Gene detail

Detailed information of BRAKERKREP00000014682.1 in Hydra viridissima

Genomic Location: QPEY01000084.1:614241...632247
NR annotation: XP_047134373.1, mutS protein homolog 4 isoform X1 [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

BRAKERKRET00000014682

atggaaaGAATTTCATCTATCTGCACAAATAGTGACTCTTCTGTCCCTAATTCAAAGCGCCAGAGGATGAGTTCAAGTTTCAATACGACATCATCAAGTGGTTTAGGTATAGAGAGAAGTGCAAAATATTCTTTAGATTTGGAGACACCACAAGTGACTTTGGATTTTGGTTTCAGAGAGAAGTCTGCTCCTGCCTTGAAATCTAGAGCTTCAGGAGTATGtgCTCCTTTATCAATAGCTCAACACACTCCTTTTCAAGAAAGCAGCTCTCATATGCCAAGCTCATGGTACACTCCAAAGACACCTGCTTCCAGAACACCATCAGGATTTAATGTTCAAACTAGCAATGTTGTTGCTCAACACACTCCTTTTCAAGAAAGCAGCTCTCATATGCCAAGCTCATGGTACACTCCAAAGACACCTGCTTCCAGAACACCATCAGGATTTAATGTTCAAACTAGCAATGTTGTTGccatTGTTGAAGGGCGTGGTATGGCAAAAGGTGAGATAGGAATGGCTTGTATTGATCTGAAAGGTGCAGAGCTAATTATCTCACAgttttcagATGGTCCCAcctatgtaaaaatattatgcaaatTGCAAATAATCCAACCAGTtgagGTTGTTATGCCTAACACCTCTTATGAAAATGGTAAGATGACACAACTATTTCAAGTGATTAGTGAACAATTCCCATATGTTACTTTAACTACAGTGCAAAGAAAGTATTTCAATGAAAGCAAAGGTCTCCAATACATAAGGCAGCTCTGTGTACCAGAATTCAATTCAGTGGAAATGGATGTTCAATCaaaATATTATTGCTTAGCAGCAGCAGCTGCGCTCTTAAAGTATGTTGAGTTTATCCAGAATGTTGTTTTTGCACCTTCTTCATTGAAAATCAGCTACAAAGGAGGGGAAAAAACAGCATTAATTgacATGACAGCTGCTCGCCATCTAGAACTACTTCAAAATTTGAGAAATCCCAAAAGTAAACAATCATTGTATGGAGTACTGAATTATACAAAGACAGCTGGTGGAGctcGTTTGTTGAGGTCTAACATATTGCAGCCTCCTTGTGATCTTCAAACCATTCTTACAAGATTTGATTGTATTGAAGAGTTagtagaaaaagaagaactttttcttaacttaCAGGCTAtaCTTGGCAGATTTCTCGATGTTGATCACTTGATATCATCTTGTGTGCAAATTCCAAAGAAAGAAGGTATCAAGgtgtttgaaagaaaaataggagaaataatttttttgaaacacaCTATTGAGCTTGTTCAAACACTACAAAATGCATTGGCTGATGgtgaaaacaatttgtttaaagcgTACTACCAATCATTAGAAGATTCTcgttttgcaaaacttttggAGCAAATACAAACTGTCATCCATGATGAAAGTCGGTATCAAAAAGgGTTATTGGATGTTGCACGTCGCACTCACTGTGAAGTAGTTGATGACATAACAGaaatgattCGCCAAGAAGCAGCATCAACAGGTCTTATGTTAACTCCAAATTATAGCAACACCAGAGcaAGATTGGAAGAGTCATTGGAAGAAATATACTTTCTATCAAACATGGTGGTTGGAgagttgatgaaaaatattcgAGATCAAATTGGTTGCTTGTATAAATTAGCTGAATGCATCTCCACATTAGATATGCTTGTTTCTCTTGCTCATGCATGCACTCTTTCTAACTACAtaCGTCCAGAATTTACAGATACTCTTGCACTAAAGCAATCACGGCATCCAGTTCTTGATCGCATGTCATCTGTTCCCATTATACCGAATGATGTgTATGCATCagatgtttcaaattttgtgaTAATCACTGGACCTAATATGAGTGGTAAATCCACATATTTACGTCAAATAGCTTTACTGCAAATTATGGCTCAATGTGGCTCTTTTGTTCCTGCTGAGTATGCATCTTTTCGATTAGCAAATCAGATATTTGTGCGGATTGGAAGTGATGATGACATTGAGACAAATTgttctacttttaaattagAGATGAAAGAAATGAACTATATTTTGCAAAATGTAAGCGACAATTCTTTGCTTATTGTTGATGAACTTGGAAGAGGCACCAGTGTTGAGGAAGGTGTTGGCATTACTTTTAGTATATGTGAATATTTGCTATCTAAAAAGGCGTTTACGTACTTTGCAACTCATTTCCAAGCTCTCTGTGATTTGGAAAACCTCTATCCCAATGTAGAAAATTACCATTTCGAGGTGCAgCAAGCGTTTGATCAAAATCTCGACGCTGAAAACATGCAGTTTACACATGTTTTGGTGAAGGGAAGAACGACTGAAGAAAATTACGGGCTGCAATTAGCGGAGATGTCCACTTTACCAGTggaattagttaaaaaagctaaagaaatAGCAATCCAACTCAATCAAAAGAGAAAAGAAAATCAGATCTCTTCAGAGTCGTCAAAGCGTGAGAAAGCGGTTTTTCGTTTAGTTACTCGGCTTTTGCAAGCAGCAAAGAATTCTCGTTTAGACGAAGAAACACTTCGTTTATACCTAGCGGGATTGAAGAGGCAGTATATCGCAGATATTTACGAACAATAG

