Gene detail

Detailed information of BRAKERFUXP00000025046.1 in Telmatactis stephensoni

Genomic Location: 000245F_pilon_pilon:49491...68678
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

BRAKERFUXT00000025046

ATGGCGGAAACTAAGCGTCTTAGTCTGGGCGAGGATAATACACTTCTGGATAATGCCGTTACAGAAAGCGCCATTCACTATTTCGACGAATTGGACTACCGAAATCATAGGCAAGTTTATGTTGGAGTACATCTTCCCTTACAGAATGCTAACCGGCCAAGTAGACGAACGAGCCGAGGTTCGAGTAGCCGTCGACATCATCATAGGCACGGACACAGAAGAAAACATAAAAGTGGTTCGAGCTCACCGACCGAAACTGATCAAGTTTCTGCCCTTCCATCTGAACGTGTACGCTTCATTCTTGGAGGCCAAGAATTCGAAGTTGAAGGTCATCAAATTTTTGCTGAACTTGATGAGTATGAAGTGACTGATGATGGCAATGGTGTTTGGAAGGAGTCAGCAAGGTGGTTGAAATTTGAAGAAGATGTCGAAGAAGTTGGTAATAGATGGAGCAAGCCTCATGTTGCTACACTGTCTTTGTACAGTCTTTTTGAATTACGCAGCTGTTTATTGCATGGAACAGTACTTCTTGATTTGAATGCTTCCAACATGGAACAAATATGTGATTTAATCTTAGATGATTTAGTATACACCAATCAGTTGGAGCAAGATAACCGTGCAAAAGTTAAAGAAGTACTTTTACAAAAACATGTTCATCAGTTTGAAAGAGCAAATGTTCGCAAACCTAAAACATCAAAGAGTATTGGACAGCACTTTGCCAACCTTGGATCTAGAAAAGCATCTGCCCCAACAGTAGCTGGAATGGAGAAGAAGAAGCCAGTGATTGAGGGATCAAAGTCTGTGCCATTCAATCTGACAGCTTTGCAAGAGGAACCTGAGCCAGTCAAAGCATTTCCCTATATACCTTCAGCTGTGTCATTAGTAGATGAAGGTGCAGAGCGTGCAGATGATGAAGAATGCAAGGATGATATTGCCAATGATACATTTGATTATAACTTCATGAAGAAAATACCCCTTGGAGCTGAAGCATCCAATGCTCTTGTGGGTGAAGTGGACTTCCTCAAAAAGCCCATCATAGCATTTGTACGGCTTGAAAATAGTCTTGTTCTTGGTGATCTGACTGAGGTACCTCTACCAACAAGGTTTATTTTTGTCATGCTGGGTCCAGCAGGTACACCAGGCAGATATCATGAGGTTGGAAGAGCTATTGCAACTTTAATGTCTGATGAGATTTTCCATGAAGTGGCTTACAGAGCTAATTGTCGTGAGGATCTTTTATCTGGTATTGATGAATTCTTAATGCAGGTGACAGTGTTACCACCAGGAGAGTGGGATCCTTCCATTCGTATAGAGCCTCCAGCAACAATTCCCTCTCAAGAAAAACGACTGGAATGGGGTTGTAAAAATGATGAAGATCATGATCCAGCTGACAGAGAAGAACATCTCCGCAGAACAGGAAGGTGTTTTGGTGGACTAATAGCAGATCTAAAAAGAAGATTACCATGGTATGCTAGAGACTTTAAAGATGCCCTCAGTCCACAATGCATTGCGTCCATTATTTTCATCTACTTTGCATGTTTGACACCAATTATTACATTTGGAGGTCTTATGAGCACCAAGACAGATAATTACATGGGAGCTGTAGAGCAAATGCTTGCCTGTTGCATTGGTGGAGTCCTGTTCTCTCTATTTGGTGGTCAGCCATTGATAATTCTTGGTGCCACAGGACCAATGCTTGTATTCGAagaaattatcttttcattCTGCACTTTGGCTGATTTAGAATACCTACCCTTTAGAATGTGGATAGGAATTTGGACCATGTTGTTCTGCTTTGTTCTTGTCATCACAGATGCAAGTTCTCTGGTGTGCTACTTTACCAGATTTACTGAAGAATGCTTTGCTACATTGATTGCACTTATATTTATTGTGGAAGGTTTTTCAAAGTTGTGGCATATCAAAGATGAACACCCAATATCAACAGGATACACTGACCATCATGCATGTAGTTGTATCATAGAAAAGTCATTCCTAGTCCCTGTACTAGAGAATGGAACTTGGGTCAATAAAACTGTTAGAAATATGTCCATATATGAGGGTGTGTCAATTCAAGATTGTGAACTTAAAGGTGGAACCCTAACTGGTTTGGCTTGCGATGAAAACGTGTTTTTTCTCTCTGCAATTTTATGTCTTGGTACCTTTGCCTTGGCTATCTCATTGAAGAGTTTCCGTACAAGTCCATATTTCCCTACAAAGCTACGTGCAAAAGTATCAGACTTTGCTGTTCTAATATCCATCCTAGTGTTTGTTGGTATTGATCTGGCATTTGGAGTCAACACTCCTAAGCTTAAAATCCCCTTGAGTTTTCGGCCTACAGCTGGTGACAAGAGAGGTTGGATAGTGCCACCATTAGGCAGAAACCCTGGGTGGATCATTGTAGCAGCCACTATTCCTGCTATTCTTGCTACAATTCTAGTGTTTATGGATCAACAGATCACTGCACTGATCGTTAACAGACGAGAACACAAACTCAAGAAAGGTGCTGGCTATCATCTTGATCTTCTTCTGGTTGCTATTATTATTGGTATTTGTTCAGTGCTTGGTCTTCCGTGGGTTGTAGCTGCCACTGTGTTATCTGTGTCCCATGTTCAGAGTTTATTTGTAGAGTCTCAATGCACTGCTCCTGGAGAGAAAACCAAGTTCCTTGGTGTAAGggAACAGCGTGTCACAGGAACTGTTATTTTTTTACTCATTGGTGTATCGGTGTTAATGACTCCTATTCTTAAGGTCATTCCAATGCCTGTattgtttggtttgtttcttTACATGGGTTTTTCAGCATTGAAAGGATTACAAttCTTTGAGCGATTGAAAATCATCTTTATGCCTGCCAAACATCAACCTGATTTGATATACCTTCGTCGTATCAAAATCACTCGTGTACATTTGTTCACTGGGATACAGTGTACATGTTTGATAGTCCTGTGGGCCATCAAGTCTACTCATGCTGCTCTGGTGTTTCCTATCATGGTTCTTATGCTTGTCGCTGTTCGCAAAATCATGGAGAAGTTTTTTACCAAACACGAGTTAGAAGTGCTAGATGACTTAATGCCAGAGACcatcaagaaaaagaaactagGAGAATCATTAGCTGATGGGATTGAAGGAGGAGAAGGTGGTGATGCGTGCGATGGGAGTGAAAGTGGAGAGGAAGATGATGTGGACGGAGAAAAGAAAGATGAACCTGAAGCTAATGGTCCTCCCCAAGTTCAAATACCAATCAATATCACCGACGAAATGACCAAAAGCTCACTGTGGAAGTCGTTCGTGAAGGACGGTGCTGTGTCTAAACGTAGTAAATGTAAAAATGACAGACACCACGGCTCACGAAGTAAACACAGGCATAAACATGGCAAACATCGAAGCAAGCATCGCGATAAAGACATTGACCAGGGCTTGTGGTTTTCAGCGGACAAAAGTAGAAGATACTTTGATGATCAACGCGATACTTGTGAACTTAGAAGGCTGACTGCCATTGAAGAAGATCCAGTGGTTGACCCAAAAGAAGCTGAGGATGTTCCCGAAGTTGTCGTTGTCATGCCGTCGTCCAATGGAATAGAAACACCAAAAGATAAGAACGAATAG

