Gene detail

Detailed information of XP_032236631.1 in Nematostella vectensis

Genomic Location: NC_064044.1:1048603...1055911
NR annotation: XP_032236631.1, survival of motor neuron-related-splicing factor 30 [Nematostella vectensis]
Species Nematostella vectensis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_032380740.2

GAACCTCGCATCCGCCTCGTTCTGGTGAAACAGGAAGCttttcaatatggcggatCCGAAAGAACTCCAGACAAATCTTACTCAATATCGCGCTCAACTCAGTCAGGTTGATGCTGCTCTTACAACAGATCCTGATAACGAGGAGTTGTTGAAGTTAAAACAGGATTTAGAGGAAGTTATTAATTTGACTTTGGATCTGTTGAAAGTTAATGTGAAAGTTCCCGAGGCAGAGCTACCCAACGCTAAGTGGAAGGTTGGACACAGATGCCAAGCTGTTTGGACACAGGATGGCAACTACTACCCTGCCACTATTGACCTCATATCAGATGACCTTTCAACATGCACTGTCACCTTTGATTACGGAAACACAGAAATTGTTAAGCTAGATTCATTAAAAGATATATCTGCAGCTTCCGCCGGTGACAAGAGACCCAGTGATAATCAAGAATCCAgttcaagtaaaaaaatatccagGAAAGAAAAGGATCAACTAAGAGAACAGAAACGGAAGAAAATGGCCAAGAAACAACTGAGAATGAAGGAACTAGAGGAACAAAGAGAGGGGGAAAAGAACAGATGGCTAGACTTCTTCAACAACTCCAAGGGAAGTAGTTCAAGCTCAACCAAGTCCAAACTGCCAAAGAATTTAAAAGGGGTTACAAAGAAAAGCATTTTCGCGTCACCGGAAACACTCAACGGAAGGGTGGGTGTTGGAACGTGCGGGATTGGTGACAAGCCGATGACATCGTTCAAGCAAGACAAAGTGGTCTACAAGAAATAGCATGAGCTAagcatgggggggggggagagggggaagggagacTTGTATAGCTATGTGGAGAGTTGTATAGCTATGGGGAGACTTGTATAGCTATGAAGAGAGTTGTATAGCTATGGAGAGAGTTGTATAGCTATGGAGAGAGTTGTATAGCTATGGGGAGACTTGTATAGCTATGGGGAGACTTGTATAGCTATGGGGAGACTTGTATAGCTATGGGGAGACTTGTATAGCTATAGGGAAACTTGTATAGCTATGGAGAGAGTTGTATAGCTATGGAGAGAGTTGTATAGCTATGAAGAGAGTTGTATAGCTATGGTTAGAGTTGTATAGCTATGGAGATAGTTGTATAGCTATGGGGAGAGTTGTATAGCTATGGAGAGAGTTGTATAGCTATGGAGAGAGTTGTATAGCTATGGAGAGAGTTGTATAGCTATGGAGAGAGTTGTATAGCTATGGAGAGAGTTGTATAGCTATGAAGAGAGTTGTATAGCTATGGTTAGAGTTGTATAGCTATGGAGAGAGTTGTATAGCTATGGGGAGACTTGTATAGCTATGGAGAGAGTTGTATAGCTATGGAGAGAGTTGTATAGCTATGGAGAGACTTGTATAGCTATGACTAACTAGATATGTACATATATGCAGCTGTATGCAGATGCATGTTTCTGCCCAAAGAGGGATATAGCTTGGGCAGATGACGGGATTTCTAAAACAGGGCATATACATAGAGCATGCCCTTAGAATACACTAATTTTATCCCTTAAACCACCTTACTAGAGTTATCAAACTCAAGAGAAAAGCAGAGCATAGGAGTATGTTTTGGATCCCACTTGGACTTTTGGGTATACAGACGAAGCAGTCATAAAACAGCAGGGGGCCTCTAAAACCAATATCATATGCATACCAGTTAGTTTCCCTGGCGTTTACAATATAACAGTGCAAAAAACTATCGAATTTTTCATGATTGTACTGGTATTTTTGTAATGTCTGTTTGGAACTGAAGCTCAAGGGCCACTCATGTTCCATGCCTGAGGAATCTGAAAATGCATAATAGACTCACACAGACTACTCCACCATACACTACTACACTACTTCCATACACCACCAGTTAAACACACGAAATGATGTTGACAAATGCAATAACATCCTAACTGTTTTACTATGTCGCTTTTAAATGTCTTCAACGGAAGGGGTTGTATTTGGCTCTTCATATCCTCCTCCTTACACATTATTTCACTGGTCCGTTCTCGGGATAATGGGCCTGTGGTTTTGAATGCTTTTGCTCGCGTAAGTTAATTTGCAATTATCTTGTTACTTTTTGCTCGTTTTACATAATGTTTGAAGCTtatcttattttaaaaagtgcTCGAAATGggagagcccccccccccccccccccacacacacacacacacactcttTGGAATCCCATAAAGAAATCGGCCCCCTATATAAGTAGCGTCAGTCTAAAATGTCATgctttttgtaaataaagtttTAGCTGTC

