Gene detail

Detailed information of HSymV2.0_g01.00157_t1 in Hydractinia symbiolongicarpus

Genomic Location: HiC_scaffold_1:5478886...5494248
NR annotation: XP_047139865.1, chromodomain-helicase-DNA-binding protein 1 isoform X1 [Hydra vulgaris]
Species Hydractinia symbiolongicarpus · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

HSymV2.0_g01.00157_t1

ATGCAGAGATTAAAGAGCTATAAGGAAGACAGCGAGGATGAAACAGACTCAGATGATCTTGTTGAATATGATGAAAAACAAACTGATATACCTACTGAACCAGTTGAAACTATTGAGAAGGTTATGCGTCATCGCAAAGGCAGACCAGAAGAAATTGGAGCTCAAACTACTATATACTCTCCAGAAAACGAGGAATTTGCAAAAAAAGGTGAACCTGACCCAGAAAACGAAACTGTTGAACTTCAGTTCTTGATTAAATGGAAAACTTGGTCTCATTTACATAACACATGGGAGACGAAAAAATCTTTAACTGAGCAAAAGTGTGGAGGGATCAAAAAATTGGAAAATTATATAAAACGAATGGATGAAATAGAGAAATGGAAAAAAATCTCATCTCCTGAAGATGTGGAATATTTTGAATGCCAAAGTGAAATGAATGAAGATATTCAGAAGCAATATCAAAAAGTGGAAAGAATTATCTCTCATCAGTTTATGCCAGAATCAGATTCTTCATATCCTGACTATCTCTGCAAGTGGCAAGGCTTGCCATACTCTGACTGCACTTGGGAAGATGGGAACTTAACTGCAAGGTTTTTTCAAAGTTATATTGACGAGTATTTAGAACGTGAACGATCTGACACCATACCTAATAAAAATGCGAAATGTTTACGACATCGTCCAAAGTTTGTACCGTTAAAAAAGCAGCCAGACTATTTAGGAAATTCTGATCTGCAACTGCGTGATTATCAGTTAGACGGTGTTAACTGGTTGGCACATGCTTGGAGTCGAGAACTGTCTGTTATTTTATCGGATGAGATGGGATTAGGCAAAACCATTCAAACTATTTCTTTTTTATCTTACCTGTTCCATACTCACTCATTATACGGGCCATTTCTTGTCGTTGTACCCCTTTCCACCATGGATGCTTGGCAAAGAGAATTCCAACTATGGGGGCCTGATATGAACTTAATAGTTTATATTGGCGATGTCAATTCGAGAACTAACATACAAGAATATGAATGGTGTTTTAAAAAAAACAGAAAACTAAAATTTAATGTTTTATTGACAACGTATGAGATGCTGCTTCGGGACAAGGAGTTACTCGGTTCACTTTATTGGGCTGCTTTATTGGTAGATGAAGCTCATCGCTTAAAAAACGATGACTCCTTGTTATACAGAATGTTGATTGATTTCCGTACAAATTTTCGCTTACTGATCACTGGTACACCCTTGCAAAACTCTTTGAAAGAACTTTGGTCGTTGATGCATTTTATTATGCCGAACAGGTTTGATGAGTGGTCCGATTTCGAGTCTGAATATTCAGTATCTGATAAAGAAGGTCTTCAGAAACTTCACAGAGATCTTGAACCCTATTTATTGAGAAGAGTGAAGAAGGATGTAGAAAAATCTCTTCCAGCTAAGGTTGAACAAATTCTCAGGATGGAAATGTCACAAGTCCAAAAACAGTACTACAAGTTGATCCTGACGAAAAATGTACAAGAGCTATGTAGAGAACTTAAGGGTAGTTTCAGTGGATTGCTAAATATCATAGTGGAGCTGAAGAAGTGCTGTAACCATAGCAACTTGATAAAACCCCTTGACCTGATGAATGAAGACCCCAACATGCTACAGACACTTATCAAAGGAAGCGGAAAGATGATACTGTTAGACAAATTGTTGTGTCGGTTGAAAGAGACAGGACATCGAGTTCTGATCTTCTCACAAATGGTTCGAATGCTTGACATCATCGCTGACTATCTGTATATGAAAAGATTCATGTTCCAGAGATTAGATGGATCAATACGCGGTGAGCAACGGAGGAGAGCTTTGGATCATTTTAATGCTGAAGGTTCACAGGATTTCTGTTTTCTTCTCTCAACTCGTGCCGGAGGTCTGGGTATTAACCTCGCATCAGCAGATACAGTAATTATTTTTGACTCTGATTGGAATCCGCAAAATGATCTGCAGGCCATGGCTCGAGCGCACAGAATTGGTCAAAAAAATCAAGTCAATATATACAGGTTTGTTACTAAGAATACAATTGAGGAGGATATTATTGAGCGAGCAAAGAAGAAGATGGTGCTCGATCATCTCATTATACAACGCATGGACACAACTGGTCGAAGAATCTTGTCGAAGAGTAGCACTGCTCCTTCCTCTAACGCACCATTTAACAAAGAGGAATTATCTTCTATTCTAAAGTTTGGTGCTGAAGACCTGTTTAAAGATGCTGACCAAGACCAGGATCAAAAGCTTCAtGCTATGGATATCGATGAAATCTTGCAGCGTGCAGAAACTCAGGAGCATCAGGATAACTTACCTTCAGTTGGCGAAGAACTGCTTTCTCAATTCAAGGTGGTTAACTATGCAGCCTTTAACGAAGAAGAAATTAAACCAACTCCTACTGCCAACCCTATGCAAAAATTATGGGAAGAAATCATTCCTgaagaagaacgaaagaaagcggaagaagaaagagaaaaagaaaagaaAGCTGAGTTGACGTTAAAGCCAAGAAGTAGAAAAACTGTGGAGAAGATGAACATTGGTCAAACGTCCAATAATAAAAAAGTAAAATCTAAAGCCATCGTGGACACTGATACATCTAGCGATTCTGATGACGACAGTGTGGAGGAGAATGATGTTGATGAAGCTAAAGGTAAAAAAGCAACGAAACGGCAAACGAAATCCAAACCTGTAAAGAAGGAGGGTGTCAAAGGGTTCTCCGACGTAGAAATAAGAAGGTTTATAAAAAGCTACAAAACGTTTGCAAGACCAATGACCAGGCTGGATTCGATTGCAGAAGATGCTGAACTTACAGATAAATCGGTGAACGAATTAAAAGAACTCGGTGAATTATTGAAGTCTTCCTGTGAACAAGCTGTAAAAGATTATCAAGAGAAGCTGTTGCAGGACGAACAATTTGACGGTAAAAAGAAAGGTGCCTCTTTGAAGATATCTGGTGTCACCATAAACGCGCCATCGGTGTTAAAAGCAGAAGTAGATTTAGAACCACTCGCTTTGTGCTTACCACAAGAACCCCGACAACAAAAAGGTTACCGATTGACCCATCCCACACGTAGCGTACATTGGGGTATCTCATGGGGCGTGGTGGAAGATTCCATGTTGTTGATTGGTATGCTGAAGTATGGTGTTGGCAATTGGGATGCTATCAAAAATGATCATGCGTTGGGACTTTCTGGAAAGATCCTTCCCATGGGAAATGGCAAGCCGCAAAATAAACATCTCCAATCTCGCGCAGATTATCTTCTGAAACTTTTAAAAGAACAGAAAACTCATCATGAACCAGAACAGAAAAAAAAAAAAATAAAGGTTCGTCCACACAAACAAGAAGATTATGTATCGCCTCACTCAGAAAGCGAGCATACCATCTCAAATACTCTgaatgaacaaaaaccaagcaagaagaagaagactaaaaagactgttgaaaagaagaaTGCAAAGACACTCAAAAAAGAGAAGACTCGCGATGAACGAATCTCAAGTCCTGCCGTGCCAGAAGAAAATCCGGTAGTGGTGATGGACTTTCGAGAAGAAATGGCCGAAGAAACTTTTAAGAAGTGCAAAGAAAAAATGCGCCCGGAAAAGAAGTCACTCCAACAACTTGATTCTCCTGACCAAAAATCTACGCCCAAAGAACAAGTGCAGACAACGAAAAAATGTTTGTTAAAAATCGGGGACCATATTGAAAGGTGCTTGGACGAGTACATGAAGGACCCTAACGAACTTGATGTATGGCGGAGTAATCTCTGGTCTTTTGTTGCAAAATTTACCGAGTTAGGACCAGCGAAACTTCACAAGCTCTATCGAGCAGCTGCTCGTAAGAGAGACGTGCAGCGTGACGAACAGAAGAAAGAGATTCAAAAACTGAAAATAAACTACACTCAATCACTTCACGAGATCGGAAAACATCTCCCTCCGGATCGTTTGGAGCTGGAAAAAGCGAGAAAAAAAGCGTTAGGTTTAAATGCTAACAATCCTGCATCGGCAAAGATACCAAAGTTGAATAAAATTAAAATACCTCACAAGAAAAAAGAAAAAGATGGAACAAATAACAATAATAAAAATACGGTACCGAATTATAAGATGCATGAAAGCCGAGATGGGTACCGTGGTCGACACGGCGGAGAGAAGATGAGCGAAAATTGGCGTCATCGAAACAAGCCGTACAACCGAGAACAGGCACCAAACTACAATACTTCACAAAAGTTAATTCTAGACAACGAAAGTGGTAACACCGTCAAAACGCAAACATATCGAGAATGGAAGGAAGCTCAGAAAGCACGGTTAGCTGCGGAAGAGAAAGCACCGCTTAAGGAGAATAGACAAAAAACATATAAAGATAAACCTTATTACGGAGATGAAAAACCTCATAATACGGAAAAACACTATGGAGATGAAAAAGCTCCGTTTAAACATGAACAATATACTTCTTACGATCCACGTAGTAAACCTCGCTATCATCGCGATTCGCAAGAATATTCGGGAGAATACTCAATATCTCCATCGTATATAAAATCTCCTTCAGCTTCTCTTTCTCCGCATAGTTACGTTGATTCTTGGTCGAGGAAAAGAACTTCAAGTAATAATAGTGAATTTGTTGCTACTAAAAAGTTGCATAGAGATCCGGAATCGTCTAACAGCAACCAATCGTGGGCAACAGGTGGGAACACGTGA

