Gene detail

Detailed information of RMX52778.1 in Pocillopora damicornis

Genomic Location: SczhEnG_1580:1...7411
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_00023715

ATGGAGGAGCTAGAGATAGCAAAGAAGAAGCGGAAAGTTGATGGTGGAGGTGCTGCCTCAACGCCAAACCATGTGATGACCAATGGAGATTCTATTGGAACAAGCGATGCAGCTTCCACTCGACCACTTTCCCATCTGCAATTTAATCCGTCCAGATTTGACCGACTCCGCCAGATTACAATTGACTGTCAAAAGAATTTTCTCCCTCAACCTAAACCTAACGGCAGCAAGATACTTCGATGTAAAGGACCTGCAAAGGAACCGAACCCGGAGATACACTCGTCGAACGATGCAAACAGCCCAAGCCCTGATCTTATTATATCGTCCGCTGGCTCATCACCGGCTCATTCGCCTAAACCATTAGATTTCAAAATGTTGTCTACGCCCCCGCGGTCGAGTAAACTGGGAGATACGAATCTTCCGATACTTGAAAACACTTCAGAACTAACCTCCTCTGATCGCCAAATGGCGTGTGTCAGACTTGTGGCGAAATTAGACGAATCTTCAAGTAAAAAGCTTTCTAATGGAGTCACCACGGATGCTAGGACTTTAAATCAGGATTCCTTGGTGGAAGTTTTGGAAGAAGGCGATCAAACGTGCCCATTAAACCCTGGCGCTAAGCCTGTCCATGTGAATGGGGAAATCAATTTGTTAGAAGGGAACAAAGGGCCAGCGGATAATGATAAAACTACTGTGAAGGATCGAAATTCACCGTCTTTTTCAGACCTGGCTCCCAGTGCTAACGCAGAGGAAACTACAAAGGACTTCAATTTTAATTCAGACGAATTCAGACAAATGGTCAAGAAAATGATCCAAGAGAGGATGAGTCAAATCCAGCAGTCAATGGATGATGACAGCCCGAACGACAAGCTCTCCGTTAGGCTAGCTGCACTTGAGAAGGAGAACAAAGCATTGAAAGAGTACGCAAAGAGAGTAGAAGATTCTGTAAAAACGATTTTAAAAGCTGAGAGCTTAAAAGCAAAGAAACGAGAAACTAAAGCTGTTCAAACCCAAGATCTTAACTGGATGAACGCTCTGCGCACGAAGACTGTGAACGCACCATCTCCCCCAGCGAGTTTAACAGCTTCCAGGCCCTCAAATGCTAGTGTCAATGTTATGACTACACCAACACCACGGCTCACCTCCACCGTAGCACCTTTGCCTGGTCACACAGTACCGCAATCAGCTCCCGTTAACTATCGCCCTGCGACTCAGAGGCAGTCGGAGCCTGTGCGTCCTCGTATCCCTGTTGCGTCAAACGTCTCTCCTCGTCCACAAGCACCTATCGCGTCGGGAGCCAATTACGTCCCTGGGCCAGCGCTCCGACCCACACCCACTCAGGCGGCAGTGCCAAGGGGTCCTGCTCCACCTGTGCGCCACTTCTCTTCGGGTCAGTCAGGGTTTAATGGCGTAAGAGCCCCTCCTCCGCCAAGTGTTCAGCCACCAAGGCCGATGATGAGGATACAGCGACCCATCACTAGCCTTCCCGGACCACGTAGCGTTGCTCCAACTCCTTCCCGCCCGTTGCCTACGGTGACGGTTCATCCACAAACTCCATCTAGTTCCACATCTGTCCGGGGTCCACATGAGTTGCCTTCGTATGGTTACAACACACAAAATGCTTATCATAACGGGCAGCATAGCCCAAGATTTCCTGTGGCTCCACAGATGAGAGCTCAAGCACCCCAGCCTCCTCAGGGTGCCCCCCCTCAAGTCTCACAAGTACCTAGACCCGCTTATCCACAGTCCCCTATTCAAGCGTCGCAGCCTCAACATATGATGCAACAACCTCATCGTCAAGAACAACAACACCCTCAACGAAACCTCCCTCCAGTCTTGGTAAGACAGAATACACCGGTGCAAATGCAGTCTCCTCCCCATGCGGTAAATCAGCAAGCTTCACCTCACTCTCAACAGCCCGGTATGGGGCATTATCAACAAGTGGTTGGACCTCCAAGACAAGTTGCTCCACCTCAACCTTCAGTTCCCCAGCAAAGCTATGCACAAGTACCTATAGGACCCCAACAGCCTGCCCAACAGGGTCTACCGCCGGGTTCAGGGCAACATCCCCCTGTATCTCCAGCAACAGAAGCTAAAGACCCCCCTCCGAAACCTAATGTCTCCATAGCGGTGGCTCCAAGCGGTATCGTTTTGTCGTGGTACATGGCTCTTGAGGAGAGACACGCGCCTATAATGAACTATCAACTGTTTGCCCTTCAGGACGGCGGAACAACGGAGAACCCTCACCAGTGGAAGAAGATTGGAGTCGTCAAGGCGTTGCCGCTTCCTATGGCTTGCACTCTGACTCAGTTTTCACCTGGCAATAAGTACCACTTCTTGGTACGTGCTACTGATGTTAATGGACGACAGGGTGAGTGCAGTGAGGCCTGCACTATTACGCTCAAGTGA

