Gene detail

Detailed information of RMX43238.1 in Pocillopora damicornis

Genomic Location: SczhEnG_3245:124941...149105
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_00014560

ATGGAGAAAGCTATCGAATGGATAAATCTCTATCCGGTAGATAGCGCAGTACGTTTTGTTAACAGTTATCCGCTGGATAGTGATTTATCCGTTGGACTTTATACAACTCTCGACCCTGGTGTTAACAGCTCAACTTATCCAGCTAATATCAGCGCACATCACAATGACGACCAGCGGTTTACCTCAAGAAATAAAGAAAGCATGGCAGCATCAAAAATTTCTCTCGACAAAGACGCCTTTTTTCGGCGAATCAAAAGGATTTACGACGCCTGGAAGAAGGAAGACAGCACGGAAGATAATGGGGCTGCTTTTCCTAGTGTCGACACAGTGGTGATTGCAGTCGGGCAGGACGAAGACGTCATTTACAGTAAATCGACAGCAATACAGCAATGGTTGTTTGGTTATGAACTGGCTGATACTGTAACAGTGCTGTGTGAGGGATCAGTTCACTTTCTTGCCAGTAAAAAGAAATATGATTTTCTGAAACCATTACAAGATATGCAAGTGAAATCCAACACTTCACCATCAATACAACTTCACTTGAGAAACAAGGGAAAGACTGTGGGTGTTTTTCAGAAAGATAATTTTCAGGGACAATTTGTTGATGAGTGGAAAAATGCATTTGAAAAGGAGTCCTTTGAAAAGGTTGACATTAGCAGTGCAGTGGCGTATGTGATGTCAGTCAGAGAGGACCAAGAGCTCACTCATGTCAAGAAAGCTGCTCAAGTTTCCTCAGATATTTTTGTCAAATACTTCAAGAAACAAGTCATGGAAATTGTAGATGATGAAAAGAGGGTGAAACATTCAAAAATTGCAGATGGAATAGAAGGAGCTTTGGAATCAAAGAAATTTTTGCAACCTGGAATGGATTCTGAACAAGTTGAGATGTGTTACTCTCCCATTATTCAGAGTGGGGGAAAATTCACACTTAAGTTCAGTACAGTAAGTAATGATGAAAAGCTTCACTATGGTACAATAATCTGCTCCCTTGGTGTTCGATACAAGTTCTACTGTTCCAACATTGTTCGCACAATGTTATATGAGCCATCGCAGGAGCAACAAGAAAACTATGATCTGCTTCTGACAACTGTGGATGTTATTATGGACAAGTTAAGACATGGAGTGAAACTTTGTGATGTTTACAATGCCGCCCTTGAACATGTTACAGAAAAGAAACCTGATTTTCAGGCTAATTTTGTGAAAAATGTTGGGTTTGGGATGGGAATTGAATTTAGGGAAGGTTCTTTACTCATAACTTCTAAAAACAATCATGTGGCAAAGAAAGGGATGGTTTTCAATATAAATGCAGGTTTCTCAGGCCTGGTTAATGATAATGCAGAGGACAGTGAGGGTAAAAACTATGCCCTTTTTATTGGAGATACTGTGTTAGTTAATGAGGACTCTCCAGCCTCTATATTAACATCAGCCAAGAAAAAGATCTCTAATATCGGCATCTTTCTCAAGGATGAGGAAGATGAAGGACAAGATCAGCAAGAAAATGGAGAGGCTGAAGAGGATCTTCTTTTGGGTCGAGAGGGGAAAGGAGCATTACTTGAAAGCAGAACAAGATATTCTGAGCTGAGAACTTCAGGGACCACTACTGAAATGACAGCAGAGGAAAGACGAAAAAAACATCAACTTGAACTAAAGGAGCAGTTGCACGAAGAAGCAAAGAGACGTCTTCTCGAGTCCAAAGGGGATACAGATGCGATTACTAAGTTGAAACCATCCAATGTAGCCTACAAACATCCTACAATTGTTCCGAGAGATAATGATGTCAGAGAACACAAGATTTTTGTTGACAAAAAATACGAGGCAGTTGTTTTACCGCTATTTGGGGTAGCTACACCGTTTCACATATCTACCATCAAGAACATCAGTTCCAGCGATGAGGGCGGTTATACCTACCTTCGAATTAATCTGTTTTGTCCTGGAAGTGCTGTCGGTCGTTCTGAAGGAAGTCTGTTCGCTCAACCCGAGGCTACATTTGTGAAAGAAGTAAATTACCGAAGCTCGAACAGCAGACCTCATGGCGCATCTCAGCCACCGGCGTCCAATCTTAACACAGCGTTTCGTCTGATAAAAGAAGTGCAGAAAAAATTCAAAACACGGGAGGCTGAAGAGAAAGAGAGACAGGGCGTGGTCCAGCAGGGAAACCTTATACTAAACCCTAACAAAGGCAATCCAAAATTGAAAGATTTGTACATAAGACCAAGTATAACTCAAAGAAGATCACCGGGCACTTTAGAAGCGCATACGAACGGTTTTAGGTTTGGAATGTATCGCGGAGAACACGTCGACATTTTGTATGGAAATGTAAAACATGCGTTTTTCCAGCCCTGCGATGGAGAAATGATCATTCTACTTCATTTTCACTTAAAGCATCCTATAATCATTGGCAAAAAGAAATACAGAGACATACAGTTCTACACTGAAGTCGGTGAAATCACAACAGACTTAGGAAAACACCAACACATGCATGACAGGGACGATCTTCAAGCAGAGCAGGCCGAAAGAGAGTTAAGGCAAAGGTTAAAATCAGTGTTCAAGAATTTTATTGACAAAGTAGAAGGAATAACTCACGGGCAAGTGGAGTTTGATGTTCCATTCAGAGACCTCGGGTTTATGGGTGTACCATCTCGGAGCACAGTATTACTTCAACCCACAACGCATTGTTTAGTTAACATTACCGAGCAGCCAACGTTCATTATCACTTTGGATGAAGTAGAACTTGTTCACTTCGAGCGAGTGCAGTTTCATCTGAAGAATTTTGACATGGTATTTGTGTTCAAAGACTACAAACGTAAAGTGGAACACGTAAATGCTATACCAATGACGTCACTGGATTCTGTCAAAGACTGGCTGAATTCATGTGACATTAAGTACACTGAAGGAATCCAGAGTTTAAACTGGGCAAAGATTATGAAAACCATCAACGATGATCCTGAAGCGTTTATCGACAATGGTGGCTGGAGTTTCTTGGATCCTGACAGCAGTGGTGAGGAAGGAGAAGACAGCGAGGAGGAAGCGGAAAGTGAGTACGCTCCGACAGAATCAGAGGAAGAGGAGTCATCGTCACAAGAAGAGTATTCTTCTGAAACAGAGACGAGCGAAGACGGCTCAGAATTCGAAGAAGAGATGGGCAGCGAAGAGGAAAGCGGAAAAGACTGGTCTGAACTTGAAGAAGAAGCGGCCAAAGCTGACCGTGATAGGGGCCAAGAAGAAACTCCATCAAAGAAGAGGAAAAAACCTAGTAGCAAACACGAATCTCCACGCAAGAAAAAACGGAAGAGTTAA

Transcript

rna-pdam_00014560

ATGGAGAAAGCTATCGaatggataaatctctatccggtaGATAGCGCAGTACGTTTTGTTAACAgttatccgctggatagtgatttatccgttggacTTTATACAACTCTCGACCCTGGTGTTAACAGCTCAACTTATCCAGCTAATATCAGCGCACATCACAATGACGACCAGCGGTTTACCTCAAGAAATAAAGAAAGCATGGCAGCATCAAAAATTTCTCTCGACAAAGACGCCTTTTTTCGGCGAATCAAAAGGATTTACGACGCCTGgaagAAGGAAGACAGCACGGAAGATAATGGGGCTGCTTTTCCTAGTGTCGACACAGTGGTGATTGCAGTCGGGCAGGACGAAGACGTCATTTACAGTAAATCGACAGCAATACAgcaATGGTTGTTTGGTTATGAACTGGCTGATACTGTAACAGTGCTGTGTGAGGGATCAGTTCACTTTCTTGccagtaaaaagaaatatgattttCTGAAACCATTACAAGATATGCAAGTGAAATCCAACACTTCACCATCAATACAACTTCACTTGAGAAACAAGGGAAAGACTGTGGGTGTTTTTcagaaagataattttcaggGACAATTTGTTGATGAGtggaaaaatgcatttgaaaaggAGTCCTTTGAAAAGGTTGACATTAGCAGTGCAGTGGCGTATGTGATGTCAGTCAGAGAGGACCAAGAGCTCACTCATGTCAAGAAAGCTGCTCAAGTTTCCTCagatatttttgtcaaatactTCAAGAAACAAGTCATGGAAATTGTAGATGATGAAAAGAGGGTGAAACATTCAAAAATTGCAGATGGAATAGAAGGAGCTTTggaatcaaagaaatttttgcaaCCTGGAATGGATTCTGAACAAGTTGAGATGTGTTACTCTCCCATTATTCAGAGTGGGGGAAAATTCACACTTAAGTTCAGTACAGTAAGtAATGATGAAAAGCTTCACTATGGTACAATAATCTGCTCCCTTGGTGTTCGATACAAGTTCTACTGTTCCAACATTGTTCGCACAATGTTATATGAGCCATCGcagGAGCAACAAGAAAACTATGATCTGCTTCTGACAACTGTGGATGTTATTATGGACAAGTTAAGACATGGAGTGAAACTTTGTGATGTTTACAATGCCGCCCTTGAACATgttacagaaaagaaacctgATTTTCAGGctaattttgtgaaaaatgttGGGTTTGGGATGGGAATTGAATTTAGGGAAGGTTCTTTACTCATAACTTCTAAAAACAATCATGTGGcaaagaaagGGATGGTTTTCAATATAAATGCAGGTTTCTCAGGCCTGGTTAATGATAATGCAGAGGACAGTGAGGGTAAAAACTATGCCCTTTTTATTGGAGATACTGTGTTAGTTAATGAGGACTCTCCAGCCTCTATATTAACATCAGCCAAGAAAAAGATCTCTAATATCGGCATCTTTCTCAAGGATGAGGAAGATGAAGGACAAGATCAGCAAGAAAATGGAGAGGCTGAAGAGGATCTTCTTTTGGGTCGAGAGGGGAAAGGAGCATTACTTGAAAGCAGAACAAGATATTCTGAGCTGAGAACTTCAGGGACCACTACTGAAATGACAGCAGAggaaagacgaaaaaaacatcaacttgAACTAAAGGAGCAGTTGCACGAAGAAGCAAAGAGACGTCTTCTCGAGTCCAAAGGGGATACAGATGCGATTACTAAgtTGAAACCATCCAATGTAGCCTACAAACATCCTACAATTGTTCCGAGAGATAATGATGTCAGAGAACACAAGATTTTTGTTGaCAAAAAATACGAGGCAGTTGTTTTACCGCTATTTGGGGTAGCTACACCGTTTCACATATCTACCATCAAGaaCATCAGTTCCAGCGATGAGGGCGGTTATACCTACCTTCGAATTAATCTGTTTTGTCCTGGAAGtgctGTCGGTCGTTCTGAAGGAAGTCTGTTCGCTCAACCCGAGGCTACATTTGTGAAAGAAGTAAATTACCGAAGCTCGAACAGCAGACCTCATGGCGCATCTCAGCCACCGGCGTCCAATCTTAACACAGCGTTTCGTCTGATAAAAGAAGtgcagaaaaaattcaaaacacgGGAGGctgaagagaaagagagacaGGGCGTGGTCCAGCAGGGAAACCTTATACTAAACCCTAACAAAGGCAatccaaaattgaaagatttgTACATAAGACCAAGTATAACTCAAAGAAGATCACCGGGCACTTTAGAAGCGCATACGAACGgttttaGGTTTGGAATGTATCGCGGAGAACACGTCGACATTTTGTATGGAAATGTAAAACATGCGTTTTTCCAGCCCTGCGATGGAGAAATGATCATTCTActtcattttcacttaaagcaTCCTATAATCATTggcaaaaagaaatacagagaCATACAGTTCTACACTGAAGTCGGTGAAATCACAACAGACTTAGGAAAACACCAACACATGCATGACAGGGACGATCTTCAAGCAGAGCAGGCCGAAAGAGAGTTAAGGCAAAGGTTAAAATCAGTGTTCAAGAATTTTATTGACAAAGTAGAAGGAATAACTCACGGGCAAGTGGAGTTTGATGTTCCATTCAGAGACCTCGGgTTTATGGGTGTACCATCTCGGAGCACAGTATTACTTCAACCCACAACGCATTGTTTAGTTAACATTACCGAGCAGCCAACGTTCATTATCACTTTGGATGAAGTAGAACTTGTTCACTTCGAGCGAGTGCAGTTTCATCTGAAGAATTTTGACATGGTATTTGTgttcaaagactacaaacgTAAAGTGGAACACGTAAATGCTATACCAATGACGTCACTGGATTCTGTCAAAGACTGGCTGAATTCATGTGACATTAAGTACACTGAAGGAATCCAGAGTTTAAACTGGGCAAAGATTATGAAAACCATCAACGATGATCCTGAAGCGTTTATCGACAATGGTGGCTGGAGTTTCTTGGATCCTGACAGCAGTGGTGAGGAAGGAGAAGACAGCGAGGAGGAAGCGGAAAGTGAGTACGCTCCGACAGAATCAGAGGAAGAGGAGTCATCGTCACAAGAAGAGTATTCTTCTGAAACAGAGACGAGCGAAGACGGCTCAGaattcGAAGAAGAGATGGGCAGCGAAGAGGAAAGCGGAAAAGACTGGTCTGAACTTGAAGAAGAAGCGGCCAAAGCTGACCGTGATAGGGGCCAAGAAGAAACTCCAtcaaagaagaggaaaaaacctAGTAGCAAACACGAATCTCCACGCAAGAAAAAACGGAAGAGTTAAACATTCTAATGTTGAGTAAATTTAAACAAGGGTTTCCAACGTTATAACTGAAGATGTCGTCTGCCGAAAGCTGCGGTAGGAAAGGAGAGCGAACTCGTGCGAACATTATTGTTCACAGTGGCTGGTGAATGCGCGACATTATGCATTCTGGTATTATTATGGATAGCACTTAGGCCGTTTTTAGTAGTTCAACTGACTGGCTAGAATTCAGTTACAACTCTCCCGTTAGACAAGTTCATGTTTGGAGGGATTTTTACTTTCGAGTGAAATTTCACGTTTCCATAAGAAGCCTGTTCATTTTTATATTGACTGGTTTGGCCCACTAGTTGCAAGTAATGGTGAGCCCTTTAATTTCCAGCGGTAACGTAATGCTTCAAATAAGACTGGCGCAAGGAACGTGCGCAGTCTTTCGTTTTTCGTTAGTCGCCTATATTCTACATCTTTTAGGTTTCTGTGAATACttgtaaagttaaaaaaatgtgttccGCCAAACGGTTTGACGTCTGTACTTTCAACGTTGCTCGAGAATTTCTCCGTTACATGCACATGTATCTGTCCAAGGTCTGATAGAAGCAATAGGTTAATAGGTGCCTTCGGTGATTGAGGCCGAGCAGTTAATTGTTCTTATTCCTGTCCGAACTTCGACAGAAATCATACGTTTGGCTTTGATACGAAAGCTTCTTTACCTAGTTACCAACACATTACTCTATATTTGTCCAATCACAGTTGAGATGCATTACTTTGATTGACATTGA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9Y5B9	FACT complex subunit SPT16 OS=Homo sapiens OX=9606 GN=SUPT16H PE=1 SV=1
