Gene detail

Detailed information of HSymV2.0_g06.10893_t1 in Hydractinia symbiolongicarpus

Genomic Location: HiC_scaffold_6:21549766...21562509
NR annotation: XP_015776225.1, PREDICTED: F-box only protein 10-like [Acropora digitifera]
Species Hydractinia symbiolongicarpus · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

HSymV2.0_g06.10893_t1

ATGACAATAATGGTAGCAAGCATCCCACTTTTAAAATCGCTGACATCCACTGATATCAAACAAGGTTTACCAGGCGAGGTATGGAGAGTGGTGTTTTCTTACTTAAAAGCTATTGATCTGTGTCGTTGCTCACAAGTATGTAAAGACTGGCGTATCCTCGTTGATAGTGTCGATGCAACAACATGGAGGTTTTTATACCTGGAACAAAAAAAGTATAAGCGATGGAAGCATCCTTACTGGCCAAATGAAACACAATCAAATGTTATTTCTTGGAAGAAATCATACAGACAACGATATTTAGTGTCTCGTTTGTGGTTAAACAATGGTGTGACAACTGCATGTTCAGTAAACTTTTTCTTTGGTAGAAGTAAAGAAAGAAAGAATTTTTATGTTGGCTCAAATAAACCTTATAAAACAATAAAGAGTGCCATTGAAAAGGCTTCTCCTTACGATCGTATATATGTCTATCCCGGAGTATATCAAGATCCAGTCATGCTTGTGATAAAAAATCCATGTGCTGTTATTGGCGTGGATGACCCAAGTAAAATTATATTAACTATGCAAATCGATGTAAGAGCAGAGTCTTTAAAATTAGAAAACTTAACAATAAAACCGATGTATCCAAGAAGAGTTCATTCATCCACAGCTCTTCTAAAGGTATTATATGGTCATGTCTTTATGTTTAACTGTATTGTGAATCAAGGTTACCTACATATCACTGCACCCGGCATAGCTGACATCAGGTCATGTACATTTACTACCGCTTTTGTTAATTTACAAGGTGTTGGTTATAGTAGTATTACAAACTGTGAATTTAAGCCTGATCGGTTTGCTATATTTGTTGAGGAACCGTTGTTTCAATTTAACTTAAGACCACCTCGCACCATGGATGAAGTTGGAGGATGGGTAGCCGCTTTAAACGAGAAAAAGTTTGATGAGTATTACTGTAGGCATATTAAAGAAAAATGTCGGAAAAGAAATGGAGATAATGAAATGAAAAAGTCCAAATCTTTTTTATCTTGCATAACTGAATCTGATCTCAGTTTGAGTGACAGTGATGCTAGTGAAGTGAGATCGAAAACAAAATCATGTTTGTCACGAAAGAGTAGAGTCAATAGTTTAGGGTCACTAAAGAGCGACAATGGTACTGAGAAAGAAACTGTGGATGCACAAACTAAAGTATTACTTAAAGCTATACAAGGTGTTGTTATTCGAAATATTAAAGTTACTGGTGGCAAGGGTGGGGTCACCTTGTGTAGAATGGGACAGGCATGGATTGAAAATTCAACATTTTCCAACTTGAGTTATGGAATTCGATGTTTACAAAATTCAAAATGTGTTGTATTAAACAACAAGATACATAGTTGTGACACAACAGGTATTTTTATAAGAGATCACTCTGTTGCATTGATTGCTGGAAATCAAATCTTTGCGAATGGTGAAGCAGGTATTGATATTCGTTCAAGTGCAAATCCGTTAATTGAACATAACGAAATTCACAGTGGTAAAAGATCAGGAATAGTTTGTTTAGATCATGGAAAGGGTGTGATTCGAGAAAATGACATTTACAATAACAAGGAAGCAGGCATTTATATTTTACATAAAGGTTGTCCTAAAATTCATAACAATCATGTGTGGTCTGGACGAGCTTCTGGCATTGCTGTGACAGAAGATGGGACTGGTCATATAACAAACAACATAATTACTGAAATGGAGTGGGCAGGTATTGACATTCGGCATGGAGGTAACCCTGTCATTTCACATAATGTGATTCAACATGGAAAATCAGATGGGATTGTTGTTGGTGAAGCTGGCAAGAGTGTTATTTTGGATAATACAATTGAAGAAAACAGTGGTTGCGGTATATGGATTTTAGACGGATCCCATCCACTCATTCACAGCAATGTAATAACGAACTCTGGAAATTCGGGAATAGCGTTTGTGAATAACAGTGATCATGAGCACGAAAAACAGAAATTGAGTGTACATATACCGCAAAACAGAGCTGCACCAGCTTTTAATCACGATGCTGACGAAAGAAGTGTTGATACAGAGGAGGAGTTTATATTCCCATCACCAATGATGTTGGAACAAGAGCCGGAATCAAGATACGTGCACGTCTCAAAGCCAGATAAAAAAGTTGCTCAGGTCGAAGGCAATACCATTGAAAACAACAAGGGGCATGGTATTTTGTATGATGGCAAAGAAGGCATTGTAATATTTAAGAATCAAATCAATCATAACTTAAAACATGGTATTAACTTAATACATTCTAGTGAAATAAGTATACAAGATAATGAGCTCAGTCATAATCACCTTTCCGGTGTAAATGTTGAACTTGGTATAAATGTATCCCTTGAGGGAAATGGATTGTACGAAAATGGAGAGTATGGAGTCAGCACAGCAGGAATTAGTACTATACTTCGCAACGATGTATTCGGTCATTCCTTACCCGGTGTATATGTTCAAACTCTTGCAGATGTTTCACTGAAAAACAACCGACTGCATGGATTAAAGCATCCATGTGTTCATGTAGAAGAACAATCGCGGTGCATTGTGGATAATAACGATTTTTACATTGGTTCTGAAGCAAAAGATTTGTACTTTCATGAAATTAGTGATGTTTCATATCTCGACAATAACAAAATTCATAAAATTGATAATAATGACTCTTGCAGAGACTTGTCAGATATTGTTTCATATACTGCTGTTGGTATAACGGATTGGAGACCTCAATGCACCAATGTGGCAACCAAGAGTGCTCCATTTTTTACCACAGTTCAAATGCATAATCAAAATCGCTCGAACAACAGGAGTTCGTTTTGTGCTCTTCTGTGA

