Gene detail

Detailed information of BRAKERKREP00000012305.1 in Hydra viridissima

Genomic Location: not available for this species
NR annotation: XP_004208576.1, alpha-actinin [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families

Sequence

CDS

BRAKERKRET00000012305

atggatgaGTTTTCTGTGTGCTTGACCAGTCCACTTTCTGTTGATATGTTACTTTTCACTGAATGGCTTGCTGGGGCAGatgATATTGAAGCAGCAAAAGTGCTTGGTTCATCCCTTCAATCAAGTATTGGGAACATTTCAACAACTTGTCTAATACAAGAAGTGAGAGAACATTATGTCCTTTTTTCTTATCTCcagcaatatttattttctccTCCATTGCTGAAGTCACCTAATTTTGCTGCACTTTCTCCAGAAACTAAAGACAAGCTTGTTTCAAGTTATTATGAGTTTGACAAGCCTGTGATACGAGAAATTCTTGGTAAGAAGATGAATGCAAAGCTTCGAAAAGATTTGGATGAAGTTAGTGAAAAAACACAAGTATCTATCAAAAGCTGTCAGAGGCAGtttgacAACATCAAAAACATCTTGAAGGTTTTCGAAGATGTTGAAGGCAACATTAAAGGTGTTCTCACAACAATGTTTCACTTCTCGGATTCACTTGTGAAAAAATACATGCCACTAATTTACGTATTTATATTTCGGTTTGAGACCTCTAAGAAAAGgCTACAGTATTTGACATATGATGATATTATCATTTGCACTGAGTTTATTATTGAGCAGTGGACATCAGATTCCACTTTATCAGGagataAGTTATTGGATTTTGATGATATTGACAGAAGTTTTCTCGAGGATCTGAGGGAACTCAGGAATTTGGTTTTAGAGAAAGACTTCATGGACCAACATAAAAGCTATTTGTTTGCCCGACTAGAAAGGAAAACAACTTTTGCccatttttcaaaaggttGTGAAGCCATTTTTcgtTTGGTCTACAGAAACTTATTTTCTCTGGGAGCCAACCTTTTTCAGACCAAAGACTTCaggaattttttcaatgactTTGTGGAAAAGgtgACTGATCCTGTTAAGCAAGCAAACTGGACTCTAAAGGAATTCGATATATTTTTGACTGAGTTATTGCATTCATGGGGAGATTTCAAAGACCAGTATACTTTCACAGCATGGTGCAATTCCCATTTAAGGAAAGTTAATGTGCAAATTGAGGAAATTTCTAGAGACTTTAGTGATGGGCTTAAACTTATGTTACTTCTTGAAGTTATTGCTGGAGAGAGACTACCAAAACCTGAAAGAGGACGGTTACGATTTCATCAAATATCAAATGTCAATAAAGCTTTAGATTTTGTTGCCAGCAAAGGTGTTAAACTGGTTTCAATTGGTGCTGAAGaaaTTGTTGACGgtaacttaaaaatgattttgggTATGATTTGGACTATCATCTTGAGATTTGCTATTCAAGATATTCTTGTTGatgAGTTTTCATCTAAAGATGGACTTTTGCTTTGGTGTCAGAGAAAAACCGCTCcatacaaaaatgtaaatgttcaaaattttcacatgAGttttaaagatgGTCTTGCATTCTGTGCACTTATTCATCGACATCGTCCTGATCTCATTGATTACAACAAGCTATCCAaggatgatCCAATGCACAACTTAAATTATGCATTTGATGTTGCTGACAAATACCTTGATATCCCACGGATGTTAGATGCTGAAGaCATGGTTAATCAGGTTAAACCTGATGAGAGAGCTGTTATGACATATGTCTCTTGCTACTATCATGCTTTCTCCAGTTCTCAACAAGCAGAAACAGCTGCAAAGCGAATTGTAAAAGTATTGAATGTAAATCAAGGTAATGAAAAAGCCATGGATGATTATGAAAATATGGCATCACAGTTACTTGATTggataaacaagaaaattccAGAACTTGAGGATCGAAGTACTGATAATACTCTTGAAGATGTTCAGAATAAACTGAATGACTTCAGAAATTATAGAGGTACTGAAAAACCACccaaagttgaagaaaaagcTGGCTTAGAAAACCTGTTTAATACCCTTCAAACTAAACTACGTTTAAGTAATCGTCCTGTGTACATGCCTTCTGAAGGAAAAATGCTGTCTgaCATAGAAAAATCATGGAGAGATTTAGAACAAGCTGAAAAAGATTTCCAAGATTGGATACTTGCAGAACTGCgcaagTTGGAGCGATTGGATCATTTAGCAATGAAGTTTAAACACAAATGTGATATCCATGAAGCTTGGTCCAATGGTCAAGATCAGTATTTGACAACTGATGATATAACTGGTGCTCCTCTTGCATCTTTGCTGGCTTCTCGCAAACGACATGAAGCATTTGAGTCTGATCTTTCTGCTCAGCAAGATCGTGTAGAGCAAATTGTGGCTATTGCTCAGGAATTAAATACACTTGGATATAGTAAAGTTGATGAAGTTAATGCACGTTGTAAAAGCATATGTGATGGATGGGATAATCTTGGAGACTTAACTGCTGAGCGCAATAACAAGTTGACAGTTGCCATTGAAATTGCAGAGCGTCTTGACAACTTATGGCTTGAATATGCAAAGAAAGCATCACCATTTAATAATTGGATGGATGGTGCAAAAGAAGACTTAATGGATATGTTTAATGTTCATTCTTTGGAAGAAATGCAAGATCTTAAAGATGCCCAGGAGAAGTTTAAAGCAAATATGCCAGCAGCACAAGAGGAGTTTGAGTCAATAATGGCTCTTGTTGATGCAATTAATTCCATGAGTAACCAAAAGAATCCATACACTAATACTAAATCTGAGGATTTAGAACAAAAGTGGATGGAAGTCCTTGAACTGATACCTAAACGAGATTCTAAGTTATCTGCTGAAACTGTTCGCCAACAGACTAATGAAAGACTTCGTGTACAGTTTGCACAAATGGCAAACCGAGTGGGTGAATGGATAAAACAAAGAACAAGTAAAATGAGAGACATTGGCATGAATGCCAGAGGTAGTCTTGAGAACCAGCTTCATGAGTTAAATGGTCTCAATGATGAAATTAATGGGTTTAAAGAACACATTTTGGAGCTTGATGCTCTAAatgctTCTGTGCAAGAGGCCTTAATTTTTGAGAATCCTCATACATCGTTGACTATGGAAATGATCCGTATTCGATTCGAACTTCTTCTCACTGGTATGACTAGAAACATCAATGAGGTTGAAAACCAGATTTTGATGAGAGATTCTATTGGTATAAGTGAAGATCAGTTGAAAGAGTTGAAGAGCTCTTTCAGCTTTTTCGacaagaacaaaaacaatcaattaGATTATAAAGAATTCAGACAATGCTTGGTCAGTCTTGGCCACAGTGTAGATGTTGAAGATAAGGGTGATGCTGAATTTGCACGTATTATGGCTATGGTTGACCCCAATCAGACAGGTTATGTAACCTTCCAGGCTTTCCTTGATTTTATGACAAGAGAAATGGCTGATACTGACAGTGCTGAGCAAGTGATGGAGTCGTTTAGAATTTTAGCCGGTgataaacCTTATATTACCGCGGATGAGTTACGACGTGAGTTGCCTCCTCAGCAAGCAGAGTATTGTATTGCTCGAATGGCTGCATATTCTGGACCTGGCGCAGTACCCGGTGCTCTTGATTATAAGTCCTTTTCTACGGCCTTATATGGTGAAAGTGATTTATAG