Q920B9	FACT complex subunit SPT16 OS=Mus musculus OX=10090 GN=Supt16h PE=1 SV=2
Q9W603	FACT complex subunit SPT16 OS=Xenopus laevis OX=8355 GN=supt16h PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003221 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00557 all species →	Peptidase_M24	Metallopeptidase family M24	Domain	Interproscan
PF08644 all species →	SPT16	FACT complex subunit (SPT16/CDC68)	Domain	Interproscan
PF08512 all species →	Rttp106-like_middle	Histone chaperone Rttp106-like, middle domain	Domain	Interproscan
PF14826 all species →	FACT-Spt16_Nlob	FACT complex subunit SPT16 N-terminal lobe domain	Domain	Interproscan
PF21091 all species →	SPT16_C	FACT complex subunit SPT16, C-terminal domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR040258 all species →	Family	FACT complex subunit Spt16	Interproscan
IPR013719 all species →	Domain	Histone chaperone RTT106/FACT complex subunit SPT16-like, middle domain	Interproscan
IPR000994 all species →	Domain	Peptidase M24	Interproscan
IPR029149 all species →	Homologous_superfamily	Creatinase/Aminopeptidase P/Spt16, N-terminal	Interproscan
IPR036005 all species →	Homologous_superfamily	Creatinase/aminopeptidase-like	Interproscan
IPR029148 all species →	Domain	FACT complex subunit Spt16, N-terminal lobe domain	Interproscan
IPR013953 all species →	Domain	FACT complex subunit Spt16 domain	Interproscan
IPR033825 all species →	Domain	FACT complex subunit Spt16, peptidase M24-like domain	Interproscan
IPR011993 all species →	Homologous_superfamily	PH-like domain superfamily	Interproscan
IPR048969 all species →	Domain	FACT complex subunit SPT16, C-terminal domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13980 all species →	CDC68 RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006368 all species →	Biological Process	transcription elongation by RNA polymerase II	Interproscan
GO:0031491 all species →	Molecular Function	nucleosome binding	Interproscan
GO:0035101 all species →	Cellular Component	FACT 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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K25639	SUPT16H, SPT16; FACT complex subunit SPT16	-	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 →