Gene detail

Detailed information of BRAKERKREP00000001065.1 in Hydra viridissima

Genomic Location: not available for this species
NR annotation: XP_012557073.1, host cell factor 2 [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families

Sequence

CDS

BRAKERKRET00000001065

ATGGCATTATCTAACATGAAATGGAAATGCGTAAAAGAACCTTCAGGACCTAGTCCTCGACCTAGACACGGTCACCGTGCAGTTTCAATAAGGGACTTAATAGTTATCTTTGGGGGAGGAAATGAGGGTATTGTTGAAGAACTTCACGTCTACAATACTGctaCAAATCAGTGGTTTGTTCCTGCAGTGCAGGGAGATATTCCACCTGGATGTGCTGCCTTTGGCTTTGTATGTGATGGGACTAGATTGCTTATCTTTGGTGGAATGGTTGAATATGGAAGATATTCAAATGAGttatatGAGCTACAAGCCAGTCGATGGGAGTGGAAGCATTTGCATCCAAAAGCACctgaaaacaatatttctcCTTGTCCAAGGCTTGGGCATAGCTTTACATTGGtgggaaagaaaattttcctttttggTGGATTGGCAAATGACAGCGAAGATCCGCGGAGTAATATTCCAAGatactTGAATGATCTTTACACACTTGACTTGACAACTCAAGAAAACTTGCAATGGGAGGTTCCTTTCACTTATGGACAACCACCTACAGCTAGAGAATCTCATTCTTGTGTACTACACACTGCAGAGAATGGGAAACATCCTCGTTTGTTTATATATGGTGGAATGAGTGGGTGCCGTCTTGGGGATGTATATATACTTGATGTTGaaaaaatgctttGGTCAAAGCCAGTAGTTCATGGTATTGCTCCTTTGCCTAGAAGTTTGCATACTTCTGTAATGATTGGTAAACGgATGTTTATTTTTGGAGGTTGGGTACCAGTAGCTATTGATGATGGAAAATCAAGCAGTGAAAAAGAATGGAAATGCACTAATACACTTGCTTGCCTAAATGTTGAAAAACTTCGTTGGGAAGCAATAAATGTTGATGGAGTTGAAGAACAAATGCCCAAGCCCAGAGCAGGTCATTCTGCTGTAAATGTACATACTCGTATGTATGTTTGGAGTGGAAGAGATGGTTATCGTAAGGCTTGGAATAATCAAGTTGAAAATGTCTGTTGTAAAGATTTGTGGTATTTAGAAACAGAGCGTCCTCCTGGTCCTTCTCGTGTTCAACTTGTTAGAGCAACTACTACTACTCTTGAGGTCTGCTGGGGAGGAATTCCAACAGctGATGCATATATTATCCAGATACAGAAATATGAAGTGCACCCTCCTGTACTTCCGTCTACTCCAATGCCAATAACAACTAAATCTGCTATAGCTTCACCTGATTTATCTAAAGTTTTGAGTCCTAGTGCTGCTCATGTTGTCCGGTTACCTATATCTTCTACCCAGTTTTCTTCACCACTTTCAATTTCTAAAACCTTACTTGCTGGTGGGCTTTCAGTTAGGCCAAAATTAACCATGTCTCAACCAAATAACCTTGTTAAAGCAACTAGTCCAAAGGGACTAACACAGATTCCAATTCAAGTTAGTggacaattaaaaaatcagcatATAACATTGGCTGCTCTAAATCAATTAACTGCCGGGAAATTGACTGGAACTAATTTAACTGCTAATGTAACCAAGACAATACAAATTGTGTCACCAAGCAAATCAGGACAGATAGTTCGTCCTCAACTGCAAGGAGCAAACCTAAACTTAGTAACTAACATTTCATCTCAACCATCTCAAGTTTCAACTTCTgctgatataaaaaatgcaaacttaAAACCTTTGTCTTCATCACCTGCTGCTACACAATATGCACTTGTTAGAGCTCAACTTCCTAGCAGTAGTGGTGGCCCTGCTCAAACTGTAACATTTATTCGTGCCATAGCTCCTAACTCTACTTCTGCAACAAATGCAGGAACCACTGTAAGTGTCACTCCTCAACAAATGGCTGCTTTGCTGAAAGGTCAACAGGGACAAAGTCAAATTCAAAAGGTTCTAAGTGCTGCTACTGGAGGAAACCAAGTTCGTGCACCAACTGTACTAAATGGTGTTGGTGTTTCCAACACAATAAGCCAACCTACTGTCAGTGTATCAGTTACTCAAAGTCCATCAAAGTTGATATCTTTGCAATTTCCTCAAAAAACTGCCTCAATTccattaaaatcaataaatgtttcatcatttttaagtaCATCAAAAACTGCTGTTACCACTCAGTCCTCTAATATTTCACCTATGGGAACACTAGTTTCTGGAATAGGAATATCTAAGAATctttcatcaattttaaatcaatgtcCACCTGTCAAGCCACAACTACCATCAGCTTTATCAAATCTGGCAATAAATTCGACTACAAATAAACTTCAGATTACTTCAAGCTCTCCTATTATCACAGACTCAACTGTCATTcatgaaacagaaaaagttgCATGCTCTGATCAAGAAAATTCTATGCATTTGAACACTATAAAACAAGCTGAATCACCTGAAGTTGCTTCAATTGCTAGTTCAAATAGTTGTGAAACAACAGGCTATGATAAAGACCTTGTTAATTCTGGTGTATTACTTGTTGATACAGCCACTTTAGACTCAAATCTGTCAATCAACCCTTCATTAGATGAagataaaacaattgaaaatgtaGTTTCAAGTTCTTTGAAATTGGATTCAGAATCTACATATAAAGAAGAAACTCAAACTGACTTAAAGTCAGCTCTTATCCTGGAAACTCctaaaatagaagaaaaagaactaATTGATGACATAAAAGAGGAACTACATAAATTGAGTCCTAACATGTCTGAAAACCTAACTGATGTTTCTATGCTAGAAGAAAAACCTGAAATAAAAGATGAGCTAATGGAAACAGATCCATCTATCGAGTCTGTTGCTGCAACCACACTTGCACAGCTAGCCTCTTATGCTGGCAATATTAATAGCATTCAAAATGCATCTGCTTCAGATATCTCAAATGACCCACTTTCAACACTAGCTGCACTTGCAACCTCTTCCCCAATTGCAACTGGTCCATTACTTCATATTGGAAATGGGCAAAATACAGATGGAATATCTGTAAGCCCAGTATTAGTGCCTGCTGGAAAGAAGgcATTAAATAAACCAATTCCTTGGTTTGATGTTGCCATGACAACTAATACATCAATTGTTGTTTCTCACTACTATGTTCCTGTAGAAGAAGGTGATGAAAATGGAGATAATGTTGTCTCAGATGGTGATTATAAAGGCATGCGTAAGGTTGAGCTTAAACCTGGTACTGCCTTCAAGTTTAGAGTTGCTGGAATTAATGTTTGTGGAAGAGGTGCATATAGTGATATAGCAGCATTTAAGACTTGTGTGCCAGGTTTTCCCGGTGCACCTTGCGctatcaaaataacaaaaaacgAAATTGGAGCTCATTTATCATGGGAACCTCCAACGAATAGTGCGGGTAAAATTCTTGAATATGCAGTATACCTGGCTGTCGACAATAAAAAAGGCGGTAAAGAAACCACGCAAACACAACTAACATTTGTGCGTGTTTATTGTGGATCGATTTCTTCGTGCACTGTGACAGCAGATACCCTTAAAAATGCTCACGTCGATTTTTCAACAAAGCCTGCCATTATCTTTAGGATTGCCGCCAAGAATGAGAAAGGGTATGGTCCTGCTACACAAGTTAGATGGCTACAAGATTTAAAGGATCTACCAGATAACAAACTAAAACGACAAGCTGATCAGAGAGGAACAAGTTGTGGAGCTCTACCACCTGAGAAGTTGTTTATGCAAGGAGGCTATGCTCTAGGATACAAATTTCACATACCAACAGACCCATATGCTATTGCTGCAGCCACTGCAAAAGAACATAGTGATCATAAACAGCGTCAAGTAATTCAAACAGTATTTGAGCCTACTGTTAAAATAGATGATGCCTATAATCGAATAACATCACCAGTTTCTCCAAATAAAAAGCGATCACGTCTTAATCCAACTGTTATTCCTTCTGTATTAACTAACCGGTCAAACTTTTCAAGACTCAAATCATCATCTCgtatttttcagaatttgGCAAAAGCAATCTATACTCCTCCTGCTATGATGAGtccaaaaagtatttttttaaccctCATGCCAACCCAAATCAATCGTCATATAAATCAGCGTGAACCAGCCGCAGATCGAAAAATGATAATGGGAAGACCCACTGAGTACAAAGGAGTAGGCGATCGACCATCGAACCATCAATATCAACTGGTACCACGAGTTACCCACCTTGAATGCTAA

