Gene detail

Detailed information of BRAKERFUXP00000040280.1 in Telmatactis stephensoni

Genomic Location: 000069F_pilon_pilon:578201...599398
NR annotation: no NCBI-NR hit recorded
Species Telmatactis stephensoni · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

BRAKERFUXT00000040280

ATGTTCAAACTAGTAAGGAGATATCGAGGCAAGTCCTCGGATGGTCACATAAAGGACAAACACGGGCAAGAATTGTTCGTTTTCAACAAGACTATTGAACATGGATTTCCACACAAGCCAAGCGCTTTAGCCCACGATCCTCAACTGCATCTGTTAGCTATTGGTACAGAGGATGGAACTCTAAGAATCTACGGAAAACCAGGAGTTCAGCTCACTGCATGTCACCAAGAAGAAACTAGGATACAAGAACTTCATTTTCTTCCAGAGCAGGGAAGAATTATCAGTGTCTGTGATGACGGTGAACAAAATAGTATCCATCTATGGGAAGTCAacaagaaggaaggaaagtcTGTTCTTGaagaagtcaaaacttgcaCTCTCGAAGGAagactgAAAAAGATTTCTGTATGTTGCCTTTCGATGAATACAAATCGGCTCTACCTAGGCACAGAGGGAGGCAACATTTACATTCTAGATATCAATTCATTTGAGTTACAAGACTATGTCATCTACCAAGATGTTGTCATGCAGAGTGTCGAGGAGgagaacaaaacaaatgcaGGATCAGTGGAAGCTATTCAAGAACATCCAGATGATTCCAACAAGATTCTAATTGGTTACAAGAAAGGACTTATTGTACTCTGGAACCACGAAACAAGCAGTGTTGTACACACCTTCCCTAACAAGATTGATCTAGAAAGTGTCGGCTGGAATAATGATGGCACCAAATTTATCAGCTCACATGCTGACGGTAGCCAACACATCTGGAGTGTTGGTAATGCAGCTATCACAACAGAGGAATCATCTACACCCTTTGGTCCATTCCCTTGCAAGGCCATCACTAAAGTAGAATGGCATGACAACTTCATTTTCTTTGCTGGTGGAATGCCAAGAGCAAGCTATGGTGACAAGAACTGTGTGTCTCTTATGCATGGATCAACAACACAAGTGGTGTTCGACTTCTCCTCCAGGGTGGTGGATTTCCTTTTAATGACAAACCCAGACACCAATGAACCAGCATGTCTTGCTGTTCTTTGTGAGCAAGAATTTGTTGTCATTGATTTGAAGACCAAAGAGCAAGGATATCCCACATTTGTTCAACCCTACCTTATCTGCTTACACTCCTCCCCTATCACAACATCATTCCATTGCCATGGCTGCCCTAGTGAACTTTGGGACCAAATTGTTGCTGCTGGAAGAGAACAAATGAAATCTGAGTACTCTGTAGAGGAATGGCCAGTAACTGGTGGAAAGTCTCTCCTTGAAGATGCCCATGACAAGAACTTGCTCATCACTGGTCATGAGGATGGCTCAATAAGGTTCTGGGATGTCTCCCAAGTAGACATGAAACTTATATACAGCTTGAACACATCCAAACTGTTTGTCAGTGACCATGAAGCGCATGACAATGGTGCACAAGAAGTGGAAGAAGAAGGCTGGCCACCATTCAAGAAGGTCGGCAACTACGACCCTTACACAGATGACCCACGTTTTGCAATCCAGAAAATCTTGTTATGTTCTGACAGTAAGAAACTTGTGGTTGCTGGTAATGGAGGACAGGTCCTGACATTCAACATCAGTGATGATGATACCAATGTGGAACTTCAGGCTATGGAAGTTGACCTTGTTGAGGACAAAGAAAAGCTTCAATGGAAAGGGCATGGACCACTGACACCCAAAGAAGGACAAATCTCTGTATCTCGTGGTTTCCAACCCAATTATGCCATCCAGTTTATCCCAGCTGCACCCATCACTGCACTTGCATTCCAAGCTAAGTGGCATGCACTTGCTGCTGGTACCTGTCATGGTTTTGGACTCCTTGATCTAGAAAACAAGAAGGTCGTCACCACCAAGTGTACAGTTTCTGACGAAGaACTTTCAAACACAGGAGAACCCATTTCCagaaagaaatcactaaagaaaTCAATCCGAGACTCTTTTAGACGACTACGCAGAAGCCGTAAAGGTACAAAGAAGAGTGCTGAGActccaaagaaagaagaaggtgCAGAAGGTGCCCCAGCTTCACCTGGAGAACAATCTCCTCCAGTTCAGAGACTTGTTCATGAAAATCGTGTTGATGAGACTGTATTGAGTATGGTCAGATGTATATACTTTGTGGATACATTCTTGAAAGATGGTGTCCACCACACTCCATCAATGTGGGTCGGCACAAATGCTGGTCAGATCTTTGTCTACAATGTCACTCTGCCAGGTGAAGAAAACAAAGAGGAAGGACTCAAAGCAGAAATGGGAAAAGAAATCAAACTTAGACACAAGGCTCCAGTTGTTTCTATCTTTGTTGTGGATAAAGATGGTTTGCCAATGTTGGGAGAGTCCAAAGAAGAAGGTGCTGAAGCTGCTGGACAACACTCCCTGGTCATCTGCTCTGAAGAACAGTTCAAAGTATTCAGTCTTCCTCATCTTAAAGCTCGTCATAAGGAAAAACTCACAGCTGTTGATGGTTCTCGTGTCCGCAAAATTGCAATCATCAATGCACACAGCAAGAGTGATGACTCTGGCATGGTTTATCACTGCCTTGCATGTCTAAGTAACCAAGGTGACCTCAGTGTGTATTCTGTCCCTCACCTTAAACTCCAACTCAAAGTTTCTTGCATGAAGAAAGAGGACATGATTGCAATTCAATCTCTGGTATTCACATCATCTGGACAAGGATTTTACTTAAGATCACCCTCAGAGTTACAGAGATTCTCCTTAACAGCTAGTGATTTacTCAAACCAGAATGTGTTCTAGAACTTGCTGAAGGCATGAGACCACCAGAGGAGGTAACCATCGAAGTCACTGAAGAGGAaccagaaaagaaagaaagaagagactcatcatcatcatcctcatcttCATCCTCTTCTTCATCAgatgaagaaaaagatgaagaaaagaagaaagccaagaaagcagaaaagaagaagagaaagaaggaaatgaAAGAGGCTGCAgcagctgctgctgctgctgctgaaaCTGCTGAAGTTGTAGTAGAGGAGAAGAAAGAAGAGGCCGAGGACAAAgcagaagagaagaaagaagaagttgAAGAAATCAAGGCAGAAGCAGAAGCTGTTGTTGAGTCTGAAGTTCCATCAGGAGAAATAGTGCTAAGAGAAGGTGAAGGCACAAGTGTCACAACAGAGGAGAAAGTAGAATCGTCTTCCCATGAAACTTTCCATCACCAAACATCAAGTTCAGAAACTAAAGGAGTTAAAGAAGAGAATGCACTTCAGTCCGAATCACAGACAGTAGAAGAATCAGATAATTCAAGATCTGTTATCACCACAAAACGAATAGTTACAAGCACCCGGGTTGTTAAGCAGACAACTTCTCATCGCATTGTAACATCAGATGGAGAAACTGTTGAAATGATTGAGGGTGTAGAAAGCCTTCAAAATGGAGATGAAAagGCTGTCAATGATGCTGAACATGATGATATGGATGGACTTGAATATGACGTGTCAAAAAGACGATCTAAGGGAAAAGGCTTTACAAGTCCAGGAAAATTAAACACTAGACGATCAGCAGAAGTTCCAGTAACCAAAACCACCGAAGGCCCATAA

