Gene detail

Detailed information of amic_s0157.g27.t1 in Acropora microphthalma

Genomic Location: sc0000157_pilon:537703...543336
NR annotation: KXJ04755.1, Transposon Tf2-8 polyprotein, partial [Exaiptasia diaphana]
Species Acropora microphthalma · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

amic_s0157.g27.t1

ATGCTGGTGGTTGGTTACAGTGATACTCAAGACGAAGCCAACAAGAACCACGATGAAAATCTACTTCGTCTGCTAAAAACAGCAAGAGAGATAAACTTAAAGTTTAACAAGAAAAAGCTCAACCTGCGAAGAAGCGAAGTGAAGTTCATGGGACACGTGCTTACATCCGATGGCCTTAAACCAGATGCAGATAAGGTCAAAGCAGTGGCCCAAATGCCAAGGCCTACCACTAAACAAGAGACCCTAAGCCTTCTAGGGTTTGTGAATTACCTCGCAAAGTTCTTGCCGCGCTTGTCGGAAGTTGCACAGCCTCTGCGCGAGCTAACAACAAAGAATGCAAGATTCGTGTGGTCAAGCCAGCACGATAAATCCTTCACAGAAGTCAAGAAGCTTGTGAGTGCACACCCGGTACTCAAAtactacgacatggatgcagaagttacgattcaatgcgacgcaaatgaaaaaggcctgggcgctactctactacagaatggccaaccagtcgcctttgcgtctaggacacttacacctgtcgagccgcgttacgctcaaattgagaaggagtgcctggcaattgtctttgcctgcaccaagttaagccaatacattacacgcagagaactcatcactgtagaatccgaccacaagcctctacagtctatcttcaaaaaatctctgttctctgcaccaggacgactacaacgcatgatattacgactacagaagtacaacatcaacgtggtctacAAACCTGGATCACAGATGTACGTGGCAGATCATCTATCACGAGCTTACCTTGCAGATCAAGGGGAGCGTAGTGATGAGTTTCAGGTGTTTGCTCTTGAGCTGGAAGAAATCAACCTGCTAAACAACGTAAAGATCACCAGCGAAAGACTTGCACAACTACAGAAAGCTACAGAACAAGACCCCATCATGCAATCACTAAAAAACACCATACTTATCGGATGGCCGGATACGCGCGTGTTATTCAAGAATCAACGCATTATTATTCCACAAGCACTCCGATCGGAAGTAATCGCGAGGTTACATTCCAGTCATCAAGGGATCGAGGCTTGTTTGAGGAAAGCGCGGGAGCGTGTGTTCTGGCCTGCAATGCAACATGATGTCAGGAATGCAGTATTAACATGCCAAGTGTGTGCAGAGTTCCAGCCAAACAATTCCAGCATGCCTATGCAATCACACGAAATACCAGACAGACCCTGGAGCAGAGTAGCTACTGATCTGTTTTCGTTGAAGTCAAAGGACTATATAGTACTGGTTGCTGCTGTTCGTGACGCCCACTGCGATTGCGTCAACTGTATTCGGTTTTTAGACAGCAGAAGCTTTGTTACTTGCTCTGACGATACTACTGTAGCTCTCTGGGATTGCAGAAATCTTAAAAGTAAAGTTATTAGCATGGAAGGACACACAGACTGGGTGAAGAGTATTGAATACCACAAGCCGTCTGGACTCCTTGTGACTTCAGCTTTTGATGATACGGTTCGTGCGTGGGACATAAACAGATACTCAAATGACGGTACAGCTCTCGGTCAAATTCTTCTGAAATTTCCATATTTGATTCGCATGAAAATATCGCCTGATGGTGACAAAATTATCCTCTCGGCCAATCCAGGGCGCTTACTTGTTATTCATAATCTATCTCTGAACAACTTGCAGTACGATATTAAAGGGGATGAAATGCCACCATCTCTACATGAGGTGTGCGATTCCTCATCACTTGTCAGTTTAGCCAGTCACCGCTGGCCGAGCAAGGCAAGGAATGCATTGGAGGTTATTCAAGATTTCCCCGAGGACTGCACTCCATGGTGCATTTCATCATTAGAGGTGCATCCGCACAGCTGGTGCAGTGTTGCACGATACACTTGCAGGAATTCAAGGAATGAGTGGACTGTTGTTCATGATATTCAGGATTTTGCTGAACACAGAGTTGGGGAGGCAACAAGTTCTTTAAGGCGTCTCACACACAGCATTCAAGAGCCAAATGTTGCAAAAGGCTACATAAAAGAACACTGTTTTAGCAGAGATGGAAGAGTCATTTGCTCGCCTTTTGGCAATTCTGCTAGAATCCTGAGTTTCAATTCACAGTGTGACGAATTGTCATCTTGTTCTCGTAACATTCCCTCTGAGCTCTGTGATTTGAAAACCCTTATCAGCCATAAGCATGCTGTTGTAACTTGTAGGTTCTCACCAAAACATCTGCTTCTTTCTTTGGGTTGTTTGGGAGGAAAGGTTAGTTTTTATGAGCCAAAGCTGTGA

