Gene detail

Detailed information of XP_032221817.2 in Nematostella vectensis

Genomic Location: NC_064040.1:7592457...7606469
NR annotation: XP_032221815.2, protein Smaug homolog 1 [Nematostella vectensis]
Species Nematostella vectensis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_032365926.2

TTCTCTTGTCACTGTGGAGATCTTTGCAGTTTTGAATTAATGAGGCGAAGGTTAATGTTTACATTTTCTTTGTACAAACATTAGTAGAGTAGAGCTGGTCAAATTTAACCTCACTGTATCTTTTGCTTCTCTCGTGGAAATTTGAGTTTTGGGAGCGTTTTATGGCATTGATGAGGTACGCAGTATTTCGCAGATACGAAACTGAGGTGAGCTAGTGGACAAAGACGAACTGCTTTCGACTCGACCAGTGCAAGCGAATTCAGGCCCCACACGCCGTAATTTAGCCGCAAACAGCGCTTCTCAGGTCAGCTTGTAAGAGGATATGAAGCCAGCCCACACGCATTTTCGGGACCAAGTCAGTGCGTTGGTAGGATGGTTCTCTAACTGGAACGAATGCGAACAGACCATAGCCCTGTACACTTTACTCAAAAGAATATCCACAACCCAGGCAAGATTCTTGTCTTTAATTCTCGAACATACATTTCGAGATGATCCGGTGGAAATCCAACTCCTGCAGCGTCAAGCGAATGACAAAGAGTTTCTGAGCAACCTTTGTCACGAGACCAAAGCTGTAGCAGTCCAACAATTACTAGCACACCTGCCACTTCTGGTCCCTGGTAATGATGAAGCCAGATTTGAGTATCTCCAACTCCTTCCTAAAATCCTCACTCACACAGTACAGCACTCAGTCCATCAAGATGAATGCATGCAGCTGCTTTCTCTAGCTCTTGTTCATCCAGCCTTTCCTCCTGAGGAGAGAAACTCACTCTTATGTTGGCTAAGCCACCTAGAAAAGACATTAGGCATTAAAGAAAGACAAAACTCTGGCCCTGCCCGGCTACAGACTACTGAAAGCTCAGACATGCCTGGGTCCTGTGATAATCTTGTACGGCACAATTACACCAGGGGGAGGGTGAATGGGTGGCGAAACCAGCCTTTAGTTCACCATGATTCAGGCCTTGGATCCTTTGAGACACAGCCTTCCTATGGTAACTACAATAGTGGTATGGGTTCATCTATGTCTTCTATTATGAGGAAGAGCCGGTCGGGCTCATTAACTCCTCCACCGCCCGTTGAGGAGCAGGACTCTGTCATGCTAGATGATTGCATGGGGGATTCTCTACAGGTAGAGATACGCCCTGGCCGATCACAGTCATTTCCTGTCGACCCACAGAGGCTCAATCACCAATTGTCACCTCAGTCTTCAACTGAGAGTGAACAGGACGAGTCTTCATTTCGGCACAAGCCAGGCAGTTTTAATGCAGAGGAAGCGCGTCCTGGAATGAAAGATGTTCCTATGTGGCTAAAAAGTCTGAGGCTTCACAAGTATGGGAGCCTGTTTTCTCAGCTGTCATATGAAGAAATGCTTAACCTGTCAGATGAATACCTGGAAAGCAAGGGGGTCACCAAGGGTGCCAGGAACAAGATTTTACTCAGCACGAGAAAGCTCCAGGAGCGATCGGATACTCTGCAGAAACTGGAAAagGAGGTTCTACAGAATGGCAAGCTACAGGCGGTTCTCAAAGAGCTCCAGCAGATAGTGAATACTCCAATTAAACCATTTACTCCATCACCAGGCGTGGCAACTAGTGGGTCAGTATCAAGCAGTAAACTCGCTGAGCAGAGTACTCCAAACCCTCCACCACACCCTGAGGACTTGCCGGGGTGGATAACTAGGGTCATGGGGAAAGCATGCACACAGATCCTGGTGTCTCGGGCTGATGAAGAACACTGTACATTATACCTTACTCTTTTGGATAAAACTCTTGCTAGTGAGGCTTTCACCCCAACACAAAAGCGCCGTCTTCAGTCGTGGAAACAGCAGTGTCAGAGGCTTGTCCGTCAGCAGCAATTTGCCAGAAGACCAAGTTCCCAGGAGAAGTCTAGGGGGTGGTACTACTTGTCAAGCCCGCCCACTGACCCAAATGCAAGTCTACAGCCTCCAGTGAGTCCAGGAACTGTAACCGTCAAGCCTCGGCATAGGAGCTCCCCTCGATGTGTCACTAACAAGACCCCGCCTGCTGTTCAATTAAGAAGTAGCAGCACAGAGACGCCACACCCGGGCCAGTCAAAACCAACTCTGGTGAGATCACATGCAATAGTGGGACGTACCAAGTCACTCCCTGTGAGAACAACCACCCCACAGCTTTCACTGCCAGAGCAAGATTCTACTGATGAGACGGAGGGGTTTGATAACAGTCTCGAGTCATTATGCCTGAGGATGACTGAGCAAGCACTATCAGatactGGTGATCAGCAATAATATGAGAAAGAAATGGCAAAGAAGTCTTCAGTCATTGAGTGCTACCAAGTAGTCATCATCAATTAGACACTAAATGGTCCTTAAAAGAATATCACTAACAGATGTCAAGAAGATATGGTCCATATAGCATGTATGTAAGATATTTAAAGAGTGCCCAAAGGGGGCATAGGACGGACCCAAACACAAGTTCTATAAATGCTGGATCTAGAGGAGAATGGAGAAGGTTTGCATCAGGCTCTTTCTTTCCATGGGGGTGTGCCATGGTTATTGCTACCAGCCTTTCAAGCTTTCAGAGTACTGGGCAGTGTTTTATTGATGTACATTGTCATAATGGATGTGTGGATTTGAGGCAAGGATGCCAAGTTACCTAAGCTATACTCTGTGACAGGCCTGCAAAGAAACCTCTAAAAGAGCTGAATGATGCTTGTAATGTAGAAAACAGACTTTGAGAGAAGGCTGACTGTTGAGTCTCTAAACAGAAGATATTTGTAGCTTATTTGTAAATATAGATAAACTATTCATTGTTCATGTTAGAAAGGTTGTGTTTGGGAAGGCTTTGTGCTTCAAATATGATTTGAAGTGCAACcaacacaaaaagaaatacataaaGCATATGTATTCTAGACTTTAAAAGTTAGGAATAAATTGAATATAGTTCATAATGTA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q8CBY1	Protein Smaug homolog 1 OS=Mus musculus OX=10090 GN=Samd4a PE=1 SV=2
Q9UPU9	Protein Smaug homolog 1 OS=Homo sapiens OX=9606 GN=SAMD4A PE=1 SV=3
Q95LV5	Protein Smaug homolog 1 OS=Macaca fascicularis OX=9541 GN=SAMD4A PE=2 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003202 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00536 all species →	SAM_1	SAM domain (Sterile alpha motif)	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR037634 all species →	Domain	Protein Smaug, SAM domain	Interproscan
IPR013761 all species →	Homologous_superfamily	Sterile alpha motif/pointed domain superfamily	Interproscan
IPR050897 all species →	Family	SMAUG/VTS1 RNA-binding	Interproscan
IPR001660 all species →	Domain	Sterile alpha motif domain	Interproscan
IPR037093 all species →	Homologous_superfamily	Smaug, PHAT domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12515 all species →	STERILE ALPHA MOTIF DOMAIN CONTAINING PROTEIN 4-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0017148 all species →	Biological Process	negative regulation of translation	Interproscan
GO:0030371 all species →	Molecular Function	translation repressor activity	Interproscan
GO:0043488 all species →	Biological Process	regulation of mRNA stability	Interproscan
GO:0000289 all species →	Biological Process	nuclear-transcribed mRNA poly(A) tail shortening	Interproscan
GO:0000932 all species →	Cellular Component	P-body	Interproscan
GO:0003729 all species →	Molecular Function	mRNA binding	Interproscan
GO:0005515 all species →	Molecular Function	protein 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
K27396	SMG; protein Smaug	-	Messenger RNA biogenesis	ko03019	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of XP_032221817.2 across 48 RNA-seq samples of Nematostella vectensis. 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.