Transcript

BRAKERFUXT00000040280

Protein

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003530 (this species only) · gene tree & orthology
Ubiquitin family	UBD\|Other\|Beta-prp · all ubiquitin genes in this species
Ubiquitin family	E3\|E3 adaptor Cullin RING\|CDC20 · all ubiquitin genes in this species
Ubiquitin family	E3\|E3 adaptor Cullin RING\|DWD · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00400 all species →	WD40	WD domain, G-beta repeat	Repeat	Interproscan
PF08596 all species →	Lgl_C	Lethal giant larvae(Lgl) like, C-terminal	Repeat	Interproscan
PF08366 all species →	LLGL	LLGL2	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR019775 all species →	Conserved_site	WD40 repeat, conserved site	Interproscan
IPR001680 all species →	Repeat	WD40 repeat	Interproscan
IPR036322 all species →	Homologous_superfamily	WD40-repeat-containing domain superfamily	Interproscan
IPR013905 all species →	Domain	Lethal giant larvae (Lgl)-like, C-terminal domain	Interproscan
IPR000664 all species →	Family	Lethal(2) giant larvae protein	Interproscan
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	Interproscan
IPR013577 all species →	Domain	Lethal giant larvae homologue 2	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10241 all species →	LETHAL 2 GIANT LARVAE PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005096 all species →	Molecular Function	GTPase activator activity	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0008593 all species →	Biological Process	regulation of Notch signaling pathway	Interproscan
GO:0019905 all species →	Molecular Function	syntaxin binding	Interproscan
GO:0030864 all species →	Cellular Component	cortical actin cytoskeleton	Interproscan
GO:0030866 all species →	Biological Process	cortical actin cytoskeleton organization	Interproscan
GO:0032878 all species →	Biological Process	regulation of establishment or maintenance of cell polarity	Interproscan
GO:0045159 all species →	Molecular Function	myosin II binding	Interproscan
GO:0050708 all species →	Biological Process	regulation of protein secretion	Interproscan
GO:0051294 all species →	Biological Process	establishment of spindle orientation	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
K06094	LLGL; lethal(2) giant larvae protein	-	Membrane trafficking	ko04131	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of BRAKERFUXP00000040280.1 across 18 RNA-seq samples of Telmatactis stephensoni. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.

18Samples

18TPM > 0

6Conditions

12.0Max TPM

4.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
Mesentery	3	3	6.26	11.98
Club-tips	3	3	5.31	6.59
Actinopharynx	3	3	3.42	5.84
Tentacles	3	3	4.49	4.95
Pedal disc	3	3	3.41	3.89
Body column	3	3	3.44	4.67

Per sample · hover a bar for the full sample record

Show the sample table (18 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR14511804	Mesentery	Mesentery	not recorded	not recorded	SRP319504	11.98
SRR14511800	Mesentery	Mesentery	not recorded	not recorded	SRP319504	3.86
SRR14511801	Mesentery	Mesentery	not recorded	not recorded	SRP319504	2.93
SRR14511811	Club-tips	Club-tips	not recorded	not recorded	SRP319504	6.59
SRR14511802	Club-tips	Club-tips	not recorded	not recorded	SRP319504	5.11
SRR14511803	Club-tips	Club-tips	not recorded	not recorded	SRP319504	4.24
SRR14511805	Actinopharynx	Actinopharynx	not recorded	not recorded	SRP319504	5.84
SRR14511807	Actinopharynx	Actinopharynx	not recorded	not recorded	SRP319504	2.96
SRR14511806	Actinopharynx	Actinopharynx	not recorded	not recorded	SRP319504	1.46
SRR14511810	Tentacles	Tentacles	not recorded	not recorded	SRP319504	4.95
SRR14511808	Tentacles	Tentacles	not recorded	not recorded	SRP319504	4.69
SRR14511809	Tentacles	Tentacles	not recorded	not recorded	SRP319504	3.84
SRR14511812	Pedal disc	Pedal disc	not recorded	not recorded	SRP319504	3.89
SRR14511813	Pedal disc	Pedal disc	not recorded	not recorded	SRP319504	3.37
SRR14511814	Pedal disc	Pedal disc	not recorded	not recorded	SRP319504	2.98
SRR14511817	Body column	Body column	not recorded	not recorded	SRP319504	4.67
SRR14511815	Body column	Body column	not recorded	not recorded	SRP319504	2.98
SRR14511816	Body column	Body column	not recorded	not recorded	SRP319504	2.67

Source: CnidoSite RNA-seq expression matrices (TSTEP_TPM, StringTie quantification over 18 runs), joined to SRA sample metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped by the descriptor carried in the expression matrix itself.

Co-expression network

Genes whose expression across the transcriptome samples of Telmatactis stephensoni 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.

Direction	Partners	Most correlated partner	PCC
Positively correlated	23	BRAKERFUXP00000025864.1	0.976363943608349
Negatively correlated	3	BRAKERFUXP00000036041.1	-0.845500480631622

Open this gene in Network Analysis → The network opens with the gene already entered and both directions selected. There you can add up to 9 more genes, switch between the positive and negative network, and export the edge list.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Telmatactis stephensoni, 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.	ready	open →
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 →