Transcript

amic_s0157.g27.t1

TGCTATTTGGTATTTGTTCTGCCCCAGAAGAGTTCGAAAGTACCCTACACGAACAACTGGGAGACCTTGAAGGCGTGGAGGTACTTCGCGACGATATGCTGGTGGTTGGTTACAGTGATACTCAAGACGAAGCCAACAAGAACCACGATGAAAATCTACTTCGTCTGCTAAAAACAGCAAGAGAGATAAACTTAAAGTTTAACAAGAAAAAGCTCAACCTGCGAAGAAGCGAAGTGAAGTTCATGGGACACGTGCTTACATCCGATGGCCTTAAACCAGATGCAGATAAGGTCAAAGCAGTGGCCCAAATGCCAAGGCCTACCACTAAACAAGAGACCCTAAGCCTTCTAGGGTTTGTGAATTACCTCGCAAAGTTCTTGCCGCGCTTGTCGGAAGTTGCACAGCCTCTGCGCGAGCTAACAACAAAGAATGCAAGATTCGTGTGGTCAAGCCAGCACGATAAATCCTTCACAGAAGTCAAGAAGCTTGTGAGTGCACACCCGGTACTCAAAtactacgacatggatgcagaagttacgattcaatgcgacgcaaatgaaaaaggcctgggcgctactctactacagaatggccaaccagtcgcctttgcgtctaggacacttacacctgtcgagccgcgttacgctcaaattgagaaggagtgcctggcaattgtctttgcctgcaccaagttaagccaatacattacacgcagagaactcatcactgtagaatccgaccacaagcctctacagtctatcttcaaaaaatctctgttctctgcaccaggacgactacaacgcatgatattacgactacagaagtacaacatcaacgtggtctacAAACCTGGATCACAGATGTACGTGGCAGATCATCTATCACGAGCTTACCTTGCAGATCAAGGGGAGCGTAGTGATGAGTTTCAGGTGTTTGCTCTTGAGCTGGAAGAAATCAACCTGCTAAACAACGTAAAGATCACCAGCGAAAGACTTGCACAACTACAGAAAGCTACAGAACAAGACCCCATCATGCAATCACTAAAAAACACCATACTTATCGGATGGCCGGATACGCGCGTGTTATTCAAGAATCAACGCATTATTATTCCACAAGCACTCCGATCGGAAGTAATCGCGAGGTTACATTCCAGTCATCAAGGGATCGAGGCTTGTTTGAGGAAAGCGCGGGAGCGTGTGTTCTGGCCTGCAATGCAACATGATGTCAGGAATGCAGTATTAACATGCCAAGTGTGTGCAGAGTTCCAGCCAAACAATTCCAGCATGCCTATGCAATCACACGAAATACCAGACAGACCCTGGAGCAGAGTAGCTACTGATCTGTTTTCGTTGAAGTCAAAGGACTATATAGTACTGGTTGCTGCTGTTCGTGACGCCCACTGCGATTGCGTCAACTGTATTCGGTTTTTAGACAGCAGAAGCTTTGTTACTTGCTCTGACGATACTACTGTAGCTCTCTGGGATTGCAGAAATCTTAAAAGTAAAGTTATTAGCATGGAAGGACACACAGACTGGGTGAAGAGTATTGAATACCACAAGCCGTCTGGACTCCTTGTGACTTCAGCTTTTGATGATACGGTTCGTGCGTGGGACATAAACAGATACTCAAATGACGGTACAGCTCTCGGTCAAATTCTTCTGAAATTTCCATATTTGATTCGCATGAAAATATCGCCTGATGGTGACAAAATTATCCTCTCGGCCAATCCAGGGCGCTTACTTGTTATTCATAATCTATCTCTGAACAACTTGCAGTACGATATTAAAGGGGATGAAATGCCACCATCTCTACATGAGGTGTGCGATTCCTCATCACTTGTCAGTTTAGCCAGTCACCGCTGGCCGAGCAAGGCAAGGAATGCATTGGAGGTTATTCAAGATTTCCCCGAGGACTGCACTCCATGGTGCATTTCATCATTAGAGGTGCATCCGCACAGCTGGTGCAGTGTTGCACGATACACTTGCAGGAATTCAAGGAATGAGTGGACTGTTGTTCATGATATTCAGGATTTTGCTGAACACAGAGTTGGGGAGGCAACAAGTTCTTTAAGGCGTCTCACACACAGCATTCAAGAGCCAAATGTTGCAAAAGGCTACATAAAAGAACACTGTTTTAGCAGAGATGGAAGAGTCATTTGCTCGCCTTTTGGCAATTCTGCTAGAATCCTGAGTTTCAATTCACAGTGTGACGAATTGTCATCTTGTTCTCGTAACATTCCCTCTGAGCTCTGTGATTTGAAAACCCTTATCAGCCATAAGCATGCTGTTGTAACTTGTAGGTTCTCACCAAAACATCTGCTTCTTTCTTTGGGTTGTTTGGGAGGAAAGGTTAGTTTTTATGAGCCAAAGCTGTGAACAATAAAGTGAGTCGACCTTG

