Gene detail

Detailed information of BRAKERKREP00000001441.1 in Hydra viridissima

Genomic Location: not available for this species
NR annotation: XP_047126263.1, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families

Sequence

CDS

BRAKERKRET00000001441

ATGGATACAGAtgaaaagaatataaaagagGAAGAAGAAGAAACTGAAGTTGTTTCTGAAGAAGAAGCCTCAgatgatgaagaaaaaaaagcatctcCAATAGTTATCAATAAAGAAATGAGTGTGAATAAAGAGTATActgaaaaaatggaaaaagataGAGCAACTCGCTTTAATTATCTTCTCAAACAAACAGAAATATTTGCACATTTTCTTAATACTGGAAAAAAACCTCCAAAAAgtcctttaaaaattaaaaaatcagattttccCACAAGTCCTACTAAAAATACTACAAGCACAGCTGCAAATGAtcatCGCCAtcgaaaaacagaaaaagaagagGATGATGAACTCCTAGAAAATTCGAAGCAATCAGAGGCACATATTGTACAATTTAATTCTTCACCTACTTatgtaaAAAATGGTAATATGAGAGATTATCAGATTCGAGGATTGAATTGGATGATTTCTTTGTATGAAAATGGTATAAATGGTATCCTTGCTGATGAAATGGGTTTAGGTAAAACATTGCAGACAATCTCTTTAATTGGTTACATGAAACATCATCGCAATAATCCTGGGCCACACATTGTCATTGTGCCGAAATCCACTTTAGCAAACTGGATGGCCGAATTCCAGAGGTGGTGTCCATCAATTCGTGCTGTGTGTCTTATTGGAAACCAAGAACAAAGAGCTGCTTTCATTAGAGAAACATTGCTTCCTGGTGAATGGGATGTACTTATCACATCATATGAAATGTGCATTCGTGAAAAAGCTGTACTCAAAAAGTTTGCATGGCGTTTCTTGGCTATAGATGAAGCCCATaggataaaaaatgaaaaatctttgctttcacAAATTGTGCGTGAGTTTAAATCATCCAATAGGCTTCTATTAACTGGCACACCATTACAAAACAATCTGCATGAACTTTGGGCATTACTTAATTTTCTTCTGCCTGATGTTTTTAATTCTGCTGAGgactTTGATGCTTGGTTTAATGCTGAAAGCATTACTGAAGAAGATCAGTTAGTGAAACGTTTACATGaaGTTCTTCGTCCATTTCTACTAAGGAGGTTGAAGAGtgaagttgaaaaaacattgctccctaaaaaagaaacaaaaatatatgttgGTCTAAGTGTTATGCAACGACAGTGGTACACAAAGTTGTTAATGAAAgatattgatattgttaatgGTGCAGGAAAAGTTGACAGAATGCGActtcttaacattttaatgcAGCTAAGAAAATGTTGTAATCATCCATATTTGTTTGATGGAGCAGAACCAGGTCCACCTTATACTACTGATCAGCATTTAGTTGACAACTGTGGGAAAATGATTGTTTTGGATATGTTACTGAAGAAGTTAAAAGATTCTGGATCTCGAGTTCTTATATTCAGTCAAATGACTCGTGTTTTGGATATATTGGAAGACTATGCAATGTGGCGAGGTTATCAATACTGTCGTCTAGATGGTCAAACTCCACATGAAGACAGAACTGCTCAAATTAACGATTTTAACTCACCTGGAAGTGATAAATTCTTATTCATGCTCAGTACTCGTGCAGGAGGACTTGGTATCAATTTAGCAACTGCTGATGTTGTGGTTATGTATGATAATGATTGGAACCCTCAAGTTGATTTGCAAGCACAGgATCGAGCTCATCGGATTGGTCAAACAAAGCAGGTTcgtgtttttaagtttataactGAAAACACTATTGAAGAAAGAATTATCGAGCGTGCTGAGATGAAACTGCGTTTAGATGCTGTGGTTATTCAACAGGGGCGGCTTGTTGATTCAGCTGCTAAAATTCAAAAggatgatattttaaatatgataagACATGGTGCTGATAAGGTATTTGCTGGTAAAGATGCAACAATTTCATCAGATGACATTGATGCTATATTAGAGCGTGGACAGAAAAAGACAGATGAAATTGCTAAGAAAATGCTTGAGTTAGGGGAAAATCAACTACAGAAATTCACTATGGACACTTCAGAAAGTATATACCAGTTTGAAGGACAAGATTTTCGTGAAACGCATGATAAACCTGGTTCCTTAAGTCATTGGATTGAGCCTCCAAAGCGTGAGCGTAAAGCCAATTATGCTGTAGatacatattttaaagagCTTATGCGTGTAAATGAGCCAAAAGCTCCAAAGGCTCCACGCCCTCCTAAGCAACCTAATGTACAagactttcaattttttccacCAAGACTCTTTGAATTACTTGATGTGGAAATCTATAGTTATCGAAAATCTATTGGCTATAAAGTCCTTCGTGACTATGATCTTCCTGATGATGAAGCCAAGCGCTTACAGAAAGAAGAACAAAGTAAGATCGATAATGCTTTACCACTGTCAGAAGAGGAAAGCATAGAAAAAGATGAACTTTTAACACAAggatTTGTCAATTGGAATAAACGagattttaatcaatttataaaagcttGTGAAAAATATGGGCGTGATGATATTAACCAGATTTGCAAAGAGGTCGAAGGGAAAACACCTGAAGAAGTAAAAGAATATGCTTCTGTATTTTGGGAACGTTGCAATGAACTAACTGATATTGACAAAATCATGTCACAGATAGAAAGAGGGGAAGCTAAAATACAACGAAGAATTAGTATAAAAGAAGCCATGGAAGCTAAgatggCTCGATACAAATCACCTTTCCATCAATTAAGAATACAGTATGGAACAAATAAAGGCAAAAATTATACTGAGGAAGAGGATAGGTTTTTAgtATGCATGATACACAAATTaggatttgaaaaagaaaatgtatatGAGGAATTGCGTCAAGCTGTACGAAATGCTCCACAATTCAGATTTGATTGGTTTATAAAGTCCCGAACAGCTGTTGAATTGCAACGTCGTTGCAATACTCTTATTACACTTATTGAACGAGAAAATCaagaaatagaagaaaaagaaaagagggAGAAGAAAAAAGGACCAAAGCCAGGACTACCCAGggGACCGAGCCAAAAACGTAAAAGTGAACCTCCTGTTGCAAAACCTGccaaaaaggtgaaaaaataa

