Gene detail

Detailed information of XP_032228601.2 in Nematostella vectensis

Genomic Location: NC_064044.1:11253434...11256767
NR annotation: XP_032228601.2, syndecan-3 [Nematostella vectensis]
Species Nematostella vectensis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_032372710.2

GCGCATGCGCTGTCTTACCGGTGGCAGCGTCTCAAAGACTGAACGACAAACACGCGCGTAAGTCCTGTTCCTTTAAACCGACTTACTTAACGAACAACTGTATTCTCATCGCCTTTACGGTTCTTAAAAACCACTTCTGCTTACCTCCCAAAGAGTCCATCTTCACAAGGTTTGCCTTCAAGACTTGGATCAAACGAAAATCTACCAAAGCTAAGACAACATCGTTAAAGCCTTTTAGATATTTCAAAAAGCCGACTTCAAACGCTATCTTTAGACTTGCGCTGTTGTGAAAGGGTATTGGAAGTGAACTCGCGGCATGGTTCGAAACTGAAGGCAGTAATTCCGAATTGCGTCTTATTTGACAAACTATGTCAGCTCGGAGTAGactattatttgtttttttcgtgTTGCTTCTGTGCGATATTGCCACGAAAGCAGAAGACGGACTTCGTGAAGTGACAACTATTGACGACAATGGGCAAAGATGGGTTCGAATAATCGACGAAAGAGCTGAAACAACATCCTCAAGCCCTGTGAGCACTGCGGAAAGCTCACTAGGAGTTGACGACGAAGATGGAGATGGCGGGTTTAGTTCCGGCGATGGGAAAATGAATGAGAGAATGAAAAACAGCGAGTTTGACGTACAAAATGATGAACCGATCAGGCGAAACGATAGTGTTGCCACGCAGCCAACTCTCGCGTTAAATACTAGCAAAGTATCATCAACTTCAACCCCAGCTGCTAAAGAAACTGCGTCTAATAATTTTAAGACAACAGTTGGTCCCACTACGGTGGCTAAAAATGTGACTGATGCGAGTACGAACGAGCTTAATGCAACCGCCACCACAAGCTCGCTAGAAGTGTCTTCCGTCAAACCGCGTGAAAATAAAACTACAACAAAACCTTTAACAACTGTGCAGGCTCATGACACGACCCCAAGCACATCACAAAGTATTTCTACGACTTTAAGACCGCAAATTATCCCCAAAACAGAACCTGTTACTCTCAAAGTGTCAACGACTGTTTCAGTACTCAAATCGAGCACACAAAGTACTCAGGGTGTGACAACCGAAACAATAGTGATACCAGAAAAAACTACGGAAATCCCTACCACTAAACCTATTTTGTCAAGCGCAACTTCTAAGCCGTCGACAAACGAAGTAGATTGGTCGGGTAAACCAACAGAATCGTCTAACATTACGTCTGAAAATGTTACCAGTAGCAAGTTCACGGTCAAACTTACTGTACCCCCAAAATCAACACAACAAAGTGTTTTGCCGACAGATGAAAAAGTTACAGGTGACGTTCAAGGGCAGAAAAGCCCGGCACCAAAAGAAAAACGAAAAGTTTTATTCGGGTTTGTGACGCTAGAGATTCTGATAGCTCTTTTGGCGGGCGCTCTGTTCTCAGTATTGCTCGTGGCTTTCTTGGTGTATCGCTTGAAGAAGAGGAATGAAGGGAGCTATGAGTTAAGTGAGACGATTGCCTTGAGGCCTAAGGAACTGGATGAGATGGGCAAAAAGAAGGAAGTGTTCGtataatgagaacaaacaGAGACTGCATGTTGGCTTATGCTCTTTGTGCGCAAGTCTACGTAAGAGGAAAGTGGGACTACAAAACCAAGAACGCTTGAGGTATTGTTACGGCTTGGAGGTGTTATAATGATGCAAGCaaaaacaacgacaacaattTCTATGGAGAGAACGCTTTGTAAGGTATTGTTACGGCTTGGGGGGTGTTACACAATGAATGCAAGAaaaaacaacgacaacaattTCAACCGAGAGAACGCTTTATGAGGTATTCTTACGGCTTGGGGGGTGTTACACAATGGATGCAGAAACATTCACAGCAGTGGTTACAAAAGATCTATGTCAGCACAACAATGACGGAATACCAGGGTCATCGCCTTGTCGCATGGACAAATTTGTCATATCCCTTGTAGAGCACTAGTAGATACCGAAAGATGTTGAATACGAGAGTGACTAGTTTTTAAGTGATTTTGGTTATATATTGAGCATGTTAAAGTTCCAACTATTATATTGTACAGTTTTACAGAACATCGGGCTGGTCTAATCATTCTAgccctttaaaaaaatgggaTACATTCCACTTCAAAAAAACTGCGAAGGAATTTCAATGAATTATGCATTGGTTGGACGAGGCGTAAAATTTAGGACTAGCCGCGACCATCAAAGTTTGAGAATCTTATCACTAAAGATCCATTTCTTGTGGTTATACGATATGGATGTATTCATGGCGAGTGGAATATTGAGACAAAACATTATATTCTGAAGCTGTCTCTGAAAGGGtgttttcattaaaatgtAGAAAGCTCTCAAACAAACATAAGGTTATAATGGCAAGGGGATAATATTGACGCAAACATAGCAAAGCCGACCAATCATAATCAATCTCAGATGACATGGTTTTAAATCCCCAATAGGTCATTTGGAGTGCGTCGAGAGAGACACTTTTTGTTGAATGACTCTGTTGATATAGTGAGAGagaaaaaattgtttttgcaaaCAGCGTAGATTATGCTgcagaaaatattttatcacGCTTCTGTGATTATGCGTGAATTTGTTAACTGAGTAAATGACTCAGTTTAATGACAGCTGCTTTGTGAAGACAAGAATTTATGAACTTCATTgtcttttctatttttaacGTGTGCCTACAAGTATATTTCGTTGTCATTTCCGCTTTTGAACTTCCGCtgaaaaaaactaaaaggGATTTGGATCAAAATGCTGCATTTTACTAATATATCTTTTTGAACAACGACACTCGGCAACGTACATAAGGCTAAGGAATATGAAACCTAATAACAGATTATCTTTCttggatttatttttattgaattgtGGATAATTCATTTTGTTACTAAATAAACAGTCTTAGAACAATGATTTTAAATTCAGATTTTGTCAACGCAAACAGTCGATCGACATCCGCCCCAAAcattaaataacaaataaaataataaaagagtaGAGATTCAAA

