Gene detail

Detailed information of RMX55640.1 in Pocillopora damicornis

Genomic Location: SczhEnG_1030:336739...351174
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_00001669

ATGACTTCAACCCGTAATATTCAAAGCATGTGTCCGTTTAGTGTGGTTGTGCTTGCCATGTGCTTTTCGTTACTGCTAACAGGGCAAGATTTCCCTGTAATTCTAAGGGAGTTAGGGGAAGCAAAATTTGAAGGATACAGGGCATTTGCACAAGGCATGCAGTTTGTTGTGGTACTTGAAGTGACTGGGAATAATGCTAATCCTCCAGATGAGATTCCTGAACATGTTTTGAGCTTGCCCATCAATGCCACAAGTTGTCCTAGTTTTAAACTCGTAATCATTGAAATGATTGGTGCTACTGATCTGACAATTGATTGTAACACCACAAATCCAAATGCCAATGTAACATTGCTGTTGGACAATGTTAGATTACCTGTTGGGGGCAGAGTTACACTTCACAAGCAAGTCTTCACTATTCACAACATTTCAACAAGAGATACAGGAAGATATAAATGTGTAACCAGTAGTGGTTCAAGCATGACAGTTTTTTGCCAGACCGTAATCTACACTTCTGAAGAGAAACAAGCATGCTGTCCAAAAGTGACTCCTGAAGTAAAGGTTATGGAGGCTGGTATGAGCACAAATTTCACTTGCAAAGCCTATACTTTTGGTAGTCTCTCAAAGTATTTTACTTTAAAGTGGTTGAGAGAAGAGAATGGAACTAGTGTGGAAATTCGTCAAGGTGACACAATGCACAAGCAAACTGTTGTATCATATGGCCATTCTGTTCTTACAATTACAAATGCACAACTTACACCAGCAGAGGGTGTAACGTATCGCTGTCAGATAACCTACAGGGGTACAGCATCTTCCTCCCTCCCTCTACGTTTGATAGTAGTCAAAGATTTTGCACCCAACATAATATTTTTAAAGTCTTTAGAGGAATCAGGAACTGTTAAGGAGAAAGATAAGTTGTCAATGCGTTGTCAAGCACGCAGCTTCCCATTGTCTAACATCACTTGGATTCATAATGGAGCAAAAATGTCAGTGTGTTTAATAACTAGAAGTCAGGATTGCATGGGGAAAAGTTACAAAGTGCTGCAAGATACCAATAAGCAGTGGCTTACCTCAATTAGCCAACTTATTATAGAGAGTACAAGTTTTCCAAGAGATAATGGGACTTACACCTGTGTAGCAAGGAACAGCAAGAGTTACGATGAAAAAAACCTGGAAATTTCCATTGAGACTGTACCCACTTTGGATAAGTCGAAGTCATTCTGGACAAGTAGAAGAATCTACTGTGAGATCAGCCAATCCAATCCATTGCCAACTTTCAAATGGCAGCATCAAAATGGCCCGTGTTTGAACTTCAATCCAGAATGTTACCCAGACAACAGCAACTGGAAAGACCTTCCCACTAGCTTTGTCATTTCCCCACCTAGTGGCGATGCCACTTACAGGAGCACTGTTGACATTCCGCTAGACACTCCGTCAGGATTTTTAAGATGTTTGGCAGCCAACACAGGAGGAAGTGATGAAAATATGATGCGATTCTTTGCTAGTGGTATGGATTCTGTCAGAATCACAACAGCAACAAAAGAGTATGATGAAGATGATACTTTAAGTATGAGATGTGTTAGGATTTGCAGAGGTAAAATGACTGGTTGGTACAAAGATGGTAGACAGCTGTTGGCGGCTACTGATCCAAGAATCAATGTAACATTCGGGACTGAGAGTGACTTGACATGGACAAATCTAGTGGTGGAAAAACTTACTGTCAATGATTCTGGAGTGTACATTTGTGCAGCTACTGACTGTCAAAGTAAACCTTTGAATGTGTCGAGGGATATCAAAGTCAACAAGGTTTTTCCACCAAGTATACTCAACTTTGAAAATCAGACAGCTTATCATCAAATTAGCTCTGAATTATTTTGTAATGTTTCTGCTCATCCGATGCCAAGTCAGGTACAGTGGTTTAGAGGCAGTCAGCCCCTTAGAAATCAAATTGAAGTCATGGACAGACTATTACCCTCGGCCTGTAAAACTCGTTCTCCTGGTTTCTATCGAGTAAATGGTGTTGTTGGGAAACTCATCATTTGTAAGCCTGCAGACACTCTTCATACAGGGTTCTACACTTGTAAAGCGGCAAATAGGAAAGGGGAAAGTAACGCTACTGCCTTTCTTAATGTACTGGAGAACCCTGTGATTATACGTCCAGCCAATGGAAGTCGTTCGGTTGAACTAGGGGAGCCATGGAATAGTACGTGCGTAGTCACTGGCAACCCTGTGCCAAAAGTAGAATGGAAAAGAGTGGATGGAAATTTAGTATTCACTCAAAAACAGTACAACAACGAGGAGGTGGTGTTAATGTTGGAGTCTGTCAGTAAAAAGGATCTCGGAATGTACTTGTGTGTAGCCGTTAATTCAAAAGGAATTGCAGTTGCATTCGTCGAATTGGCAGAGGCAGACAACCCCCAACCGAGCACGGCTCCAGAAGGATCAAGCAGAAAGATGCTCATCGCTCTCAGTGTTGTTGGAGTGCTTCTCTTTGTCCTTCTTATCGTCATCTTAGTCTGTTATGTATTTTTTCGCCGCCAGCGTCAGAAGATTAAAGAATATCAGAGTCAGTTTTTCCCTGTGACTTTTGAACACGCTATGATAGCACGTGGAATGGAGTTTTTAACTTCAAAACAGCAAACTAACTCGGCATACGTAAGTATCACAGGAGACAACCGACCTGCCAATGATTATTACGTCACACCCTATAATACAGAATCCAACTTTCCGCAAACAAGTTTAGCTGGCTTAAACAGACAAACGAGTGACGATGTTGAGTCCAGTCCCTCTCTCCCGTTGTCTCGAGACATGGATACCGAGCAGGAACTGGATCAAGACGAAAGATATAGAATGGTGGATCTAGGGGCCGGTGGAAGCCTGTCAGGGAACGAGAGCGGAATAAGTTTGGAGGAGGGCAACGACGAAGCTTCTGCAGTAGCAGAATTAAGGCCTCTTCGTGTTTCTGCTATACCTACCTCAAAAGTAACCGCTAAAGCAAAACTTAAGTCAAATTCTAAAGAAACTGAAATATAA