Transcript

HSymV2.0_g01.00157_t1

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P40201	Chromodomain-helicase-DNA-binding protein 1 OS=Mus musculus OX=10090 GN=Chd1 PE=1 SV=3
O14646	Chromodomain-helicase-DNA-binding protein 1 OS=Homo sapiens OX=9606 GN=CHD1 PE=1 SV=2
B6ZLK2	Chromodomain-helicase-DNA-binding protein 1 OS=Gallus gallus OX=9031 GN=CHD1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003380 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13907 all species →	CHD1-like_C	Chromodomain-helicase-DNA-binding protein 1-like, C-terminal	Domain	Interproscan
PF18375 all species →	CDH1_2_SANT_HL1	CDH1/2 SANT-Helical linker 1	Domain	Interproscan
PF00176 all species →	SNF2-rel_dom	SNF2-related domain	Domain	Interproscan
PF00271 all species →	Helicase_C	Helicase conserved C-terminal domain	Domain	Interproscan
PF00385 all species →	Chromo	Chromo (CHRromatin Organisation MOdifier) domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR025260 all species →	Domain	Chromodomain-helicase-DNA-binding protein 1-like, C-terminal domain	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR040793 all species →	Domain	CDH1/2, SANT-Helical linker 1	Interproscan
IPR038718 all species →	Homologous_superfamily	SNF2-like, N-terminal domain superfamily	Interproscan
IPR000953 all species →	Domain	Chromo/chromo shadow domain	Interproscan
IPR000330 all species →	Domain	SNF2, N-terminal	Interproscan
IPR016197 all species →	Homologous_superfamily	Chromo-like domain superfamily	Interproscan
IPR049730 all species →	Domain	SNF2/RAD5-like, C-terminal helicase domain	Interproscan
IPR014001 all species →	Domain	Helicase superfamily 1/2, ATP-binding domain	Interproscan
IPR002464 all species →	Conserved_site	DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site	Interproscan
IPR001650 all species →	Domain	Helicase, C-terminal domain-like	Interproscan
IPR023780 all species →	Domain	Chromo domain	Interproscan
IPR023779 all species →	Conserved_site	Chromo domain, conserved site	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45623 all species →	CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 3-RELATED-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0140658 all species →	Molecular Function	ATP-dependent chromatin remodeler activity	Interproscan
GO:0000785 all species →	Cellular Component	chromatin	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0003682 all species →	Molecular Function	chromatin binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006338 all species →	Biological Process	chromatin remodeling	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:0016887 all species →	Molecular Function	ATP hydrolysis activity	Interproscan
GO:0034728 all species →	Biological Process	nucleosome organization	Interproscan
GO:0042393 all species →	Molecular Function	histone 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
K11367	CHD1; chromodomain-helicase-DNA-binding protein 1	EC:5.6.2.-	Chromosome and associated proteins	ko03036	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_g01.00157_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

