Gene detail

Detailed information of BRAKERKYLP00000011848.1 in Mastigias papua

Genomic Location: chr17:9521683...9534222
NR annotation: CAH3117783.1, unnamed protein product [Pocillopora meandrina]
Species Mastigias papua · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

BRAKERKYLT00000011848

ATGGAATCGAGGCTTAGGCCATGGTCTCAATTTGGTGCAGAGGCAAATAGTTTACAAATGGCGGCCAAACTAGAGCGTAAAAAAACTTCTAATATTTTTTCGTTCGTTAACAAGCAACTAAAACTATTAGATTTAGAAAGAAATGCAGAGATTGACGAATCTGTTGATGCAAGGAGATCTTGTAGCATTAAGGACCTCGAAAAGCGAGGAGTTTGTGTATCAAAGCTTTACGTAAGAAGTGAATGCACGGGATTGTATGGAAAACATCTTGTGAGTTTTGGCCGTGGGAAAGAGAAGCGATTAAAGGGGAAAGACAAGATCAGCCAAGATGCCAAGGATCAAGCTGTATCACATTGTTTATCAAACGGGGATATAGTTGGAGTTCAAGAATCTTCATCAGAACTTAAGGAGGAAAATATTGCATCTGGGATCATAACGAAAGTTGATGATGATACAATCACTGTggcatttgaaaatgaatttgagGGTTCATCGTTATCAGATGCATTCAAGCTCATAAAACTTTGCAATGATGTCACATACAAGCGATTGAAGAGTGCTCTTGGCACTCTGAACaatgcaaagaaacattcaCATCTAAAAGATGTGCTATTTCACCAGACACCACTTGGGGCAGATTTGATGCTTGTCAAGGAAGATAAGTTTATTCCTTTGGATTCTAATCTCAATGATTGTCAGATTGAGGCTGTCAAATTTGCATTGAACCAAAAAGAGATTGGCATCATCCATGGTCCACCAGGAACTGGTAAAACCACTACAGTTATAGAAATCATAAAGCAAGCAgtaaaatttctcaatttcaagGTTCTCGCATGTGCTCCatcaaatgtagctgtggaTAACCTCGTTGCAAAGCTAGCTACTGCAAAAATAAAGATTGTGCGTCTTGGCCACCCAGCTCGAGTTTACCCTCACTTGCAAAGATATTCATTGGATGCTGTTTTGTTGAATTCAGATTCTGCAGAAATCGTTAAAAGTGTTAGGGACGATATTCAATCAATTTTGGAGAAGATCAAGAAATGCAAGAGTGGGTCTGACACCAGAAAGCTGAGAAGCGAGCTCAGGTTCTTGAAGAAGGAACTCTTCGAGAGGGAACGCAAAGCAATCAAGTCTGTTCTCTCATCAGCTGATGTTattttatcaacaacaacaagtgCATCTGATGAGGGTCCTTTAAAGCATTTAAATGAAGACCATTTTGATCTGATTATTATTGACGAAGCAGCTCAGGCATTAGAAGCTAGCTGCTGGATTCCACTTAACCATGGAAACAGGTGCATTTTAGCTGGTGACCATCAACAACTACCGCCTACAATCATAAGTCAAGAAGCAGCAAAAAAAGGTCTTGAAGTAACCTTGATGGAAAGAGCAATCATAGAGTTTGGAGATTCAATTGTGAGAATGCTGACAACCCAATACAGAATGAACAGTGTGATAATGGACTGGCCGTCAAAACAGCTATACAATGGCAAACTAACTGCAGATAATTCAGTTGAAAGTCATCTCTTGTCAGATCTACATGAAGTGGTATCAGATGAAAACACCTCAGTTCCCTTGCTCTTCATCGACACCGCTGGTTGTTGTATGTACGAGCTTAAGCAAGAGAGTGAAGAATCTAAAGGGAATGAATACGAGGCTCAATTAGTTTTATCTCATGTCGAGGCTCTTTTGAGTGCAAATGTTGAAGAGGAATCAATTGGAATAATTACACCGTATAATTTGCAGGTGGAGCTTGTTCGTCAATTACTTTCATCGCGGTATCCAAAGTTAGAGGTTCGATCAGTAGATGGCTTTCAAGGAAGGGAAAAGGAAGCCATCATCATATCACTTGTTCGTTCAAATGACGAAGGTGATGTTGGATTTTTAAAGGAAGACCGACGCATAAATGTAGCTATAACAAGAGCAAGACGCCACTTGGCTGTGATTGGTGACTCCTCAACGATATGTCATCATCATTTCCTTAAGTCGTTTTATGATTATGTATCTGATCATGGCGAAGTAAGATCAGCACAGAGCTATACATTTGCCCGTATGACACAGAATACAGACAATGTTACGAATGAATTTTTAAGAGACTTTAGGGATTTGATTTGTGTAAATAATGATGCCAAAGACTATGGTCTCACAGACATAAAGAACACGGGCAAACATTCATCGGATTCGAGAAGTGTACAAACTGATACTCGCAGAGAAGGTAGTAAAAAGCATCCTTCTGTTTTGGATTCCAACTATGAGAATCAAGAAGGCTTTCTTGTTGAGCAATGCAATTATATTGCTGAAGGCAATAGGATTGAGTGTGAAGACACAAGTCTTAACGCTGAAGCTTCAAACTTATCTAAGTATACGAGAGAGATAATAGAAAAGATGGTTACTGACTTTGTCAATTCTGACACTGAAGACAATATGGTTTTCGATTCCACGATGAGTAGCAGAGAGCGCTTTTGGGTACATGAGATGGCAGAAAAGTATGGACTTGCTCACTGGAGCGGTGGAGATGGAATAGATCGATTTATTACAATTAAGAAGAGAAAAAAGAAGCAAGACAATGCCAATGGTGAGGCTATCAAAAGAGTGGTAGATGCAGAGTTGACCGTAACCTGTCTCACTTGCAGTAGGTCAATTCCAAAAGATAATTTGCAATTGCATTCACTGCGctgcagaaaatttgaaagtgaaGGAGTAAAGAAAGAAAGGTATTCGGCACAGAATGATCATAAAAGGAAAGTACAATCAAAAGGTAatagaaaagagaagaaaaaaacGGCCGAGGAGGATGTGGACGCGTTAATTGCCGAGTTTGCAAAGGGTGACTCTACTTGCAGGTTTGATTCATGCAAGAATAGTGTTTTGACTTTAGGCCAGAAATGTAAATTTTGCACTAGAACGTTTTGCTTGAAGCATGGCCTTGCAGAAGTACATGGCTGTGGGGAGGCGGCAAAAGTCGATGCAAGAAGATCATTTGAACGGAACAATCAGAAAGCAAGGACTAGAGCATTGAATGACACTCAGAAAAATTATGTAAAAAAGAAACTGAATGAAAAAATTGTggaaatggaaaagaaaagGACTGGAAATAATGCAAAGAAAAAGTAG

