Gene detail

Detailed information of HSymV2.0_g09.16744_t1 in Hydractinia symbiolongicarpus

Genomic Location: HiC_scaffold_9:19527620...19562759
NR annotation: XP_012554613.1, transcription factor IIIB 90 kDa subunit [Hydra vulgaris]
Species Hydractinia symbiolongicarpus · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

HSymV2.0_g09.16744_t1

ATGAAGATGGGAGTGTCTTGTAAAAATTGTGGAGGGACTGAAATTGATCATGATCAAGCACGAGGTGATGCTGTTTGTATTGGCTGTGGTTCAGTGGTTGAAAGTCTTTGCATTGTCAGTGAAATTGAGTTCCAAGAAAACAGCGCTGGCAATGCTTCAGTGATTGGCCAGTTTGTGTCTGCTGAAGGACAACATCACAGCATGGGCTCAAACTTAAAATATGGCACTGGAAGAGATCACAGACAAGTGATTTTGGATAATGGTAAGCAACTGATCAATCAAATGGGAAGTCAATTAAAAATGAGTCATCATTGCTTAGATTCCGCATTTATGTTTTACAAAATGGCTGTCAGCAAAAGGTTTACATCTGGTCGGAAAACTATTCATGTAATTGGTGCATGTTTGTATCTTGTTTCAAGAACAGAAAAGACGCCACATATGTTGCTTGATGTTTGCGACGTAGTTCAGTGTGACGTTGTAACTTTGGGTAGAGTATTTCTACAACTTGCTCGAGAACTGTGTATTGATTGTCCCATAGTTGACCCCAGTTTGTACATTCATCGATTTGCACACCAACTTGATTTTGGTGAGAAAGAGAATGAAATATCAATGACAGCGCTTCGTATTATGGCACGTATGAAAAAAGACTGGATACATTTCGGGCGGAGACCATCTGCATTATGTGGAGCTGCTTTAATTATTGCTGGTAAACTCTTTAGCTACAATGTTACCATGACTGATATCGTTAAATTAGTTCGAATGAGCAAGACCACAGTGTTTAAAAGACTAATGGATTTTAGTAAAACCGCAACTGGTAAACTGACCACAGACGAGTTTAAAACAGTAGATCTCGAAGAGGAAGCAGATCCCCCTTCCTACACTGCTGGAAGAAATCGTGTGAAGTTTGCACAAGAACTTGGAGATAATTATAGATTTGTGTCTAGTGATATTTTATCACAAGTAGTCAAAACACAAGAAAAGCTGGAAGTTCTATTAGAAAAACGAAAAACTATACACAAAGATTTGGAAATTACAAAATCGGAAGCAGAATCGTTTGATTATAGAAAAGAATTACCTTCTGACTACTCGTTATATACTTATGAGTTAGACGAAAATGGAGGTTTAAAGAATCCTTTGTTTGTCATTCATAATGAAAATGATATGAATTCAGAAAAACTTGAGGAGAGCGGCAAAAGTCATGCCAGCAGTACTTTGTTATTAGATTCTAAAACAAAATCAGAACCAGTGGATGTGTTTAAAGAAGAAAAAATATTGAAGGGTGAAGAAGAAAATGACGAAATTGAGTTGGATGACATCGATGATAAAGAAATTGATAAACTACTGTTAACAGAGGATGAAATAAAAATAAAAACTGAAATATGGCTGGAAGAAAATAAAGAGTATTTATTAAAAATGAAAGaaaaagaagaggaacaaaaaagaaaagaagaggaagaaAGTAAAGGCGGAATAAAAAGGAAAAAGAAAACATACAAAAGAAAGCAAAAAGATCGTCCAATTTGCGACACAGCCGATGAAGCTATAAAAACAATGCTCGCAGAGAGAAAGTTATCGAGTAAAATCAACTATGATGTTCTGCGAGGTCTGAGGTCTGAAGATAAAAATCAGGATTTTAAAGTGATGAAAAACGAACGTAATACCGACAGTGAAGCAGACGTTGTTGATACAAACATTAAAGTAGAGGATAAACCGCAGCTGCTGGAAAGTATTATGTATGAATCGGGCCCTATGAAACGAACCAATAAGAGAAACGCAAAGACAACTTTTATCTCGCTTGGTTCTCCAGATACTAAAAGGGTGAAGGTTGAACAGGAACAAAGAAATCTTACTCAAAGTTTAGAAACAATACCAGTGATTGAAAAGCAGAAACCTAAAGTGGAAGAAATGCAACCAATTGTAGAATCAGGTCCTGTGAGTACGAATGTGGACGATGATGACTATGTAGAAGATGAGGAGGAGGGGGAGGTTATAACAGCATCAGCATTGTTTGCTAAAGAAGTTGATGATTACGACACCTACGGTTATGATGATGGAGATACATTCTACTGA

Transcript

HSymV2.0_g09.16744_t1

CGAAAACATCTTGAAGAAAAATCTCGGCCATCCGTGCGTTTAAAAAGGACCTGGTTGACTTTGTTTACTATACATTTCGTTTCGTTTACGTAAGTGGAGGTTCGTGATAAATGGAAAAGTCACCCGAAGCCTGGTACGACGTGCTCTTGCAAGGCGACAGTTGGAAATACGCTCATTTAGACCAAGTTCTTCCCGTGGAATGAAGATGGGAGTGTCTTGTAAAAATTGTGGAGGGACTGAAATTGATCATGATCAAGCACGAGGTGATGCTGTTTGTATTGGCTGTGGTTCAGTGGTTGAAAGTCTTTGCATTGTCAGTGAAATTGAGTTCCAAGAAAACAGCGCTGGCAATGCTTCAGTGATTGGCCAGTTTGTGTCTGCTGAAGGACAACATCACAGCATGGGCTCAAACTTAAAATATGGCACTGGAAGAGATCACAGACAAGTGATTTTGGATAATGGTAAGCAACTGATCAATCAAATGGGAAGTCAATTAAAAATGAGTCATCATTGCTTAGATTCCGCATTTATGTTTTACAAAATGGCTGTCAGCAAAAGGTTTACATCTGGTCGGAAAACTATTCATGTAATTGGTGCATGTTTGTATCTTGTTTCAAGAACAGAAAAGACGCCACATATGTTGCTTGATGTTTGCGACGTAGTTCAGTGTGACGTTGTAACTTTGGGTAGAGTATTTCTACAACTTGCTCGAGAACTGTGTATTGATTGTCCCATAGTTGACCCCAGTTTGTACATTCATCGATTTGCACACCAACTTGATTTTGGTGAGAAAGAGAATGAAATATCAATGACAGCGCTTCGTATTATGGCACGTATGAAAAAAGACTGGATACATTTCGGGCGGAGACCATCTGCATTATGTGGAGCTGCTTTAATTATTGCTGGTAAACTCTTTAGCTACAATGTTACCATGACTGATATCGTTAAATTAGTTCGAATGAGCAAGACCACAGTGTTTAAAAGACTAATGGATTTTAGTAAAACCGCAACTGGTAAACTGACCACAGACGAGTTTAAAACAGTAGATCTCGAAGAGGAAGCAGATCCCCCTTCCTACACTGCTGGAAGAAATCGTGTGAAGTTTGCACAAGAACTTGGAGATAATTATAGATTTGTGTCTAGTGATATTTTATCACAAGTAGTCAAAACACAAGAAAAGCTGGAAGTTCTATTAGAAAAACGAAAAACTATACACAAAGATTTGGAAATTACAAAATCGGAAGCAGAATCGTTTGATTATAGAAAAGAATTACCTTCTGACTACTCGTTATATACTTATGAGTTAGACGAAAATGGAGGTTTAAAGAATCCTTTGTTTGTCATTCATAATGAAAATGATATGAATTCAGAAAAACTTGAGGAGAGCGGCAAAAGTCATGCCAGCAGTACTTTGTTATTAGATTCTAAAACAAAATCAGAACCAGTGGATGTGTTTAAAGAAGAAAAAATATTGAAGGGTGAAGAAGAAAATGACGAAATTGAGTTGGATGACATCGATGATAAAGAAATTGATAAACTACTGTTAACAGAGGATGAAATAAAAATAAAAACTGAAATATGGCTGGAAGAAAATAAAGAGTATTTATTAAAAATGAAAGaaaaagaagaggaacaaaaaagaaaagaagaggaagaaAGTAAAGGCGGAATAAAAAGGAAAAAGAAAACATACAAAAGAAAGCAAAAAGATCGTCCAATTTGCGACACAGCCGATGAAGCTATAAAAACAATGCTCGCAGAGAGAAAGTTATCGAGTAAAATCAACTATGATGTTCTGCGAGGTCTGAGGTCTGAAGATAAAAATCAGGATTTTAAAGTGATGAAAAACGAACGTAATACCGACAGTGAAGCAGACGTTGTTGATACAAACATTAAAGTAGAGGATAAACCGCAGCTGCTGGAAAGTATTATGTATGAATCGGGCCCTATGAAACGAACCAATAAGAGAAACGCAAAGACAACTTTTATCTCGCTTGGTTCTCCAGATACTAAAAGGGTGAAGGTTGAACAGGAACAAAGAAATCTTACTCAAAGTTTAGAAACAATACCAGTGATTGAAAAGCAGAAACCTAAAGTGGAAGAAATGCAACCAATTGTAGAATCAGGTCCTGTGAGTACGAATGTGGACGATGATGACTATGTAGAAGATGAGGAGGAGGGGGAGGTTATAACAGCATCAGCATTGTTTGCTAAAGAAGTTGATGATTACGACACCTACGGTTATGATGATGGAGATACATTCTACTGATACAAATATATAGTTACGATGGAGATACACTATATTGACAAATATTGTTTTGATTGTGGAGATTTACTCTATACTACTGTCAAACATATTGTCATGATAATAGAGATACCTTTTGCTGAAATAAATATATTATCTACCAACCGTTAGATGATCAGCG