48Samples

44TPM > 0

16Conditions

34.0Max TPM

19.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole 6 week old aboral regenerate · regenerate 96hpa	3	3	18.55	20.14
whole 6 week old aboral regenerate · regenerate 144hpa	3	3	14.81	18.78
whole 6 week old aboral regenerate · regenerate 0hpa	3	3	20.80	25.84
whole 6 week old aboral regenerate · regenerate 2hpa	3	3	33.36	34.01
whole 6 week old aboral regenerate · regenerate uncut	3	3	21.55	29.65
whole 6 week old aboral regenerate · regenerate 4hpa	3	2	16.07	26.37
whole 6 week old aboral regenerate · regenerate 120hpa	3	3	18.72	19.83
whole 6 week old aboral regenerate · regenerate 36hpa	3	3	21.69	26.83
whole 6 week old aboral regenerate · regenerate 24hpa	3	3	24.32	29.75
whole 6 week old aboral regenerate · regenerate 20hpa	3	3	21.03	25.48
whole 6 week old aboral regenerate · regenerate 16hpa	3	3	22.46	26.60
whole 6 week old aboral regenerate · regenerate 72hpa	3	2	12.29	20.28
whole 6 week old aboral regenerate · regenerate 60hpa	3	3	18.12	19.47
whole 6 week old aboral regenerate · regenerate 48hpa	3	2	12.37	23.95
whole 6 week old aboral regenerate · regenerate 8hpa	3	3	19.85	22.04
whole 6 week old aboral regenerate · regenerate 12hpa	3	2	16.00	28.76

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR6320863	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	20.14
SRR6320836	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	19.76
SRR6320837	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	15.76
SRR6320847	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	18.78
SRR6320841	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	13.87
SRR6320838	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	11.77
SRR6320846	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	25.84
SRR6320840	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	20.36
SRR6320839	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	16.20
SRR6320861	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	34.01
SRR6320848	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	33.19
SRR6320842	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	32.88
SRR6320843	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	29.65
SRR6320844	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	20.31
SRR6320845	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	14.69
SRR6320872	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	26.37
SRR6320849	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	21.85
SRR6320873	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	0.00
SRR6320882	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	19.83
SRR6320850	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	18.94
SRR6320883	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	17.40
SRR6320855	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	26.83
SRR6320851	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	21.85
SRR6320852	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	16.40
SRR6320854	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	29.75
SRR6320856	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	24.74
SRR6320853	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	18.48
SRR6320857	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	25.48
SRR6320860	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	20.85
SRR6320859	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	16.76
SRR6320880	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	26.60
SRR6320858	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	21.08
SRR6320881	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	19.71
SRR6320862	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	20.28
SRR6320865	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	16.60
SRR6320864	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	0.00
SRR6320867	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	19.47
SRR6320866	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	19.39
SRR6320869	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	15.49
SRR6320870	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	23.95
SRR6320871	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	13.16
SRR6320868	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	0.00
SRR6320874	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	22.04
SRR6320876	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	19.64
SRR6320875	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	17.88
SRR6320877	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	28.76
SRR6320879	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	19.23
SRR6320878	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	0.00

Source: CnidoSite RNA-seq expression matrices (NVECT_TPM, StringTie quantification over 48 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.