Transcript

BRAKERKYLT00000011848

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q60560	DNA-binding protein SMUBP-2 OS=Mesocricetus auratus OX=10036 GN=IGHMBP2 PE=1 SV=1
Q9EQN5	DNA-binding protein SMUBP-2 OS=Rattus norvegicus OX=10116 GN=Ighmbp2 PE=1 SV=1
P38935	DNA-binding protein SMUBP-2 OS=Homo sapiens OX=9606 GN=IGHMBP2 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004169 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF21138 all species →	SMUBP-2_HCS1_1B	Helicase SMUBP-2/HCS1, 1B domain	Domain	Interproscan
PF01424 all species →	R3H	R3H domain	Domain	Interproscan
PF13086 all species →	AAA_11	AAA domain	Domain	Interproscan
PF01428 all species →	zf-AN1	AN1-like Zinc finger	Family	Interproscan
PF13087 all species →	AAA_12	AAA domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR048761 all species →	Domain	Helicase SMUBP-2/HCS1, 1B domain	Interproscan
IPR000058 all species →	Domain	Zinc finger, AN1-type	Interproscan
IPR036867 all species →	Homologous_superfamily	R3H domain superfamily	Interproscan
IPR001374 all species →	Domain	R3H domain	Interproscan
IPR041677 all species →	Domain	DNA2/NAM7 helicase, helicase domain	Interproscan
IPR014001 all species →	Domain	Helicase superfamily 1/2, ATP-binding domain	Interproscan
IPR047187 all species →	Domain	Upf1-like, C-terminal helicase domain	Interproscan
IPR003593 all species →	Domain	AAA+ ATPase domain	Interproscan
IPR035896 all species →	Homologous_superfamily	AN1-like Zinc finger	Interproscan
IPR041679 all species →	Domain	DNA2/NAM7 helicase-like, C-terminal	Interproscan
IPR050534 all species →	Family	Coronaviruses polyprotein 1ab	Interproscan
IPR004483 all species →	Family	Helicase SMUBP-2/Hcs1-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR43788 all species →	DNA2/NAM7 HELICASE FAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0004386 all species →	Molecular Function	helicase activity	Interproscan
GO:0016887 all species →	Molecular Function	ATP hydrolysis activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0043139 all species →	Molecular Function	5'-3' DNA helicase activity	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0005524 all species →	Molecular Function	ATP 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
K19036	IGHMBP2; ATP-dependent RNA/DNA helicase IGHMBP2	EC:5.6.2.5 EC:5.6.2.3	Translation factors	ko03012	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 Mastigias papua 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 Mastigias papua, 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 →