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q92994	Transcription factor IIIB 90 kDa subunit OS=Homo sapiens OX=9606 GN=BRF1 PE=1 SV=1
Q8CFK2	Transcription factor IIIB 90 kDa subunit OS=Mus musculus OX=10090 GN=Brf1 PE=1 SV=1
Q9P6R0	Transcription factor IIIB 60 kDa subunit OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=brf1 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003241 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF07741 all species →	BRF1	Brf1-like TBP-binding domain	Domain	Interproscan
PF08271 all species →	TF_Zn_Ribbon	TFIIB zinc-binding	Domain	Interproscan
PF00382 all species →	TFIIB	Transcription factor TFIIB repeat	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR011665 all species →	Domain	Brf1, TBP-binding domain	Interproscan
IPR000812 all species →	Family	Transcription factor TFIIB	Interproscan
IPR013137 all species →	Domain	Zinc finger, TFIIB-type	Interproscan
IPR013150 all species →	Domain	Transcription factor TFIIB, cyclin-like domain	Interproscan
IPR036915 all species →	Homologous_superfamily	Cyclin-like superfamily	Interproscan
IPR013763 all species →	Domain	Cyclin-like domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11618 all species →	TRANSCRIPTION INITIATION FACTOR IIB-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000126 all species →	Cellular Component	transcription factor TFIIIB complex	Interproscan
GO:0000995 all species →	Molecular Function	RNA polymerase III general transcription initiation factor activity	Interproscan
GO:0001006 all species →	Molecular Function	RNA polymerase III type 3 promoter sequence-specific DNA binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006352 all species →	Biological Process	DNA-templated transcription initiation	Interproscan
GO:0006383 all species →	Biological Process	transcription by RNA polymerase III	Interproscan
GO:0070897 all species →	Biological Process	transcription preinitiation complex assembly	Interproscan
GO:0097550 all species →	Cellular Component	transcription preinitiation complex	Interproscan
GO:0017025 all species →	Molecular Function	TBP-class 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
K15196	BRF1, GTF3B; transcription factor IIIB 90 kDa subunit	-	Transcription machinery	ko03021	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of HSymV2.0_g09.16744_t1 across 44 RNA-seq samples of Hydractinia symbiolongicarpus. 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.

44Samples

44TPM > 0

3Conditions

137.9Max TPM

84.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
Whole embryo	36	36	80.28	122.73
Whole embryo · Triptolide 20 uM	4	4	105.30	137.86
Whole embryo · DMSO 0.5%	4	4	96.74	115.14

Per sample · hover a bar for the full sample record

Show the sample table (44 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR24482170	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	122.73
SRR24482168	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	121.09
SRR24482163	Whole embryo	Whole embryo	6 hpf	not recorded	SRP436676	121.08
SRR24482172	Whole embryo	Whole embryo	30 mpf	not recorded	SRP436676	115.66
SRR24482166	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	112.56
SRR24482171	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	108.39
SRR24482161	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	106.00
SRR24482169	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	100.84
SRR24482165	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	98.93
SRR24482162	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	97.78
SRR24482167	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	94.23
SRR24482173	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	93.89
SRR24482175	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	88.27
SRR24482174	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	86.95
SRR24482176	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	84.83
SRR24482134	Whole embryo	Whole embryo	5 hpf	not recorded	SRP436676	82.39
SRR24482142	Whole embryo	Whole embryo	30 mpf	not recorded	SRP436676	81.48
SRR24482138	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	78.60
SRR24482136	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	78.33
SRR24482140	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	78.11
SRR24482145	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	74.59
SRR24482141	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	74.36
SRR24482143	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	72.53
SRR24482177	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	70.88
SRR24482135	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	70.16
SRR24482144	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	67.38
SRR24482137	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	60.50
SRR24482159	Whole embryo	Whole embryo	24 hpf	not recorded	SRP436676	60.02
SRR24482133	Whole embryo	Whole embryo	6 hpf	not recorded	SRP436676	59.28
SRR24482139	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	58.51
SRR24482158	Whole embryo	Whole embryo	48 hpf	not recorded	SRP436676	57.82
SRR24482153	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	56.54
SRR24482160	Whole embryo	Whole embryo	24 hpf	not recorded	SRP436676	42.52
SRR24482157	Whole embryo	Whole embryo	48 hpf	not recorded	SRP436676	41.65
SRR24482156	Whole embryo	Whole embryo	72 hpf	not recorded	SRP436676	38.80
SRR24482155	Whole embryo	Whole embryo	72 hpf	not recorded	SRP436676	32.39
SRR24482146	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	137.86
SRR24482147	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	123.87
SRR24482149	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	83.63
SRR24482150	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	75.84
SRR24482154	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	115.14
SRR24482148	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	112.52
SRR24482151	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	80.38
SRR24482152	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	78.92

Source: CnidoSite RNA-seq expression matrices (HSYMB_TPM, StringTie quantification over 44 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 Hydractinia symbiolongicarpus 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	24	HSymV2.0_g03.05884_t1	0.96984282703647
Negatively correlated	4	HSymV2.0_g06.11236_t1	-0.824555830477038

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 Hydractinia symbiolongicarpus, 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 →