Transcript

BRAKERKRET00000001065

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9V4C8	Host cell factor OS=Drosophila melanogaster OX=7227 GN=Hcf PE=1 SV=2
D3ZN95	Host cell factor 1 OS=Rattus norvegicus OX=10116 GN=Hcfc1 PE=1 SV=1
Q61191	Host cell factor 1 OS=Mus musculus OX=10090 GN=Hcfc1 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004526 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13415 all species →	Kelch_3	Galactose oxidase, central domain	Repeat	Interproscan
PF13418 all species →	Kelch_4	Galactose oxidase, central domain	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR003961 all species →	Domain	Fibronectin type III	Interproscan
IPR036116 all species →	Homologous_superfamily	Fibronectin type III superfamily	Interproscan
IPR013783 all species →	Homologous_superfamily	Immunoglobulin-like fold	Interproscan
IPR015915 all species →	Homologous_superfamily	Kelch-type beta propeller	Interproscan
IPR043536 all species →	Family	Host cell factor	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46003 all species →	HOST CELL FACTOR	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0003713 all species →	Molecular Function	transcription coactivator activity	Interproscan
GO:0006338 all species →	Biological Process	chromatin remodeling	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0035097 all species →	Cellular Component	histone methyltransferase complex	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

No KEGG orthology assignment for BRAKERKREP00000001065.1.

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000001065.1 across 29 RNA-seq samples of Hydra viridissima. 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.

29Samples

6TPM > 0

7Conditions

4.3Max TPM

0.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	0	0.00	0.00
Whole	6	5	3.05	4.33
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	1.92	1.92
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	0	0.00	0.00
symbioic hydra M9 strain · symbioic hydra rep1	1	0	0.00	0.00
symbioic hydra M9 strain · symbioic hydra rep2	1	0	0.00	0.00
unannotated	1	0	0.00	0.00

Per sample · hover a bar for the full sample record · show / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR21134050	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134051	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134052	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134053	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134054	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134055	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134056	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134057	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134058	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134059	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134061	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134062	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134063	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134064	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134065	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134066	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134067	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	4.33
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	4.17
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397	3.72
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	3.47
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	2.59
SRR10058802	Whole	Whole	not recorded	not recorded	SRP220397	0.00
DRR048593	aposymbioic hydra M9 strain · aposymbioic hydra rep1	not recorded	not recorded	aposymbioic hydra rep1	DRP003902	1.92
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	0.00
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	0.00
DRR048596	symbioic hydra M9 strain · symbioic hydra rep2	not recorded	not recorded	symbioic hydra rep2	DRP003902	0.00
ERR13389755	unannotated	not recorded	not recorded	not recorded	ERP162636	0.00

Source: CnidoSite RNA-seq expression matrices (HVIRI_TPM, StringTie quantification over 29 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.