTGGGAGGCCTGTGCAACAAGACACTTCAACCTCTGATAGCTCAGATGATGAAAGCAATGTAGAAAATGCTTATCGAGGACCAAAACCCGTGTCTATATTTCACCGGGGGAGGAGTAGGGGGAGAGGAAGTAAGGTGGGGAGAGGTGACAAGGGAAACAGTGTGGTTAAGGTGGAAAACCGTGACGTAGGCCGTGACGATGACGTAATAAAATCAGCGTCTGTAACCAAGAGGAGGAAAAACAGAGGCAGAGGAAAGCGGGGACGACGCTAA

Transcript

amic_s0256.g18.t1

CATCTAATTTAGCATATCATGAAATCGAAGTTGTGACGGTGAAGTCAGCGGAATTCTTTTCGGTTAGATGCGCGGGAAATTTCAACATGGCGGGTGGCTTTTCTTTTGAAATAATCTCGTGACTTTTGAATCAGATAGAATGGACTCTGCAGAGAAAAGGGAAAACGAGCTCGACCTTTATTTTTGTGTTTCGAATTCATTGTGAATTGTGAGTGAATTCTAGACCTTTGCTGTTTGCTGCTTCGCTTGACTTTAATTTTGTTACTCGGCCAGTTTATATGGGGGTTAAAGGTCTGTGGCAGCTTTTGGAATGCGTGGGACGACCAATTACACTGGAATCATTAGAGAAAAAAGTACTGGGAGTTGATGCCAGTCTGATTCTTAACCAATCGGTGAAGGGACTGCGTGATAAGAATGGGAATCCTGTTTACAATGCGCATCTTGTTGGTTTGTTCAATCGATTGTGCAAGTTGTTGTATTACAGGATAAAACCTGTTTTTGTTTTCGATGGTGGAGTCCCAAATCTGAAGAAAAAGACTTTGGCAGCAAGAAAGGAGAGGAGGTTCAAAGCAATTCATGGATCCAGCAAAGCTGCAGAGAAAATCATCAAGAACTACTTAAAGGCAAAGGCTCTTGAAACTGTCACGGGGAGAAAAAGTGCTGTTGTTCCAAGGAGCAAAAGTCCAAGAGAACCTGATGTGTTCGAGCTTCCTCCATTACCTTCAACTTCTTCTGCTGCAAACGAAGGCTTTTCAGAAGAAGATGATATTCCAATACTGGATCATTTTCGCAGTCAACAGATGGAGCAAACGTACCAGGACCCTGCAACAATTAATATTGACTCACAAGATTTCAAGTCCTTGCCCGCAGAGATACAGCATGAACTTATCAAAGAGGTGAAAGAGGAAAGAAAGTGGAGAAACAAACATGACATGCCGCAGCAATCAAGAGATTTTTCGTGCTTTCAACTGGATAGAGTCTTGAAGCGAGGCAAAATGAATCAACGACTGGATGAACTTTGTAAGGAAATGAACAGCAAGAATTCAGGAGATCTTGTAGAAATGACTTCACAGGATTCATTGGGAGAAAACTCTGATGTTAAATCGCAAAAGATTTTGTCTGAAGATTCAGCTCATTACATCCTGATTAAGAGTACTGGAAACAGCCAAGGCAATGAGAAAGATCAGGAGGAAGAAGGATTGTCTTCAAACACAGATTTTTCTAGAGAGGGAGGATTTTTTCGTGATGGCGAAGACTGTAAAATAATCAGTTGGACCAATCCTCTCCCTAAAACAACAGTAACAGTGAAGCCTCCATGCTTTGACATTCCTGATCTTTCTACCAGCGATTCAGAGATGTTGTCCCCTCTGGTAGATAAACCATCAAAAGACATTTTCATGAAAAGTCCTACTCAAACAAACACAACTGCTTTTGATTTCTCCTCCATAAAGGAGGATGAGACTATTAATAAAATTGGTTTAAATGAGGATGAGAAAGTTGGAAGAGAAAGTGATGCACGAAAACTACAAAAACAAAACACTGACAATAATGAAATGTTGAATAGGAAAGAGTTGGAAGAGTTGAAAATGGATAATATTTGTAATCAGCAAGAAGGGACAAGTCAGGAAGGAAATAAGAATGATAGTCTCCTTACTGAGATTATAAACAAAAAGAAGGAACTTGAAGACCTCATCAAGAAGTGGGAGGTCTCTAATAAATCGAAAACACCAATTAGTTTGATGGCTTCTACTGTTGATGAGGATGTTGGCAAAGAAGAGAGCGTAATAACACCCCTTCACAGTTCACAGGACAGACAACAGGAGATCAAGATTGAAGGGGAAGAAACTAATCCAATAGTGTTGATTATTGGGGATGACAATGTTGATGAAGAAAAATCTGAGAGCTATGTTTGTGTCTTGGAGAATGACTCTGACGAAGGAAGCTCTGTGGAGGAAATTGGTGCTTCTCTTGAACCTTCAAAAAGTGTTCTTGGTTCTAAACATGAAGTGAGTGAAATTGGAATTCAGCAGACTGTTTCAAGATCACAAGAAGAATCCATGTTGATTTATGATGAAGAAAATGCAGCCATAGAGACGACAGAAATCAAACTGGTCTCTTCTAGTGTTGTCATGAATACTGAGCTTACAGACCATGCTACCGTGGCTAGCACAGAACAAGACATCAGCCCTTCCTGTTCGCATGAAATTATTGATAGTATAGAGATTCAAGATTCTTCAGATGAGAGTGGCATTGGCACAACTGTGGATGAACAAGAGGCTGGCCCCTCTGGGGTCCCTGTGGAATGGCAGGAAGCTACCACAGTGGAGAACTTGGAGGAAATCCAGAGGAACATTGAGACTGAACAAAAAAGCCTGGCGACTGAAAAAGCACGACAGAACCGTATAGCAGCTACAGTATCCAATGAAATGTTCACTGAATGCCAGGAGCTCCTACAGTTGTTTGGTGTCCCATTCCTTGTGAGCCCAATGGAGGCAGAAGCGCAATGTGCAGCATTGGATGCACTCGGCTTAACAGATGGTTCCATCACGGATGACAGTGATATTTTCCTATTTGGAGGAACGAGAATTTACAAGAACATCTTTAATCAGAACAAACACGCTGAGTTGTATCGCAGCGATGCAGTGCAACGAGATCTTGCTTTGGATCGATCAAGTCTTATTTGCATTGCTTTTGTAACCGGCAGCGACTACACTGAAGGAATACAAGGGGTTGGTCCTGTTGGCGCAATGGAGATATTGCAGGAATTTCCTGGTGAAGGTCTAGAAGGGCTGAAAAAATTCAAAAGCTGGCATAAGGAAACTCAAGAACAAACAAAGATTCCTAAAGAAACTAAAGTTAAAAGGAAGATGCGATCTGTTGTGTTACCAAGAGATTTTCCCTCGGAAGAAGTGTTTGAAGCTTATTTGCATCCTGTTGTCGATGAATCAACGGAGCAGTTTGAATGGGGAAAACCAGATTTGCATTCTCTTAGATTGTTTGCTTCCGACAAACTGGGCTGGTCAACAGCAAGAACCGATGAGATTTTGTTGCCAGTTTTAAAACAACTTAATAAGGATGAGGCACAAATGAAGATCGATAGTTATTTCCAAGTGGCTTTTGATGAGAAAAGAAGCATAAAAAGTAAGCGAATTCGTCAAGTGCTGAATCGTACGTTCAACCCGATTGAaaaggaaagcagtgaaaatcaaagcaaagAAGAAACCAGCAATCAAGACGAAGCGTCAAAGAGGGCGACGCGTCAGAGAAAACGACCACTGGCAACAGAAAAGGAGGCAGAGAAATCACAAGAAAAGAACGATAGTGTGAAGAAAGCAAAACTATTGGAGAAGGAAGAAGGTGATGGTGCGCGAGCGCACTTGAAGGGAAAAGAATTGATGGTTGAAATTACTCCTTTACAGCTTCCTTGTTCGTCAGGAAAAGGGCTTAATTCGTCTCAAAAAGGTGCTGAAAGCAAATTCGTTGCAGCAAGGAAGACGAGGGCAACAAGAAAGCTTGATTTGACTTCTCAAATTGCGGTTAACAAGAGAAAGGATTATTCTACTAGTGATAGCAGCGACAGTGATGGTTGCGATGACGTCATTTACGAACGATATGAGCGGCCTGTGCAGGGATTTCGCTCGATAAGGACACCTGGGAGGCCTGTGCAACAAGACACTTCAACCTCTGATAGCTCAGATGATGAAAGCAATGTAGAAAATGCTTATCGAGGACCAAAACCCGTGTCTATATTTCACCGGGGGAGGAGTAGGGGGAGAGGAAGTAAGGTGGGGAGAGGTGACAAGGGAAACAGTGTGGTTAAGGTGGAAAACCGTGACGTAGGCCGTGACGATGACGTAATAAAATCAGCGTCTGTAACCAAGAGGAGGAAAAACAGAGGCAGAGGAAAGCGGGGACGACGCTAAGATGACGTCAACGATCTTGCGTGGTTCGTGGACGGATCACCACTGTCGCGCGTGTCTAACGCGTTGTGGGTCTGCTGCTCGGCGTGTATTTTGTTTAGGTCAGACATCATTTGGGAAGTCTAGCTCGAATTTATGGAAGGTGGATGGAGCAATTACCGAGAAAGTAAGACAAGGAATCCTTCTGTCAAATTTTGACAGGCCGGCTATCTGTTTCTCGTTTCTAATGTGTGCATTTTAACTGACAAATCGGTGCGATGGCATGTCCTCTACACAACACAATCATTGTGCTTCTGGCTAATTTAACTTCTCTGGACATGCGCAGAACGAGTTCCAGTCACAGGCTACTGTGCTTCGTGCTTGAAACCAAATATTTCCCCACTCCACCGCGCCAAACTGCAGAGAAAACAATTGCTTTGCTGAGCATTTTGTAGTCCAAGTGGAGTTTTCTGTGATGAAATAGAAATCGTTTGTAGGCGAACTTCCACTTACAAACCTTCCCTGGTTAGTTGATATAGCTTCAAGGTGTCGCCGCCATCTGATAGGCCGTAAAAGGTGTTTCGTCAGAGCGAATGGCGAAGGACTCAGGCTGGAAACCAAATCGATAATTCGACCTTTATCAACGGCAaatgaatttctagtttctaa