Transcript

BRAKERKRET00000012305

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q7PKQ5	Alpha-actinin, sarcomeric OS=Anopheles gambiae OX=7165 GN=Actn PE=3 SV=2
L7UZ85	Alpha-actinin OS=Dermatophagoides farinae OX=6954 PE=1 SV=1
P18091	Alpha-actinin, sarcomeric OS=Drosophila melanogaster OX=7227 GN=Actn PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002750 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00307 all species →	CH	Calponin homology (CH) domain	Domain	Interproscan
PF08726 all species →	EFhand_Ca_insen	Ca2+ insensitive EF hand	Domain	Interproscan
PF00435 all species →	Spectrin	Spectrin repeat	Domain	Interproscan
PF13499 all species →	EF-hand_7	EF-hand domain pair	Domain	Interproscan
PF05427 all species →	FIBP	Acidic fibroblast growth factor binding (FIBP)	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002048 all species →	Domain	EF-hand domain	Interproscan
IPR001715 all species →	Domain	Calponin homology domain	Interproscan
IPR036872 all species →	Homologous_superfamily	CH domain superfamily	Interproscan
IPR011992 all species →	Homologous_superfamily	EF-hand domain pair	Interproscan
IPR018159 all species →	Repeat	Spectrin/alpha-actinin	Interproscan
IPR014837 all species →	Domain	EF-hand, Ca insensitive	Interproscan
IPR002017 all species →	Repeat	Spectrin repeat	Interproscan
IPR001589 all species →	Conserved_site	Actinin-type actin-binding domain, conserved site	Interproscan
IPR018247 all species →	Binding_site	EF-Hand 1, calcium-binding site	Interproscan
IPR008614 all species →	Family	Acidic fibroblast growth factor intracellular-binding protein	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11915 all species →	SPECTRIN/FILAMIN RELATED CYTOSKELETAL PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005509 all species →	Molecular Function	calcium ion binding	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0030036 all species →	Biological Process	actin cytoskeleton organization	Interproscan
GO:0030054 all species →	Cellular Component	cell junction	Interproscan
GO:0030864 all species →	Cellular Component	cortical actin cytoskeleton	Interproscan
GO:0042995 all species →	Cellular Component	cell projection	Interproscan
GO:0051015 all species →	Molecular Function	actin filament 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

No KEGG orthology assignment for BRAKERKREP00000012305.1.

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

Expression pattern (RNA-seq)

Transcript abundance of BRAKERKREP00000012305.1 across 29 RNA-seq samples of Hydra viridissima. This gene has no row in the species' RNA-seq expression matrix, so every value below is shown as zero — the matrix simply does not cover this transcript. 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

0TPM > 0

7Conditions

0.0Max TPM

0.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
whole body	18	0	0.00	0.00
Whole	6	0	0.00	0.00
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	0	0.00	0.00
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
SRR21134050	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134051	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134052	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134053	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134054	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134055	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134056	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134057	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134058	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134059	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134061	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134062	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134063	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134064	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134065	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134066	whole body	whole body	not recorded	not recorded	SRP392977
SRR21134067	whole body	whole body	not recorded	not recorded	SRP392977
SRR10058802	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397
DRR048593	aposymbioic hydra M9 strain · aposymbioic hydra rep1	not recorded	not recorded	aposymbioic hydra rep1	DRP003902
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902
DRR048596	symbioic hydra M9 strain · symbioic hydra rep2	not recorded	not recorded	symbioic hydra rep2	DRP003902
ERR13389755	unannotated	not recorded	not recorded	not recorded	ERP162636

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.