Protein

UniProt (Swiss-Prot top hit)

No Swiss-Prot hit above the reporting threshold for this gene.

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0011185 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01034 all species →	Syndecan	Syndecan domain	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR027789 all species →	Domain	Syndecan/Neurexin domain	Interproscan
IPR001050 all species →	Family	Syndecan	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10915 all species →	SYNDECAN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0009986 all species →	Cellular Component	cell surface	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0016477 all species →	Biological Process	cell migration	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 XP_032228601.2.

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

Expression pattern (RNA-seq)

Transcript abundance of XP_032228601.2 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

42TPM > 0

16Conditions

20.1Max TPM

8.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole 6 week old aboral regenerate · regenerate 96hpa	3	3	12.44	16.87
whole 6 week old aboral regenerate · regenerate 144hpa	3	3	10.14	13.57
whole 6 week old aboral regenerate · regenerate 0hpa	3	3	11.80	14.17
whole 6 week old aboral regenerate · regenerate 2hpa	3	3	9.22	9.53
whole 6 week old aboral regenerate · regenerate uncut	3	3	10.04	12.04
whole 6 week old aboral regenerate · regenerate 4hpa	3	3	11.50	20.06
whole 6 week old aboral regenerate · regenerate 120hpa	3	2	7.45	11.24
whole 6 week old aboral regenerate · regenerate 36hpa	3	3	7.77	9.59
whole 6 week old aboral regenerate · regenerate 24hpa	3	3	9.57	11.17
whole 6 week old aboral regenerate · regenerate 20hpa	3	3	8.05	10.26
whole 6 week old aboral regenerate · regenerate 16hpa	3	3	9.04	10.66
whole 6 week old aboral regenerate · regenerate 72hpa	3	2	6.56	11.26
whole 6 week old aboral regenerate · regenerate 60hpa	3	3	8.86	9.75
whole 6 week old aboral regenerate · regenerate 48hpa	3	2	6.91	11.16
whole 6 week old aboral regenerate · regenerate 8hpa	3	2	6.21	11.87
whole 6 week old aboral regenerate · regenerate 12hpa	3	1	3.23	9.68

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	16.87
SRR6320837	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	10.53
SRR6320836	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	9.91
SRR6320847	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	13.57
SRR6320841	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	9.50
SRR6320838	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	7.36
SRR6320846	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	14.17
SRR6320840	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	11.34
SRR6320839	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	9.88
SRR6320848	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	9.53
SRR6320842	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	9.20
SRR6320861	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	8.93
SRR6320843	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	12.04
SRR6320844	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	10.77
SRR6320845	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	7.30
SRR6320873	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	20.06
SRR6320872	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	9.15
SRR6320849	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	5.30
SRR6320882	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	11.24
SRR6320883	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	11.11
SRR6320850	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	0.00
SRR6320851	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	9.59
SRR6320852	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	7.58
SRR6320855	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	6.15
SRR6320856	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	11.17
SRR6320854	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	9.84
SRR6320853	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	7.70
SRR6320857	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	10.26
SRR6320860	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	8.34
SRR6320859	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	5.56
SRR6320880	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	10.66
SRR6320858	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	8.37
SRR6320881	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	8.09
SRR6320862	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	11.26
SRR6320865	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	8.41
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	9.75
SRR6320866	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	9.30
SRR6320869	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	7.52
SRR6320870	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	11.16
SRR6320871	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	9.56
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	11.87
SRR6320875	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	6.76
SRR6320876	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	0.00
SRR6320877	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	9.68
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.