Transcript

HSymV2.0_g06.10893_t1

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9UK96	F-box only protein 10 OS=Homo sapiens OX=9606 GN=FBXO10 PE=1 SV=3
Q7TQF2	F-box only protein 10 OS=Mus musculus OX=10090 GN=Fbxo10 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006286 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00646 all species →	F-box	F-box domain	Domain	Interproscan
PF13229 all species →	Beta_helix	Right handed beta helix region	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR011050 all species →	Homologous_superfamily	Pectin lyase fold/virulence factor	Interproscan
IPR001810 all species →	Domain	F-box domain	Interproscan
IPR036047 all species →	Homologous_superfamily	F-box-like domain superfamily	Interproscan
IPR012334 all species →	Homologous_superfamily	Pectin lyase fold	Interproscan
IPR022441 all species →	Repeat	Parallel beta-helix repeat-2	Interproscan
IPR051550 all species →	Family	SCF Complex Subunits and Alginate Epimerases	Interproscan
IPR039448 all species →	Domain	Right handed beta helix domain	Interproscan
IPR006626 all species →	Repeat	Parallel beta-helix repeat	Interproscan
IPR006633 all species →	Domain	Carbohydrate-binding/sugar hydrolysis domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR22990 all species →	F-BOX ONLY PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0006511 all species →	Biological Process	ubiquitin-dependent protein catabolic process	Interproscan
GO:0042981 all species →	Biological Process	regulation of apoptotic process	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
K10296	FBXO10; F-box protein 10	-	Ubiquitin system	ko04121	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_g06.10893_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

193.1Max TPM

91.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
Whole embryo	36	36	96.74	193.10
Whole embryo · Triptolide 20 uM	4	4	73.96	123.81
Whole embryo · DMSO 0.5%	4	4	56.75	86.94

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
SRR24482145	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	193.10
SRR24482138	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	191.98
SRR24482144	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	178.44
SRR24482141	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	178.17
SRR24482177	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	175.97
SRR24482140	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	174.52
SRR24482142	Whole embryo	Whole embryo	30 mpf	not recorded	SRP436676	174.04
SRR24482134	Whole embryo	Whole embryo	5 hpf	not recorded	SRP436676	172.06
SRR24482143	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	171.54
SRR24482135	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	168.75
SRR24482136	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	166.67
SRR24482139	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	166.38
SRR24482137	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	162.10
SRR24482174	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	136.51
SRR24482172	Whole embryo	Whole embryo	30 mpf	not recorded	SRP436676	121.11
SRR24482133	Whole embryo	Whole embryo	6 hpf	not recorded	SRP436676	112.87
SRR24482173	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	110.13
SRR24482175	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	108.49
SRR24482153	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	89.34
SRR24482176	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	75.93
SRR24482171	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	51.63
SRR24482165	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	43.73
SRR24482169	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	43.39
SRR24482163	Whole embryo	Whole embryo	6 hpf	not recorded	SRP436676	41.33
SRR24482167	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	39.54
SRR24482168	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	33.80
SRR24482161	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	31.62
SRR24482166	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	30.53
SRR24482170	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	30.38
SRR24482162	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	30.17
SRR24482160	Whole embryo	Whole embryo	24 hpf	not recorded	SRP436676	17.31
SRR24482159	Whole embryo	Whole embryo	24 hpf	not recorded	SRP436676	16.47
SRR24482157	Whole embryo	Whole embryo	48 hpf	not recorded	SRP436676	13.15
SRR24482155	Whole embryo	Whole embryo	72 hpf	not recorded	SRP436676	11.49
SRR24482156	Whole embryo	Whole embryo	72 hpf	not recorded	SRP436676	11.35
SRR24482158	Whole embryo	Whole embryo	48 hpf	not recorded	SRP436676	8.83
SRR24482149	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	123.81
SRR24482150	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	117.08
SRR24482146	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	30.69
SRR24482147	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	24.28
SRR24482152	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	86.94
SRR24482151	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	82.48
SRR24482154	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	29.98
SRR24482148	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	27.60

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	39	HSymV2.0_g06.10274_t1	0.981381762465357
Negatively correlated	3	HSymV2.0_g11.19702_t1	-0.910453612811876

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 →