Transcript

rna-pdam_00023715

TAGCATCAATTCACGCATGACAACTGCATGATGTCAAGTCGTAAACGGGATTCAAACACTACAGGATAAATTTATGAATACATTTTAACTCTTTGTTTTGGCGAAACCTCCCGGCACacgaagaaaacaatatatcGGGAGATTCATACCCTGTAGTTACACTTGGATCTACTACTGAACGACTTGAGTTTCAGGGCCAGTAACTTACCGGTTGATTCAAAGATCGGCGGTTGATGAACGAATCGAACGGACGTATGTACCAACAGTTCAAATCGCACTAGGTGAATCATTCTTGTTCGAGCAAGTAGAACCCTTAAATTGGAGGGAACTTGTCAGATAGACTTATGGAGTTATGGAGGAGCTAGAGATAGCAAAGAAGAAGCGgaaAGTTGATGGTGGAGGTGCTGCCTCAACGCCAAACCATGTGATGACCAATGGAGATTCTATTGGAACAAGCGATGCAGCTTCCACTCGACCACTTTCCCATCTGCAATTTAATCCGTCCAGATTTGACCGACTCCGCCAGATTACAATTGACTGTCAAAAGAATTTTCTCCCTCAACCTAAACCTAACGGCAGCAAGATACTTCGATGTAAAGGACCTGCAAAGGAACCGAACCCGGAGATACACTCGTCGAACGATGCAAACAGCCCAAGCCCTGATCTTATTATATCGTCCGCTGGCTCATCACCGGCTCATTCGCCTAAACCAttagatttcaaaatgttgtcTACGCCCCCGCGGTCGAGTAAACTGGGAGATACGAATCTTCCGATACTTGAAAACACTTCAGAACTAACCTCCTCTGATCGCCAAATGGCGTGTGTCAGACTTGTGGCGAAATTAGACGAATCTTCAAGTAAAAAGCTTTCTAATGGAGTCACCACGGATGCTAGGACTTTAAATCAGGATTCCTTGGTGGAAGTTTTGGAAGAAGGCGATCAAACGTGCCCATTAAACCCTGGCGCTAAGCCTGTCCATGTGAATGGGGAAATCAATTTGTTAGAAGGGAACAAAGGGCCAGCGGATAATGATAAAACTACTGTGAAGGATCGAAATTCACCGTCTTTTTCAGACCTGGCTCCCAGTGCTAACGCAGAGGAAACTACAAAGGActtcaattttaattcagaCGAATTCAGACAAATGGTCAAGAAAATGATCCAAGAGAGGATGAGTCAAATCCAGCAGTCAATGGATGATGACAGCCCGAACGACAAGCTCTCCGTTAGGCTAGCTGCACTTGAGAAGGAGAACAAAGCATTGAAAGAGTACGCAAAGAGAGTAGAAGATTCTGTAAAAACGATTTTAAAAGCTGAGAGcttaaaagcaaagaaacgaGAAACTAAAGCTGTTCAAACCCAAGATCTTAACTGGATGAACGCTCTGCGCACGAAGACTGTGAACGCACCATCTCCCCCAGCGAGTTTAACAGCTTCCAGGCCCTCAAATGCTAGTGTCAATGTTATGACTACACCAACACCACGGCTCACCTCCACCGTAGCACCTTTGCCTGGTCACACAGTACCGCAATCAGCTCCCGTTAACTATCGCCCTGCGACTCAGAGGCAGTCGGAGCCTGTGCGTCCTCGTATCCCTGTTGCGTCAAACGTCTCTCCTCGTCCACAAGCACCTATCGCGTCGGGAGCCAATTACGTCCCTGGGCCAGCGCTCCGACCCACACCCACTCAGGCGGCAGTGCCAAGGGGTCCTGCTCCACCTGTGCGCCACTTCTCTTCGGGTCAGTCAGGGTTTAATGGCGTAAGAGCCCCTCCTCCGCCAAGTGTTCAGCCACCAAGGCCGATGATGAGGATACAGCGACCCATCACTAGCCTTCCCGGACCACGTAGCGTTGCTCCAACTCCTTCCCGCCCGTTGCCTACGGTGACGGTTCATCCACAAACTCCATCTAGTTCCACATCTGTCCGGGGTCCACATGAGTTGCCTTCGTATGGTTACAACACACAAAATGCTTATCATAACGGGCAGCATAGCCCAAGATTTCCTGTGGCTCCACAGATGAGAGCTCAAGCACCCCAGCCTCCTCAGGGTGCCCCCCCTCAAGTCTCACAAGTACCTAGACCCGCTTATCCACAGTCCCCTATTCAAGCGTCGCAGCCTCAACATATGATGCAACAACCTCATCGTCAAGAACAACAACACCCTCAACGAAACCTCCCTCCAGTCTTGGTAAGACAGAATACACCGGTGCAAATGCAGTCTCCTCCCCATGCGGTAAATCAGCAAGCTTCACCTCACTCTCAACAGCCCGGTATGGGGCATTATCAACAAGTGGTTGGACCTCCAAGACAAGTTGCTCCACCTCAACCTTCAGTTCCCCAGCAAAGCTATGCACAAGTACCTATAGGACCCCAACAGCCTGCCCAACAGGGTCTACCGCCGGGTTCAGGGCAACATCCCCCTGTATCTCCAGCAACAGAAGCTAAAGACCCCCCTCCGAAACCTAATGTCTCCATAGCGGTGGCTCCAAGCGGTATCGTTTTGTCGTGGTACATGGCTCTTGAGGAGAGACACGCGCCTATAATGAACTATCAACTGTTTGCCCTTCAGGACGGCGGAACAACGGAGAACCCTCACCAGTGGAAGAAGATTGGAGTCGTCAAGGCGTTGCCGCTTCCTATGGCTTGCACTCTGACTCAGTTTTCACCTGGCAATAAGTACCACTTCTTGGTACGTGCTACTGATGTTAATGGACGACAGGGTGAGTGCAGTGAGGCCTGCACTATTACGCTCAAGTGAATCATCTTAggcaaaaacagaaactgttTTGTACAGCTCATTATCAGCACTAATGGTACTTA

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)	OG0001295 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF16794 all species →	fn3_4	Fibronectin-III type domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR003961 all species →	Domain	Fibronectin type III	Interproscan
IPR013783 all species →	Homologous_superfamily	Immunoglobulin-like fold	Interproscan
IPR036116 all species →	Homologous_superfamily	Fibronectin type III superfamily	Interproscan
IPR026085 all species →	Family	Activating transcription factor 7-interacting protein	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23210 all species →	ACTIVATING TRANSCRIPTION FACTOR 7 INTERACTING PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0003712 all species →	Molecular Function	transcription coregulator activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005667 all species →	Cellular Component	transcription regulator complex	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0090309 all species →	Biological Process	obsolete positive regulation of DNA methylation-dependent heterochromatin formation	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 RMX52778.1.

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 →