Transcript

BRAKERKRET00000001441

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q91ZW3	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 OS=Mus musculus OX=10090 GN=Smarca5 PE=1 SV=1
O60264	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 OS=Homo sapiens OX=9606 GN=SMARCA5 PE=1 SV=1
P28370	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 1 OS=Homo sapiens OX=9606 GN=SMARCA1 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000968 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00271 all species →	Helicase_C	Helicase conserved C-terminal domain	Domain	Interproscan
PF09110 all species →	HAND	HAND	Domain	Interproscan
PF00176 all species →	SNF2-rel_dom	SNF2-related domain	Domain	Interproscan
PF09111 all species →	SLIDE	SLIDE	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001650 all species →	Domain	Helicase, C-terminal domain-like	Interproscan
IPR049730 all species →	Domain	SNF2/RAD5-like, C-terminal helicase domain	Interproscan
IPR009057 all species →	Homologous_superfamily	Homeobox-like domain superfamily	Interproscan
IPR036306 all species →	Homologous_superfamily	ISWI, HAND domain superfamily	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR017884 all species →	Domain	SANT domain	Interproscan
IPR001005 all species →	Domain	SANT/Myb domain	Interproscan
IPR038718 all species →	Homologous_superfamily	SNF2-like, N-terminal domain superfamily	Interproscan
IPR044754 all species →	Domain	Isw1/2, N-terminal	Interproscan
IPR015194 all species →	Domain	ISWI, HAND domain	Interproscan
IPR014001 all species →	Domain	Helicase superfamily 1/2, ATP-binding domain	Interproscan
IPR000330 all species →	Domain	SNF2, N-terminal	Interproscan
IPR015195 all species →	Domain	SLIDE domain	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:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0006338 all species →	Biological Process	chromatin remodeling	Interproscan
GO:0031491 all species →	Molecular Function	nucleosome binding	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0140658 all species →	Molecular Function	ATP-dependent chromatin remodeler activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0000785 all species →	Cellular Component	chromatin	Interproscan
GO:0003682 all species →	Molecular Function	chromatin binding	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
K11654	SMARCA5, SNF2H, ISWI; SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5	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 BRAKERKREP00000001441.1 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

20TPM > 0

7Conditions

4.1Max TPM

1.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	10	1.06	4.14
Whole	6	6	2.72	3.38
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	2.47	2.47
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	1	1.77	1.77
symbioic hydra M9 strain · symbioic hydra rep1	1	1	1.32	1.32
symbioic hydra M9 strain · symbioic hydra rep2	1	1	1.28	1.28
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
SRR21134051	whole body	whole body	not recorded	not recorded	SRP392977	4.14
SRR21134053	whole body	whole body	not recorded	not recorded	SRP392977	3.85
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977	2.37
SRR21134050	whole body	whole body	not recorded	not recorded	SRP392977	2.24
SRR21134064	whole body	whole body	not recorded	not recorded	SRP392977	1.63
SRR21134059	whole body	whole body	not recorded	not recorded	SRP392977	1.55
SRR21134057	whole body	whole body	not recorded	not recorded	SRP392977	1.19
SRR21134056	whole body	whole body	not recorded	not recorded	SRP392977	1.10
SRR21134055	whole body	whole body	not recorded	not recorded	SRP392977	0.55
SRR21134066	whole body	whole body	not recorded	not recorded	SRP392977	0.40
SRR21134052	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134054	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134058	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
SRR21134065	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134067	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR10058802	Whole	Whole	not recorded	not recorded	SRP220397	3.38
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397	3.22
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	2.82
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	2.78
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	2.27
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	1.85
DRR048593	aposymbioic hydra M9 strain · aposymbioic hydra rep1	not recorded	not recorded	aposymbioic hydra rep1	DRP003902	2.47
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	1.77
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	1.32
DRR048596	symbioic hydra M9 strain · symbioic hydra rep2	not recorded	not recorded	symbioic hydra rep2	DRP003902	1.28
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.