Transcript

BRAKERFUXT00000025046

Protein

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000857 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00955 all species →	HCO3_cotransp	HCO3- transporter family	Family	Interproscan
PF07565 all species →	Band_3_cyto	Band 3 cytoplasmic domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR003020 all species →	Family	Bicarbonate transporter, eukaryotic	Interproscan
IPR003024 all species →	Family	Sodium bicarbonate cotransporter	Interproscan
IPR016152 all species →	Homologous_superfamily	Phosphotransferase/anion transporter	Interproscan
IPR011531 all species →	Domain	Bicarbonate transporter-like, transmembrane domain	Interproscan
IPR013769 all species →	Domain	Band 3 cytoplasmic domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11453 all species →	ANION EXCHANGE PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005452 all species →	Molecular Function	solute:inorganic anion antiporter activity	Interproscan
GO:0006820 all species →	Biological Process	monoatomic anion transport	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0008510 all species →	Molecular Function	sodium:bicarbonate symporter activity	Interproscan
GO:0015701 all species →	Biological Process	bicarbonate transport	Interproscan
GO:0022857 all species →	Molecular Function	transmembrane transporter activity	Interproscan
GO:0050801 all species →	Biological Process	monoatomic ion homeostasis	Interproscan
GO:0051453 all species →	Biological Process	regulation of intracellular pH	Interproscan
GO:0055085 all species →	Biological Process	transmembrane transport	Interproscan
GO:0008509 all species →	Molecular Function	monoatomic anion transmembrane transporter activity	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
K13861	SLC4A10, NCBE; solute carrier family 4 (sodium bicarbonate transporter), member 10	-	Transporters	ko02000	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERFUXP00000025046.1 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

28.2Max TPM

17.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
Mesentery	3	3	21.75	23.94
Club-tips	3	3	19.75	27.83
Actinopharynx	3	3	17.58	25.31
Tentacles	3	3	21.04	24.91
Pedal disc	3	3	19.38	28.22
Body column	3	3	6.46	8.06

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	23.94
SRR14511801	Mesentery	Mesentery	not recorded	not recorded	SRP319504	21.69
SRR14511800	Mesentery	Mesentery	not recorded	not recorded	SRP319504	19.62
SRR14511811	Club-tips	Club-tips	not recorded	not recorded	SRP319504	27.83
SRR14511802	Club-tips	Club-tips	not recorded	not recorded	SRP319504	21.49
SRR14511803	Club-tips	Club-tips	not recorded	not recorded	SRP319504	9.93
SRR14511806	Actinopharynx	Actinopharynx	not recorded	not recorded	SRP319504	25.31
SRR14511805	Actinopharynx	Actinopharynx	not recorded	not recorded	SRP319504	16.69
SRR14511807	Actinopharynx	Actinopharynx	not recorded	not recorded	SRP319504	10.73
SRR14511809	Tentacles	Tentacles	not recorded	not recorded	SRP319504	24.91
SRR14511808	Tentacles	Tentacles	not recorded	not recorded	SRP319504	24.31
SRR14511810	Tentacles	Tentacles	not recorded	not recorded	SRP319504	13.89
SRR14511813	Pedal disc	Pedal disc	not recorded	not recorded	SRP319504	28.22
SRR14511812	Pedal disc	Pedal disc	not recorded	not recorded	SRP319504	22.99
SRR14511814	Pedal disc	Pedal disc	not recorded	not recorded	SRP319504	6.92
SRR14511816	Body column	Body column	not recorded	not recorded	SRP319504	8.06
SRR14511815	Body column	Body column	not recorded	not recorded	SRP319504	6.72
SRR14511817	Body column	Body column	not recorded	not recorded	SRP319504	4.58

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	0	not in this network	-
Negatively correlated	34	BRAKERFUXP00000021703.1	-0.790475734194589

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 →