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q7ZV80	Survival of motor neuron-related-splicing factor 30 OS=Danio rerio OX=7955 GN=smndc1 PE=2 SV=1
Q3T045	Survival of motor neuron-related-splicing factor 30 OS=Bos taurus OX=9913 GN=SMNDC1 PE=2 SV=1
O75940	Survival of motor neuron-related-splicing factor 30 OS=Homo sapiens OX=9606 GN=SMNDC1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0008255 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF06003 all species →	SMN_Tudor	Survival motor neuron protein (SMN), Tudor domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002999 all species →	Domain	Tudor domain	Interproscan
IPR010304 all species →	Domain	Survival motor neuron, Tudor domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13681 all species →	SURVIVAL OF MOTOR NEURON-RELATED-SPLICING FACTOR 30-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0006397 all species →	Biological Process	mRNA processing	Interproscan
GO:0000381 all species →	Biological Process	regulation of alternative mRNA splicing, via spliceosome	Interproscan
GO:0071011 all species →	Cellular Component	precatalytic spliceosome	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
K12839	SMNDC1, SPF30; survival of motor neuron-related-splicing factor 30	-	Spliceosome	ko03041	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_032236631.1 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

42TPM > 0

16Conditions

27.3Max TPM

16.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole 6 week old aboral regenerate · regenerate 96hpa	3	3	17.15	19.32
whole 6 week old aboral regenerate · regenerate 144hpa	3	3	14.37	18.38
whole 6 week old aboral regenerate · regenerate 0hpa	3	3	13.46	14.13
whole 6 week old aboral regenerate · regenerate 2hpa	3	3	19.92	25.51
whole 6 week old aboral regenerate · regenerate uncut	3	3	13.87	14.75
whole 6 week old aboral regenerate · regenerate 4hpa	3	2	14.22	22.12
whole 6 week old aboral regenerate · regenerate 120hpa	3	2	12.67	20.90
whole 6 week old aboral regenerate · regenerate 36hpa	3	3	21.14	27.30
whole 6 week old aboral regenerate · regenerate 24hpa	3	2	15.54	24.70
whole 6 week old aboral regenerate · regenerate 20hpa	3	3	21.42	24.89
whole 6 week old aboral regenerate · regenerate 16hpa	3	3	16.49	21.45
whole 6 week old aboral regenerate · regenerate 72hpa	3	3	21.89	26.56
whole 6 week old aboral regenerate · regenerate 60hpa	3	3	17.94	19.82
whole 6 week old aboral regenerate · regenerate 48hpa	3	2	13.90	22.46
whole 6 week old aboral regenerate · regenerate 8hpa	3	3	18.10	18.66
whole 6 week old aboral regenerate · regenerate 12hpa	3	1	6.07	18.22

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	19.32
SRR6320836	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	17.53
SRR6320837	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	14.59
SRR6320847	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	18.38
SRR6320838	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	12.76
SRR6320841	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	11.97
SRR6320846	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	14.13
SRR6320839	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	13.58
SRR6320840	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	12.68
SRR6320861	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	25.51
SRR6320842	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	18.79
SRR6320848	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	15.47
SRR6320843	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	14.75
SRR6320844	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	13.95
SRR6320845	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	12.90
SRR6320849	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	22.12
SRR6320872	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	20.54
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	20.90
SRR6320883	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	17.12
SRR6320850	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	0.00
SRR6320855	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	27.30
SRR6320851	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	18.80
SRR6320852	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	17.34
SRR6320854	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	24.70
SRR6320853	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	21.92
SRR6320856	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	0.00
SRR6320859	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	24.89
SRR6320857	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	20.24
SRR6320860	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	19.13
SRR6320880	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	21.45
SRR6320881	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	14.56
SRR6320858	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	13.47
SRR6320864	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	26.56
SRR6320862	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	19.80
SRR6320865	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	19.31
SRR6320866	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	19.82
SRR6320867	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	18.20
SRR6320869	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	15.82
SRR6320870	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	22.46
SRR6320871	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	19.23
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	18.66
SRR6320875	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	18.00
SRR6320876	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	17.65
SRR6320877	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	18.22
SRR6320878	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	0.00
SRR6320879	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.