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P35689	DNA excision repair protein ERCC-5 OS=Mus musculus OX=10090 GN=Ercc5 PE=1 SV=4
P28715	DNA excision repair protein ERCC-5 OS=Homo sapiens OX=9606 GN=ERCC5 PE=1 SV=3
P14629	DNA excision repair protein ERCC-5 homolog OS=Xenopus laevis OX=8355 GN=ercc5 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002929 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00867 all species →	XPG_I	XPG I-region	Family	Interproscan
PF00752 all species →	XPG_N	XPG N-terminal domain	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001044 all species →	Family	XPG/Rad2 endonuclease, eukaryotes	Interproscan
IPR006085 all species →	Domain	XPG, N-terminal	Interproscan
IPR006086 all species →	Domain	XPG-I domain	Interproscan
IPR029060 all species →	Homologous_superfamily	PIN-like domain superfamily	Interproscan
IPR036279 all species →	Homologous_superfamily	5'-3' exonuclease, C-terminal domain superfamily	Interproscan
IPR008918 all species →	Conserved_site	Helix-hairpin-helix motif, class 2	Interproscan
IPR006084 all species →	Family	XPG/Rad2 endonuclease	Interproscan
IPR019974 all species →	Conserved_site	XPG conserved site	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR16171 all species →	DNA REPAIR PROTEIN COMPLEMENTING XP-G CELLS-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003697 all species →	Molecular Function	single-stranded DNA binding	Interproscan
GO:0004519 all species →	Molecular Function	endonuclease activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006289 all species →	Biological Process	nucleotide-excision repair	Interproscan
GO:0004518 all species →	Molecular Function	nuclease activity	Interproscan
GO:0004520 all species →	Molecular Function	DNA endonuclease activity	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0003824 all species →	Molecular Function	catalytic activity	Interproscan
GO:0016788 all species →	Molecular Function	hydrolase activity, acting on ester bonds	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
K10846	ERCC5, XPG, RAD2; DNA excision repair protein ERCC-5	-	DNA repair and recombination proteins	ko03400	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 →