Transcript

rna-pdam_00001669

ATGACTTCAACCCGTAATATTCAAAGCATGTGTCCGTTTAGTGTGGTTGTGCTTGCCATGTGCTTTTCGTTACTGCTAACAGGGCAAGATTTCCCTGTAATTCTAAGGGAGTTAGGGGaagcaaaatttgaaGGATACAGGGCATTTGCACAAGGCATGCAGTTTGTTGTGGTACTTGAAGTGACTGGGAATAATGCTAATCCTCCAGATGAGATTCCTGAACatgttttgagctTGCCCATCAATGCCACAAGTTGTCCTAGTTTTAAACTCGTAATCATTGAAATGATTGGTGCTACTGATCTGACAATTGATTGTAACACCACAAATCCAAATGCCAATGTAACATTGCTGTTGGACAATGTTAGATTACCTGTTGGGGGCAGAGTTACACTTCACAAGCAAGTCTTCACTATTCACAACATTTCAACAAGAGATACAGGAAGATATAAATGTGTAACCAGTAGTGGTTCAAGCATGACAGTTTTTTGCCAGACCGTAATCTACACTTCTGAAGAGAAACAAGCATGCTGTCCAAAAGTGACTCCTGAAGTAAAGGTTATGGAGGCTGGTATGAGCACAAATTTCACTTGCAAAGCCTATACTTTTGGTAGTCTCTCAAAGTATTTTACTTTAAAGTGGTTGAGAGAAGAGAATGGAACTAGTGTGGAAATTCGTCAAGGTGACACAATGCACAAGCAAACTGTTGTATCATATGGCCATTCTGTTCTTACAATTACAAATGCACAACTTACACCAGCAGAGGGTGTAACGTATCGCTGTCAGATAACCTACAGGGGTACAGCATCTTCCTCCCTCCCTCTACGTTTGATAGTAGTCAAAGATTTTGCACCcaacataatatttttaaagtctTTAGAGGAATCAGGAACTGTTAAGGAGAAAGATAAGTTGTCAATGCGTTGTCAAGCACGCAGCTTCCCATTGTCTAACATCACTTGGATTCATAATGGAGCAAAAATGTCAGTGTGTTTAATAACTAGAAGTCAGGATTGCATGGGGAAAAGTTACAAAGTGCTGCAAGATACCAATAAGCAGTGGCTTACCTCAATTAGCCAACTTATTATAGAGAGTACAAGTTTTCCAAGAGATAATGGGACTTACACCTGTGTAGCAAGGAACAGCAAGAGTTACGATGAAAAAAACCTGGAAATTTCCATTGAGActgtACCCACTTTGGATAAGTCGAAGTCATTCTGGACAAGTAGAAGAATCTACTGTGAGATCAGCCAATCCAATCCATTGCCAACTTTCAAATGGCAGCATCAAAATGGCCCGTGTTTGAACTTCAATCCAGAATGTTACCCAGACAACAGCAACTGGAAAGACCTTCCCACTAGCTTTGTCATTTCCCCACCTAGTGGCGATGCCACTTACAGGAGCACTGTTGACATTCCGCTAGACACTCCGTCAGGATTTTTAAGATGTTTGGCAGCCAACACAGGAGgaagtgatgaaaatatgaTGCGATTCTTTGCTAGTGGTATGGATTCTGTCAGAAtcacaacagcaacaaaagaGTATGATGAAGATGATACTTTAAGTATGAGATGTGTTAGGATTTGCAGAGGTAAAATGACTGGTTGGTACAAAGATGGTAGACAGCTGTTGGCGGCTACTGATCCAAGAATCAATGTAACATTCGGGACTGAGAGTGACTTGACATGGACAAATCTAGTGGTGGAAAAACTTACTGTCAATGATTCTGGAGTGTACATTTGTGCAGCTACTGACTGTCAAAGTAAACCTTTGAATGTGTCGAGGGATATCAAAGTCAACAAGGTTTTTCCACCAAGTATACTCAACTTTGAAAATCAGACAGCTTATCATCAAATTAGCtctgaattattttgtaatgtttctGCTCATCCGATGCCAAGTCAGGTACAGTGGTTTAGAGGCAGTCAGCCCCTTAGAAATCAAATTGAAGTCATGGACAGACTATTACCCTCGGCCTGTAAAACTCGTTCTCCTGGTTTCTATCGAGTAAATGGTGTTGTTGGGAAACTCATCATTTGTAAGCCTGCAGACACTCTTCATACAGGGTTCTACACTTGTAAAGCGGCAAATAGGAAAGGGGAAAGTAACGCTACTGCCTTTCTTAATGTACTGGagaaCCCTGTGATTATACGTCCAGCCAATGGAAGTCGTTCGGTTGAACTAGGGGAGCCATGGAATAGTACGTGCGTAGTCACTGGCAACCCTGTGCCAAAAGTAGAATGGAAAAGAGTGGATGGAAATTTAGTATTCACTCAAAAACAGTACAACAACGAGGAGGTGGTGTTAATGTTGGAGTCTGTCAGTAAAAAGGATCTCGGAATGTACTTGTGTGTAGCCGTTAATTCAAAAGGAATTGCAGTTGCATTCGTCGAATTGGCAGAGGCAGACAACCCCCAACCGAGCACGGCTCCAGAAGGATCAAGCAGAAAGATGCTCATCGCTCTCAGTGTTGTTGGAGTGCTTCTCTTTGTCCTTCTTATCGTCATCTTAGTCTGTTATGTATTTTTTCGCCGCCAGCGTCAGAAGATTAAAGAATATCAGAGTCAGTTTTTCCCTGTGACTTTTGAACACGCTATGATAGCACGTGGAATGGagtttttaacttcaaaacagCAAACTAACTCGGCATACGTAAGTATCACAGGAGACAACCGACCTGCCAATGATTATTACGTCACACCCTATAATACAGAATCCAACTTTCCGCAAACAAGTTTAGCTGGCTTAAACAGACAAACGAGTGACGATGTTGAGTCCAGTCCCTCTCTCCCGTTGTCTCGAGACATGGATACCGAGCAGGAACTGGATCAAGACGAAAGATATAGAATGGTGGATCTAGGGGCCGGTGGAAGCCTGTCAGGGAACGAGAGCGGAATAAGTTTGGAGGAGGGCAACGACGAAGCTTCTGCAGTAGCAGAATTAAGGCCTCTTCGTGTTTCTGCTATACCTACCTCAAAAGTAACCGCTAAAGCAAAACTTAAGTCaaattctaaagaaactgaaatataa

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)	OG0000375 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13927 all species →	Ig_3	Immunoglobulin domain	Domain	Interproscan
PF21314 all species →	TM_ErbB1	Epidermal growth factor receptor transmembrane-juxtamembrane segment	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR013783 all species →	Homologous_superfamily	Immunoglobulin-like fold	Interproscan
IPR007110 all species →	Domain	Immunoglobulin-like domain	Interproscan
IPR036179 all species →	Homologous_superfamily	Immunoglobulin-like domain superfamily	Interproscan
IPR003598 all species →	Domain	Immunoglobulin subtype 2	Interproscan
IPR049328 all species →	Domain	Epidermal growth factor receptor-like, transmembrane-juxtamembrane segment	Interproscan
IPR003599 all species →	Domain	Immunoglobulin subtype	Interproscan
IPR050958 all species →	Family	Cell Adhesion and Cytoskeletal Organization	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45080 all species →	CONTACTIN 5	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0007156 all species →	Biological Process	homophilic cell adhesion via plasma membrane adhesion molecules	Interproscan
GO:0008046 all species →	Molecular Function	axon guidance receptor activity	Interproscan
GO:0030424 all species →	Cellular Component	axon	Interproscan
GO:0043025 all species →	Cellular Component	neuronal cell body	Interproscan
GO:0050808 all species →	Biological Process	synapse organization	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 RMX55640.1.

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 →