86.5Max TPM

62.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
Whole embryo	36	36	61.83	86.48
Whole embryo · Triptolide 20 uM	4	4	66.43	70.06
Whole embryo · DMSO 0.5%	4	4	59.32	64.97

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	86.48
SRR24482138	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	85.84
SRR24482140	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	85.50
SRR24482144	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	82.58
SRR24482142	Whole embryo	Whole embryo	30 mpf	not recorded	SRP436676	82.11
SRR24482143	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	81.95
SRR24482141	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	81.95
SRR24482134	Whole embryo	Whole embryo	5 hpf	not recorded	SRP436676	81.87
SRR24482136	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	78.75
SRR24482170	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	76.16
SRR24482135	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	75.62
SRR24482168	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	73.30
SRR24482171	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	72.02
SRR24482137	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	68.94
SRR24482172	Whole embryo	Whole embryo	30 mpf	not recorded	SRP436676	68.10
SRR24482166	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	67.82
SRR24482173	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	66.43
SRR24482133	Whole embryo	Whole embryo	6 hpf	not recorded	SRP436676	63.49
SRR24482165	Whole embryo	Whole embryo	4 hpf	not recorded	SRP436676	62.96
SRR24482163	Whole embryo	Whole embryo	6 hpf	not recorded	SRP436676	62.31
SRR24482169	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	62.20
SRR24482174	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	61.63
SRR24482139	Whole embryo	Whole embryo	2 hpf	not recorded	SRP436676	61.18
SRR24482153	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	60.88
SRR24482167	Whole embryo	Whole embryo	3 hpf	not recorded	SRP436676	60.06
SRR24482177	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	59.27
SRR24482175	Whole embryo	Whole embryo	Unfertilized egg	not recorded	SRP436676	56.30
SRR24482161	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	52.75
SRR24482176	Whole embryo	Whole embryo	1 hpf	not recorded	SRP436676	50.26
SRR24482162	Whole embryo	Whole embryo	7 hpf	not recorded	SRP436676	46.08
SRR24482159	Whole embryo	Whole embryo	24 hpf	not recorded	SRP436676	32.36
SRR24482158	Whole embryo	Whole embryo	48 hpf	not recorded	SRP436676	30.04
SRR24482160	Whole embryo	Whole embryo	24 hpf	not recorded	SRP436676	29.73
SRR24482157	Whole embryo	Whole embryo	48 hpf	not recorded	SRP436676	28.17
SRR24482156	Whole embryo	Whole embryo	72 hpf	not recorded	SRP436676	22.66
SRR24482155	Whole embryo	Whole embryo	72 hpf	not recorded	SRP436676	8.00
SRR24482149	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	70.06
SRR24482150	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	67.50
SRR24482146	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	65.79
SRR24482147	Whole embryo · Triptolide 20 uM	Whole embryo	7 hpf	Triptolide 20 uM	SRP436676	62.37
SRR24482151	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	64.97
SRR24482152	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	61.31
SRR24482154	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	56.89
SRR24482148	Whole embryo · DMSO 0.5%	Whole embryo	7 hpf	DMSO 0.5%	SRP436676	54.12

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	15	HSymV2.0_g13.22323_t1	0.949675338195823
Negatively correlated	11	HSymV2.0_g08.14378_t1	-0.936086814543947

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 →