Gene detail

Detailed information of XP_048588683.1 in Nematostella vectensis

Genomic Location: NC_064042.1:1877772...1892009
NR annotation: XP_048588683.1, neurocan core protein [Nematostella vectensis]
Species Nematostella vectensis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_048732726.1

ccccccccccccccccccaactctTACCACCTTCCATTAGCAGGACTGGGGCTACGCGATTGGAATAACCAAAATATCCATTTCACGACTGCAACGAGGAAGGCTGgtaccaaaacaaatacaagtGCTACCGGTATTTCCTTGATAGTCACGTGCGCTGGGAGGAAGCATCACGTGCATGCCACGTGCACGGTGGCGTCATGGGTGTGTTCAACTCTATTGACAAGCTGGATTTTGTAAGCTACCACGTGCCAACCCTGAACAACAGCATCTCTCGCATATTTGTGGGACTTCGAAAGACAGGTGGAGTGTGGACGTGGAGTTACAATAATCTCACCCCAGGAGCACAGCTATGGGAATCAGACGCACCAGCCTCGCAAGGACCTCTGGGAGCTGTTACCATAGCAACCGGTAGACTCGTTGACGTACCTGACTCTGGAGATCACAAGCTGCCCTTCGTCTGCGAGAAAAACCTACCTTAGTGTGTCGAGTGTTATCAACCGAATACCTGTGGTAGAGCCTAGTGACTAGGATGGATTTTAGTTATTATTGCTGTcaatcatttgtgtaattttcttttaaataatCCATTGATATTGTGTAGACATtagaatttaagaacatccttaagaacattttcagacTTTTTCAGAAAAAAGAGAGTGGGGAAATTTCCATCACCTGGTCGAATTTCCAGTAGATCAATCAAAATTCGTACGATTACGTATTCTATTTTTGAGGTAACTGCTCGGGACAAGAGACGGCTATCCCAAGAAACtcatgtaaatattttttttaattcggtAAGCTCTTTCGCACACTATTATAGAAGGGTATATCGGTGAAAGAAGTCTTGTTCATGTATTCATGTATTCAGCTTGCTTGTCCACTCTACTATGTGCGAGCATGAATTTGCTGGTTGCGCTCCGTCTAGCGTGTGGTAATATATATACGAGTGCATATGTTTTTACTGAGAGGTAATTGGCAAAGTCTGAAACtctaaaaatacattttaaagaATGGTAGATAGATATCTAAATAGAAAAGGTGCTTGTTGATCCGTTACAGCCGAATTCGGTGTATAGCGATGCCATAAAAGTAGACGATAGAGCGGTCGCCCTATCTTTTAGGGCATTAAATTTAACCAACtgcaataaataaaattcttACGCTTTTGatattatccattaaagggtCTCACGGATTTCACAGTGATTTTAGAGCTTAAGGTTAGAAAttgcttcgaccacacccaatgtgctatcttcTAGGGTTGAAAAGTGCCATCCCTTAAGGGGTTTTCGGCTTTTCTGTTCCACCAGTCAGACCATTCTGATTCATGCCCTGTTGAAAccgtttttaaattttaaaaacaaaatacaaaattcaGAGGCATTCCACCGTTTTAGTCGAACAATAAACTCTCTAACTTGTAACCTTTCAAGTTGGTCCCTACCGTCGTTTCAAGCATTTCCCTATCTAAAAGATATTCCTAGCACGTATAGTTTTATTATATTCAAAGAAGGAATTTTAAAGGCAAACAAGAGACAACGCAGGGGTCCAAACAATTTACAGATGCATGATTCAATCCCTCGGCATCCCAGGTAGATGTCTCGGGCGTCCATAAGGAAGTATCGTCACCAACAGAAACGATAATGCTAGTCGTGTGAACGATTTTACCGCAGCTTTCCACATAAGTAATCATATCTTCGATTCGTCATCAGCTCCCGTGTCTATTGTACCACAACCGCTTGACCTTGCGCACTTGctcaacatttaaaaaaaaaatctgcttgtttttcttttacccAAAATTTGCCCCTCCATTCAATACATACTGTAGCCCGGTAGATGGTGTTTAGGTATCAATCCAATGTGGGCATACATTTTTCGTGATTTTCAGAatttgggatccctgtggtttttAATACAAGCCTTGTAAGGGGATATCCGATGCGGTTATTTTCGGAATGTTTGCGTActccgattttttttagacttttgTTATGTTATAAAGGTGATCTAATTAATACAAAAACGTTGAAAACCCTTGCAATTAGTTCGATCTTCAACCGTAGATTGATTGgaggggcatgtgcccccagtgccccaccccctgctggTCCTGAATAGCTATCCAGTGTGACACGATTGTTGTGTCACTGTCGTTCACTCTCACAACCGTTCTGTTCTCTGATTGCTTAGTTGCGTATTTCGTTTTGACTCGACGACGCCCTTTGGAGAGAAACCACACTAAAGGATGCAACAGCGCTAAAGGATGAAAGATTTTATTGTATCAgtcttttttcttattttcctGTTCTTCTTTTCATGTTTTTCTAATTCTGAGTTTACTTACTTCAATTTCATGGACATTCCCGCTCATGCTTTGGTGGGTTATGTCGTGGAGGTGTTCAACACGAGTGACTCTCCCAGCTGCCAAGCAAAGTGTTTCGATGTGAACTCTTGTGTGTCGGTAAATTTCGGAAGAAGAAGCGCGAATGATTCTCAGTTCACTTGTGAAGTTAACAACTCTACACATTTGCTGCAACCACTTGGCCTGAGACGAAGGCCAGGATTCACTTACTTTGGTGTGGCGGATCCCTGTTTCTCAAATCCTTGTCTGAACGGAGGCACGTGTACCGCTGACCAGTCCAACTGGACGTATTGCTGTAGCTGTGGAGTGTCTTTCTCGGCAGCCCCATATTTGGATGATCACTGTGGCACAGAGTTGGGGTTCGTTCAACACGGTGTGTTCAGAAACGTTTTCAACGCAGCTGCCAGCGTCAGATATGTAATAAAATTCAACGAGGCCAATCGCTTGTGCCAAGTATTTGGTGCACGCTTGGCCACCATTGCACAAGTGGACCAGGCGTGGAAATTCGGCTTATTTGAGTGCAGgTATGGCTGGGTAGCAGAAGGGTTCGCTGCTCTTCCAATACGTCTTCCTCTCAGAGGATGCATGACAGTTATGAAACAAAGTCTTGTTCACAGAAGCTATTATTCCACAACGACAGCTAAGCTCGATGCTTACTGCTACAAAGAAACAGATAACTGCAACGAGGAAGGCTGgcaccaaaacaaatacaagtGCTACCGGTTTTTCCTTGATAGTCACGTGCGCTGGGAGGAAGCATCACGTGCATGTCACGTGCACGGTGGCGTCATGGGTGTGTTCAACTCTATTGAAAAGCTGGATTTTGTACGCTACCACGTGCCAACCCTGAACAACAGCACCTCTCGCATATTTGTGGGGCTTCGAAAGACAGGTAAAGTGTGGACGTGGAGTTACAATAATCTCACCCCAGAAGCTGAGCTATGGGAATTAGGCGCGCCACCCTCGCAAGGACCTCTGGGAGCTGTTACCATAGTAACCGGTAGACTTGTTGACGTACCTGACTCTGGAGATCACAAGCTGCCTTTCGTCTGCGAGAAAAACCTGCCGTAACAGCAGTAGTAGCTCAGTGTTACAATCCCTGGGATTCACACAAGTAAACATAGCCAGTATTATAAACATGGATGAACTAGCCAAGGTTGCACTTTGCTTTAGGCCACCCTCGCAGATTTTAGAGCTCAAATATATCGTAAAGATTTGGAATGTTCTCTTATTCTTTCTTCTTCAGCTTTTTGTTGCCTTCCCATCAACCTCTCTTGAACTTTAGACATCGGGTAATGCTTATCCTTTTAAATTCTTTTAGGGGCTCTCAGGTTAATGGTTAGTGATTTTAAGTTTTCACCAAAGCTCTCATGAGCTCAAAAATTTTCTTAATCGAGACTTTTGCCGCTATGACTCACGCTAGGCGGCGCTTCTGGACTCTTCACGCTAAGGCTGCGAGGGTGACTCACGGTTGAGGTCCTGTATTACCCATAATGTAATAACAcatcacccataaatgtaataacaagtcacccataaatgttataacacgTCAccaataaatgtaataacgcaTCACCCATAGATGTAATAACACATaaacccataaatgtaataacacttcacatataaatgtaataacacgtcaaccataaatgtaataacacgtcacccataaatgtaataacacaatAACACATGAAACAATAATGCAGTTAAATTCTTGCGTATTTATTCTTCTTTCATAGCATAGAAATCATAGAAAATCAGGGACCATTCCTCCTCACAGCGGTTAATAGACATATGTCACGCAGGGAATTAACGCAGGGTGGCGGGATTCGCTAGTACTTGGTCACGCGAGGAATTAACGCAAGGTAACGGGACTCGCTCTTTTAATAACTTTATAATTTTAGACTAATATAATTTTAGACTATTAACTTTATCATTTTAGACTTTTAACATTGAAGGCTTTTAtcattttagacttttatcaTGGAGCGTTTTTGTTTAGTTAGGGGTCTGTGACAGTTGATCCCTCCCTAATTGTAGGCGTGTCCATATTGTTTTCAAGTGATACTCGAGAATCGTAAATCGAGCGCCTATTCCCGTTCCGTACGCATTAACTACCGGTAGAAAGCTGGATCTGATTTCACGCACAGGTAGCTCTAGGTATCATCTAGGTCTAGCGAAATAACTGTGGTATAGCGAGATTCGGTATCAAGAAAGCGAGTGTAAAAATGGTTGGAATGATGTCAATCATTATGATAACACGTGAAGcttgccatgcgcactagcacAGCAAGCATGTATTGTGCTACCTCCGTAGTCATGCCATGCGCACTAACACAGCAAGCATGTAGTGTGTTACCTCCGTAGTCAATAATAACCATGTAATCATTAAGTACGTCACGGCAAGTCCAAGGGTAACTCACTGGCACTCCCACGTTGGAAGGTCACCCTTCGTACACGCATTGGCTAAGGACCTACTAAACGAAGCTTTTCGGGATGTCAGTTAAGGGTTTCTGAATGGGCATGCCGTCTTAGGAGCATATAAAAGGGATGCGGTAGATACCCTAAAACATCTTGTAAACTTCTTTTAGTCCTTCGTCGTGTAACAACGTACAGAAGTAAAACCCGGTAGCTACCCACAAA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P81282	Versican core protein OS=Bos taurus OX=9913 GN=VCAN PE=1 SV=2
P13611	Versican core protein OS=Homo sapiens OX=9606 GN=VCAN PE=1 SV=3
Q62059	Versican core protein OS=Mus musculus OX=10090 GN=Vcan PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001789 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00193 all species →	Xlink	Extracellular link domain	Domain	Interproscan
PF00059 all species →	Lectin_C	Lectin C-type domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000538 all species →	Domain	Link domain	Interproscan
IPR001304 all species →	Domain	C-type lectin-like	Interproscan
IPR016187 all species →	Homologous_superfamily	C-type lectin fold	Interproscan
IPR000742 all species →	Domain	EGF-like domain	Interproscan
IPR016186 all species →	Homologous_superfamily	C-type lectin-like/link domain superfamily	Interproscan
IPR003609 all species →	Domain	PAN/Apple domain	Interproscan
IPR043210 all species →	Family	CD44 antigen-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10225 all species →	HYALURONAN RECEPTOR	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005540 all species →	Molecular Function	hyaluronic acid binding	Interproscan
GO:0007155 all species →	Biological Process	cell adhesion	Interproscan
GO:0004888 all species →	Molecular Function	transmembrane signaling receptor activity	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	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_048588683.1.

