Gene detail

Detailed information of RMX37214.1 in Pocillopora damicornis

Genomic Location: SczhEnG_4198:101275...112065
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_00019037

ATGCCTTCACGGTATGATAGCGTGAGAAGTGTTTTTGAACAAGCTCAGCGTAGTTTTCAACAGCACAAGCTGTTAGCGGATTTGAAAAAGCTCCACGACAAGTCCTCTCCTGATGAATTTCTGGAAAGTTTCTTGTTACATTTGAAACATGCGATGGTTGTTTTTAATAGAGAACCTGCTGTTGAAAGAGTCATCGAGTTCGTGGCCAAGTACGCAACGCTAAAAGATCATCGTACCTCTCAAACTGAACAGGATGGCAATAGAAGTGATGGGGAGGAAGATGATTACAGCAATGTTTTCCTTGACTCCGTCTTCACTTTCTTGCTGGACTCGCATGATGCTAAAGACAAAGCTGTAAGATTCCGTGTCTGTCAGCTAATCAACAAGCTCTTGAATAACATGGGTGATGATGCTGTTATTGATGACGATCTGGCAGAGAGGATATTTGAGAGCATGTTGATACGGCTCCACGACAAGTTTCCTGCTGTGAGAGTGCAAGCTGTTGCAGCTATTTCCAGGCTCCAGGACCCCTCAGATCCTGAGTGCATTGTAATATCCACATACTTAAAACTCATGTCAAATGACTCCAGTGTTGAAGTGCGCAGAGCTGTGCTCCTGAATGTTGCTCTTACTTCTCAGACATTGGAGGGAATAATAGGAAGAACCCAAGATTTGACAGAATCAGTACGAAAGTTAGCTTATCGTATCCTAGCAGAGAAGGTGAACATAAAATCATTTACAATTGCCCAGCGTGTGCAACTGCTTTCCAATGGCTTGCATGACAGATCAGAGGCCATTAAGGAAGTTTGTGCAAAGGAGCTTCTTGGACAGTGGTTGAACAATTTTGATGGGGATGTGGTCAAACTTCTGAAATGCTTAGATGTTGATGGATGCACAGAGGTTGCAGAACTGGCTTTAAAGACATTGCTGAATGGATTACCAAAGGAAGACCTTCAAGGTTACATTGATTCTTTAAAGAAAGGACAACAAGAAGAAGGCCCTGCAAAAATTAGCTATGAAAATCTAGATGCTGAGACAGCATTTTATTGGAGATGTCTTGGAGAACATTTGAAGTTCATGGGGGTGAATGGTGAAGCACTTTTGGATGAACTTCTACCTGAAGTATCAGTATTTTGCAAATACATTCAAGGGTATGTTGACAACTGTTTGTCCAGAATATCTTCAGAAGAGTCTTATCATTCAGGAAGTCAACAGAACTTTATCACCAGGCAACTTTTGATTCTTGTGGGAGTAATGGACCTCTCTGATGAAGTTGGAAGAAAGAATCTTTGCCAGATGATCCATGACTTGTTGGTACACATGGAGATCCAGGAGTCATTGGTGGATGTCCTACATGACAGATATGTAGGTGTTCAACCAGAAGAAAGCAGTAGAATCCAGGAGCTTGTTGAGATTATTGCTGATGTTCGACAACCTATTGTGATGATTGAGACTCCTCAAAACAAGGAAGAAAAACGAGTATGGGAACTTAAGGTTGCTGGAATCAGTGTTAAACTTAATCAGTACCGTGATGAAATGGAACAGTGTGTGACAAACCAGGATTTTGCTAAGGCAGCTGAACTCAAACAGCAAATTACAGATCTGGAAGAACAGAAAGAAATACTTGATTCACAAGAGAACTCCTTTTCCCAGACTATTAGGGAAGAAAAGGATGATCCTGATACGTTATTGAAGTGTTTAACCATTGCATCTGAGATGCTGCAGGGTGTGGCAACAAGTGGACTGAATCCAACACTAACCACTTTGGTTCAAACTCTGATTCTGCCTGGTGTTCAGAATGAAGATCCCTTAGTGCGTAACATGGCTATCAAATGCTTGGGTTTGTGTGCCCTCCTTTCTTGTGAATTTGCCCGCACACATCTTGTACTTTTTCTTCAGGTGGCCCAACTAGACCAAGAGCTTGTTCGCACAACTGCCCTTCAGGTTGTTTTTGATCTTCTTCTAAAGTTTGGTCTTGAGGCTTTCAAAGTCAATACTTCAGTCCATGATGAGGGGGATGACCCCCCTTCCTCTGACTCAGAACAGGACAAATCAGACAATGAAAATGATGAAAATGAAGGAGGTGAAGATGTCACAGAAAAGAAAGAGGATGAAGATGTGGAAGAGACCGAGGCTCGAGATACGGACACTGCTGCAAGTGTGCTTACAATACTTACTGGAATTCTAGAGAGCGAGAGCAATGACCTTAGGAATGTGGCTGCTGAAGGATTGGCCAAGTTGTTGCTCTCAGGTCGTGTTCTGAGTGCCAAACTTTTTTCACGACTTCTGTTGCTGTGGTACAACCCTACCACTGAGGATGATGTAAACCTGCGGCACTGCTTGGGTGTCTTTTTCCCAGTTTTTGCCTTTGCTTCACGCATGAATCAGGAGCTGATTGAAGAGGCATTCTTTCCCACACTGAAGACATTATTTAGTGCCCCTATGTCATCTCCTCTGGCATCAGTTAACATCAATAATGTGGCAGAGTTGCTGGTGGATTTAACAAATGGAAAATACTTGGAAAAGAAAGAAAAATCACATGTTGATGCCAATGAGGCATACAGCATTCATGCTTCTCTCAGCATTGCAATTGCTAATGAGATTTTGTCTTGTCCTGATGCTCCCGGTGTGCGAGTTCTGTGCAAGGTACTGACTATGATGGACTTGACTGGCTGTACACAGTCCACAGTCAAGGAAATTAAAGTCCTTACAGGAAGGCTGATGGAGGAAATTGAAGAGAATATGTCCCTGAAATCATTGAGCAAGTTAAATAAAATGCTGGAAACTCTCACAGATAAGGAGATTGATAGTGTCTCAGAGACTGAATTAGACAATGGCAATCAGGAAAATGCAGAGAAAACAGAGGAACCCAATGAAGGTACTATTAATGAGAAAGCTACTGTTGATGACATAGACACTTGGCAAAGATTAGAGGAAAATACCTGTGTACTTCAGGAACAAGCAAAATGCAACACAGAGGATACAGACACCATGGGTGACAAAAACTCTGAAGTCCTGAATGAAAACCAAGCTGACAACAAACCAAAAGAAATTAAATCAAGAAGAAAGAGTAAGAAGCAAGTAGGGTCAAAGTCAGTTGCCAGGGATAAAGAGCTTAGCCCTGTTGCTTTGGGTGAGGAAACACCAGCTCGGCAAACAAGATCAAGCAGAAAAAGCAAGACAAATGTTAATAAAATGGTCAAGTCTGTGATAGATTCAGAGGACAATGACAGCAATGGAAAAGAAAATGTTTCAAGCAATGATGCTGATGATGTGTTCCTCAAATGA

Transcript

rna-pdam_00019037

ATGCCTTCACGGTATGATAGCGTGAGAAGTGTTTTTGAACAAGCTCAGCGTAGTTTTCAACAGCACAAGCTGTTAGCGGATTTGAAAAAGCTCCACGACAAGTCCTCTCCTGATGAATTTCTGGAAAGTTTCTTGTTACATTTGAAACATGCGATGGTTGTTTTTAATAGAGAACCTGCTGTTGAAAGAGTCATCGAGTTCGTGGCCAAGTACGCAACGCTAAAAGATCATCGTACCTCTCAAACTGAACAGGATGGCAATAGAAGTGATGGGGAGGAAGATGATTACAGCAATGTTTTCCTTGACTCCGTCTTCACTTTCTTGCTGGACTCGCATGATGCTAAAGACAAAGCTGTAAGATTCCGTGTCTGTCAGCTAATCAACAAGCTCTTGAATAACATGGGTGATGATGCTGTTATTGATGACGATCTGGCAGAGAGGATATTTGAGAGCATGTTGATACGGCTCCACGACAAGTTTCCTGCTGTGAGAGTGCAAGCTGTTGCAGCTATTTCCAGGCTCCAGGACCCCTCAGATCCTGAGTGCATTGTAATATCCACATACTTAAAACTCATGTCAAATGACTCCAGTGTTGAAGTGCGCAGAGCTGTGCTCCTGAATGTTGCTCTTACTTCTCAGACATTGGAGGGAATAATAGGAAGAACCCAAGATTTGACAGAATCAGTACGAAAGTTAGCTTATCGTATCCTAGCAGAGAAGGTGAACATAAAATCATTTACAATTGCCCAGCGTGTGCAACTGCTTTCCAATGGCTTGCATGACAGATCAGAGGCCATTAAGGAAGTTTGTGCAAAGGAGCTTCTTGGACAGTGGTTGAACAATTTTGATGGGGATGTGGTCAAACTTCTGAAATGCTTAGATGTTGATGGATGCACAGAGGTTGCAGAACTGGCTTTAAAGACATTGCTGAATGGATTACCAAAGGAAGACCTTCAAGGTTACATTGATTCTTTAAAGAAAGGACAACAAGAAGAAGGCCCTGCAAAAATTAGCTATGAAAATCTAGATGCTGAGACAGCATTTTATTGGAGATGTCTTGGAGAACATTTGAAGTTCATGGGGGTGAATGGTGAAGCACTTTTGGATGAACTTCTACCTGAAGTATCAGTATTTTGCAAATACATTCAAGGGTATGTTGACAACTGTTTGTCCAGAATATCTTCAGAAGAGTCTTATCATTCAGGAAGTCAACAGAACTTTATCACCAGGCAACTTTTGATTCTTGTGGGAGTAATGGACCTCTCTGATGAAGTTGGAAGAAAGAATCTTTGCCAGATGATCCATGACTTGTTGGTACACATGGAGATCCAGGAGTCATTGGTGGATGTCCTACATGACAGATATGTAGGTGTTCAACCAGAAGAAAGCAGTAGAATCCAGGAGCTTGTTGAGATTATTGCTGATGTTCGACAACCTATTGTGATGATTGAGACTCCTCaaaacaaggaagaaaaacgagTATGGGAACTTAAGGTTGCTGGAATCAGTGTTAAACTTAATCAGTACCGTGATGAAATGGAACAGTGTGTGACAAACCAGGATTTTGCTAAGGCAGCTGAACTCAAACAGCAAATTACAGATCTGgaagaacagaaagaaataCTTGATTCACAAGAGAACTCCTTTTCCCAGACTATTAGGGAAGAAAAGGATGATCCTGATACGTTATTGAAGTGTTTAACCATTGCATCTGAGATGCTGCAGGGTGTGGCAACAAGTGGACTGAATCCAACACTAACCACTTTGGTTCAAACTCTGATTCTGCCTGGTGTTCAGAATGAAGATCCCTTAGTGCGTAACATGGCTATCAAATGCTTGGGTTTGTGTGCCCTCCTTTCTTGTGAATTTGCCCGCACACATCTTGTACTTTTTCTTCAGGTGGCCCAACTAGACCAAGAGCTTGTTCGCACAACTGCCCTTCAGGTTGTTTTTGATCTTCTTCTAAAGTTTGGTCTTGAGGCTTTCAAAGTCAATACTTCAGTCCATGATGAGGGGGATGACCCCCCTTCCTCTGACTCAGAACAGGACAAATcagacaatgaaaatgatgaaaatgaaggagGTGAAGATGtcacagaaaagaaagaggatGAAGATGTGGAAGAGACCGAGGCTCGAGATACGGACACTGCTGCAAGTGTGCTTACAATACTTACTGGAATTCTAGAGAGCGAGAGCAATGACCTTAGGAATGTGGCTGCTGAAGGATTGGCCAAGTTGTTGCTCTCAGGTCGTGTTCTGAGTGCCAAACTTTTTTCACGACTTCTGTTGCTGTGGTACAACCCTACCACTGAGGATGATGTAAACCTGCGGCACTGCTTGGGTGTCTTTTTCCCAGTTTTTGCCTTTGCTTCACGcatgaaTCAGGAGCTGATTGAAGAGGCATTCTTTCCCACACTGAAGACATTATTTAGTGCCCCTATGTCATCTCCTCTGGCATCAGTTAACATCAATAATGTGGCAGAGTTGCTGGTGGATTtaacaaatggaaaatacttggaaaagaaagaaaaatcacatgTTGATGCcaatgagGCATACAGCATTCATGCTTCTCTCAGCATTGCaattgctaatgagatttTGTCTTGTCCTGATGCTCCCGGTGTGCGAGTTCTGTGCAAGGTACTGACTATGATGGACTTGACTGGCTGTACACAGTCCACAgtcaaggaaattaaagtcCTTACAGGAAGGCTGATGGAGGAAATTGAAGAGAATATGTCCCTGAAATCATTGAGcaagttaaataaaatgctGGAAACTCTCACAGATAAGGAGATTGATAGTGTCTCAGAGACTGAATTAGACAATGGCAATCAGGAAAATGCAGAGAAAACAGAGGAACCCAATGAAGGTACTATTAATGAGAAAGCTACTGTTGATGACATAGACACTTGGCAAAGATTAGAGGAAAATACCTGTGTACTTCAGGAACAAGCAAAATGCAACACAGAGGATACAGACACCATGGGTGACAAAAACTCTGAAGTCCTGAATGAAAACCAAGCTGacaacaaaccaaaagaaattaaatcaagAAGAAAGAGTAAGAAGCAAGTAGGGTCAAAGTCAGTTGCCAGGGATAAAGAGCTTAGCCCTGTTGCTTTGGGTGAGGAAACACCAGCTCGGCAAACAAGATCAAGCAGAAAAAGCAAGACAAATGTTAATAAAATGGTCAAGTCTGTGATAGATTCAGAGGACAATGACAgcaatggaaaagaaaatgtttcaagcaATGATGCTGATGATGTGTTCCTCAAATGA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9YHB5	Condensin complex subunit 3 OS=Xenopus laevis OX=8355 GN=ncapg PE=1 SV=1
Q9BPX3	Condensin complex subunit 3 OS=Homo sapiens OX=9606 GN=NCAPG PE=1 SV=1
Q10429	Condensin complex subunit 3 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=cnd3 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004541 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF12719 all species →	Cnd3	Nuclear condensing complex subunits, C-term domain	Repeat	Interproscan
PF02151 all species →	UVR	UvrB/uvrC motif	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR027165 all species →	Family	Condensin complex subunit 3	Interproscan
IPR025977 all species →	Domain	Nuclear condensin complex subunit 3, C-terminal domain	Interproscan
IPR001943 all species →	Domain	UVR domain	Interproscan
IPR016024 all species →	Homologous_superfamily	Armadillo-type fold	Interproscan
IPR011989 all species →	Homologous_superfamily	Armadillo-like helical	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR14418 all species →	CONDENSIN COMPLEX SUBUNIT 3-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000793 all species →	Cellular Component	condensed chromosome	Interproscan
GO:0000796 all species →	Cellular Component	condensin complex	Interproscan
GO:0007076 all species →	Biological Process	mitotic chromosome condensation	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	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
K06678	YCG1, CAPG; condensin complex subunit 3	-	Chromosome and associated proteins	ko03036	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 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 →