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q8AVS9	DDB1- and CUL4-associated factor 10 OS=Xenopus laevis OX=8355 GN=dcaf10 PE=2 SV=1
Q6NWH1	DDB1- and CUL4-associated factor 10 OS=Danio rerio OX=7955 GN=dcaf10 PE=2 SV=2
Q5FW06	DDB1- and CUL4-associated factor 10 OS=Xenopus tropicalis OX=8364 GN=dcaf10 PE=2 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0008363 (this species only) · gene tree & orthology
Ubiquitin family	UBD\|Other\|Beta-prp · all ubiquitin genes in this species
Ubiquitin family	E3\|E3 adaptor Cullin RING\|DWD · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00400 all species →	WD40	WD domain, G-beta repeat	Repeat	Interproscan
PF17917 all species →	RT_RNaseH	RNase H-like domain found in reverse transcriptase	Domain	Interproscan
PF17921 all species →	Integrase_H2C2	Integrase zinc binding domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	Interproscan
IPR036322 all species →	Homologous_superfamily	WD40-repeat-containing domain superfamily	Interproscan
IPR001680 all species →	Repeat	WD40 repeat	Interproscan
IPR041373 all species →	Domain	Reverse transcriptase, RNase H-like domain	Interproscan
IPR043128 all species →	Homologous_superfamily	Reverse transcriptase/Diguanylate cyclase domain	Interproscan
IPR019775 all species →	Conserved_site	WD40 repeat, conserved site	Interproscan
IPR041588 all species →	Domain	Integrase zinc-binding domain	Interproscan
IPR039085 all species →	Family	DDB1- and CUL4-associated factor 10	Interproscan
IPR043502 all species →	Homologous_superfamily	DNA/RNA polymerase superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR14588 all species →	DDB1- AND CUL4-ASSOCIATED FACTOR 10	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0080008 all species →	Cellular Component	Cul4-RING E3 ubiquitin ligase complex	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

No KEGG orthology assignment for amic_s0157.g27.t1.

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 →