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

Expression pattern (RNA-seq)

Transcript abundance of XP_048588683.1 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

12TPM > 0

16Conditions

0.6Max TPM

0.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole 6 week old aboral regenerate · regenerate 96hpa	3	0	0.00	0.00
whole 6 week old aboral regenerate · regenerate 144hpa	3	2	0.08	0.19
whole 6 week old aboral regenerate · regenerate 0hpa	3	1	0.00	0.01
whole 6 week old aboral regenerate · regenerate 2hpa	3	1	0.02	0.05
whole 6 week old aboral regenerate · regenerate uncut	3	3	0.42	0.62
whole 6 week old aboral regenerate · regenerate 4hpa	3	0	0.00	0.00
whole 6 week old aboral regenerate · regenerate 120hpa	3	1	0.04	0.11
whole 6 week old aboral regenerate · regenerate 36hpa	3	0	0.00	0.00
whole 6 week old aboral regenerate · regenerate 24hpa	3	1	0.03	0.08
whole 6 week old aboral regenerate · regenerate 20hpa	3	0	0.00	0.00
whole 6 week old aboral regenerate · regenerate 16hpa	3	1	0.03	0.09
whole 6 week old aboral regenerate · regenerate 72hpa	3	0	0.00	0.00
whole 6 week old aboral regenerate · regenerate 60hpa	3	0	0.00	0.00
whole 6 week old aboral regenerate · regenerate 48hpa	3	1	0.05	0.15
whole 6 week old aboral regenerate · regenerate 8hpa	3	1	0.02	0.07
whole 6 week old aboral regenerate · regenerate 12hpa	3	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
SRR6320836	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	0.00
SRR6320837	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	0.00
SRR6320863	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	0.00
SRR6320847	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	0.19
SRR6320838	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	0.06
SRR6320841	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	0.00
SRR6320846	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	0.01
SRR6320839	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	0.00
SRR6320840	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	0.00
SRR6320861	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	0.05
SRR6320842	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	0.00
SRR6320848	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	0.00
SRR6320844	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	0.62
SRR6320845	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	0.46
SRR6320843	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	0.19
SRR6320849	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	0.00
SRR6320872	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	0.00
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	0.11
SRR6320850	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	0.00
SRR6320883	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	0.00
SRR6320852	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	0.00
SRR6320855	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	0.00
SRR6320854	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	0.08
SRR6320853	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	0.00
SRR6320856	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	0.00
SRR6320857	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	0.00
SRR6320859	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	0.00
SRR6320860	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	0.00
SRR6320880	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	0.09
SRR6320858	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	0.00
SRR6320881	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	0.00
SRR6320862	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	0.00
SRR6320864	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	0.00
SRR6320865	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	0.00
SRR6320866	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	0.00
SRR6320867	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	0.00
SRR6320869	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	0.00
SRR6320870	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	0.15
SRR6320868	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	0.00
SRR6320871	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	0.07
SRR6320875	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	0.00
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	0.00
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.