Transcript

BRAKERKRET00000014682

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
O15457	MutS protein homolog 4 OS=Homo sapiens OX=9606 GN=MSH4 PE=1 SV=2
Q99MT2	MutS protein homolog 4 OS=Mus musculus OX=10090 GN=Msh4 PE=2 SV=1
F4JP48	DNA mismatch repair protein MSH4 OS=Arabidopsis thaliana OX=3702 GN=MSH4 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003274 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF05192 all species →	MutS_III	MutS domain III	Domain	Interproscan
PF00488 all species →	MutS_V	MutS domain V	Domain	Interproscan
PF05188 all species →	MutS_II	MutS domain II	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036678 all species →	Homologous_superfamily	MutS, connector domain superfamily	Interproscan
IPR036187 all species →	Homologous_superfamily	DNA mismatch repair protein MutS, core domain superfamily	Interproscan
IPR007696 all species →	Domain	DNA mismatch repair protein MutS, core	Interproscan
IPR000432 all species →	Domain	DNA mismatch repair protein MutS, C-terminal	Interproscan
IPR007860 all species →	Domain	DNA mismatch repair protein MutS, connector domain	Interproscan
IPR045076 all species →	Family	DNA mismatch repair MutS family	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11361 all species →	DNA MISMATCH REPAIR PROTEIN MUTS FAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0006298 all species →	Biological Process	mismatch repair	Interproscan
GO:0030983 all species →	Molecular Function	mismatched DNA binding	Interproscan
GO:0003690 all species →	Molecular Function	double-stranded DNA binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0007131 all species →	Biological Process	reciprocal meiotic recombination	Interproscan
GO:0140664 all species →	Molecular Function	ATP-dependent DNA damage sensor activity	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
K08740	MSH4; DNA mismatch repair protein MSH4	-	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 BRAKERKREP00000014682.1 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

17TPM > 0

7Conditions

77.5Max TPM

27.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole body	18	7	19.68	77.53
Whole	6	6	45.94	74.91
aposymbioic hydra M9 strain · aposymbioic hydra rep1	1	1	37.74	37.74
aposymbioic hydra M9 strain · aposymbioic hydra rep2	1	1	42.73	42.73
symbioic hydra M9 strain · symbioic hydra rep1	1	1	43.88	43.88
symbioic hydra M9 strain · symbioic hydra rep2	1	1	50.06	50.06
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
SRR21134053	whole body	whole body	not recorded	not recorded	SRP392977	77.53
SRR21134050	whole body	whole body	not recorded	not recorded	SRP392977	73.10
SRR21134052	whole body	whole body	not recorded	not recorded	SRP392977	67.53
SRR21134064	whole body	whole body	not recorded	not recorded	SRP392977	39.54
SRR21134060	whole body	whole body	not recorded	not recorded	SRP392977	38.69
SRR21134054	whole body	whole body	not recorded	not recorded	SRP392977	36.35
SRR21134056	whole body	whole body	not recorded	not recorded	SRP392977	21.50
SRR21134051	whole body	whole body	not recorded	not recorded	SRP392977	0.00
SRR21134055	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
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
SRR21134066	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	74.91
SRR10058804	Whole	Whole	not recorded	not recorded	SRP220397	47.39
SRR10058805	Whole	Whole	not recorded	not recorded	SRP220397	41.16
SRR10058803	Whole	Whole	not recorded	not recorded	SRP220397	39.28
SRR10058806	Whole	Whole	not recorded	not recorded	SRP220397	38.47
SRR10058807	Whole	Whole	not recorded	not recorded	SRP220397	34.41
DRR048593	aposymbioic hydra M9 strain · aposymbioic hydra rep1	not recorded	not recorded	aposymbioic hydra rep1	DRP003902	37.74
DRR048594	aposymbioic hydra M9 strain · aposymbioic hydra rep2	not recorded	not recorded	aposymbioic hydra rep2	DRP003902	42.73
DRR048595	symbioic hydra M9 strain · symbioic hydra rep1	not recorded	not recorded	symbioic hydra rep1	DRP003902	43.88
DRR048596	symbioic hydra M9 strain · symbioic hydra rep2	not recorded	not recorded	symbioic hydra rep2	DRP003902	50.06
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.