Gene detail

Detailed information of XP_048590645.1 in Nematostella vectensis

Genomic Location: NC_064044.1:12549685...12565178
NR annotation: XP_048590645.1, NPC intracellular cholesterol transporter 1 isoform X1 [Nematostella vectensis]
Species Nematostella vectensis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

LOC5514760

ATGCAATTCGCAGCGTTTGTTTTAGTAGTGGTTTCTCTGTGCACGTCAACTACCGAGGCGGAAGAATATGCACCGATCCACAAAGAAGGGTACTGTGTTTGGTACGGCCAGTGCACGGAGCCAGGCCAAACGCCGGCGTTGAATTGCCTTTATAACGAACCGGCAAAAGAATTGAACGACACCAAAGCAATGAATATTTTGAAAAACCTCTGTCCAAAGATAGCCCAAGGTGGGAAGACTTGTTGTGACCTGAGGCAATTGGAAGCATTAGACTCAAATTTGAACACGCTGCGCCAGTTTACAAGCCGCTGTCCTGCTTGTTGGCAAAACATGCTTGATATGTACTGCGAGTCAACTTGTAGCCCGGACCAATCACTGTTTATGGACCCAACAAGCGTTGTAGGTTTTCCCCCGTACACCCCCTACATGATTAACACGATCAACTACTATATTGCCCCTGAATACAAAGATCAGCTTTTCAAATCCTGTAAGGATGTTATTTTTCCTGGGAACAATGAGAAAATCCTGAATTTGCTGTGTGGTCAAAGTGCAGAGACTTGCAGCCCACAAAAGTTGTTGGAGTATATGGGGAGTACATCTAACGGACAAGCACCCTTTGACATTCATTACCCTGAAATTATTCGCCCTAACATGACGTGGATGAACCAAACTGCTTATAAATGTAGTGAAAGCTTCATTAATCCACTCACGAACCGCACATCAGCGAAGTGTAGTTGTCAAGATTGCCATGGGTCTTGTCCAGTTCTTCCTCCAGAACCTCCCACCCCAAAACAGAAAACCATCATTGGCTTGAGCATCCTCAGTTTTGTCTTACTGGTGGTCTTTATTGGGTTTTTCATTCTCTTCATGGGCATCTCATGCTACAAGATCTTAAGCAAGCCGGCTTACATGCGTTTACCAGACAATGTCGTTGCAAGGGGAGTAGTCTACACTGAGGAACGCCCTCCATCTAATGTCATCAATGTTGAAATCGCACGAAAGCCTGGTTGCTTTGAGGTTATGGGCGTAGCTATGGAACAAAAGCTCCGCAAGATCTTCTCTTTGTGGGGACTATGGTGCAGTAATCATCCATATACTGTTATAGTTGGCTGTATTGTTTTTGTTGGCATACTTGCTGGGGGAGTCGGTTACTATTCAATCATCAAAGACCCAGTCAAGTTGTGGTCTGCTCCCCAGAGCCGTGCAAGACAAGAAAAGGACCTTTTTGATAGCAAGTTCTCACCGTTTTATCGTACAGAACAACTGATCATCACAGTTAACCAAAATTATCCCCAGAATCACACAGGCTACAAGCAGTATCCTGATGATAAATTCATCCCTTTTGGACCTATCTTCCACTTGGACTTACTGAATCAGGCATTAGATCTCCAGAACTATCTCACTGATATGGTAGTGCCACACACAGAGAATGGCAAAACCACCAACATCACACTTGAGGATGTATGCTTTAAGCCGCTGGCACCCCTGAACACCAAGTGCACCATACAAAGTGTATTTCAGTATTTTCAGAACAGCAAAGAGTTGCTGAACAAGTGTAGGACAAGTTTGGGATATGACTGTTACAAACCTCACCCAGCTGACTACTTCCATGACGATTTTCACGATCACATTCTCTACTGCACCAGTGCTCCAACATCTCTTGAAGATTTCAAGTGGGGTGGAGGCCCATGCCTTGGTGAAAACGGTGTTCCAGTCAACCCAAACATCGCCCTAGGAGGCTTTGAAGGGACTGACTACAACAACGCCTCTGCCCTCATCATCACGTTCGTCGTGGAAAACCACAGGGATGAGAAGAAGAATGCCAAGGCAGAGTCATGGGAGAAGGCGTTTATTGACCACATGAAGAGCTATGTCGAACATCCTGAGAACAGTAACTTGACCATCAGTTTCTCGTCAGAGAGGTCGATTCAGGACGAGTTAGACCGTGAGAGTGAGACTGACATTGCCACCATCTTGGTCAGCTATACCATCATGTTTGTTTACATTACCATCGCTCTTGGTCAGATCAACTCCTGTGAGAGAATCATGATTGACTCCAAGTTCACCCTTGGCTTCTGTGGTATCATAATCGTCCTGTGCTCTGTCATCTGCTCCATCGGCTTCTGGAGTTATGTGGGCGTGCCTGCCACCTTAATCATCATTGAGGTTATCCCGTTCCTCGTACTAGCTGTCGGGGTGGATAACTTCTTCATCATGGTCCAGGCTTACCAGAGGATCAATCGTTACAGCAATGAGCCTGTCTCAAAAAAGATCAGTTGTGCCCTTGGTGAAGTTGCACCCAGTATGCTACTTTCATCACTCTCAGAATCTGTTGCTTTTGGATTTGGTGCGATGTCCGACATGCCTGCAGTTAAGGTTTTCTCTCTCTATGCCTCCTTCGCTGTCGCCGTTGACTTCATCCTCCAGATCACATGGTTTGTGGCTCTTATGTCACTTGACGCCAAGCGACAGGAAACCAATCGCTGGGACATCATGTGCTGTGTCAAGCAGAAGAAGACAGAGCATCGTGAGCAAGATGGCTTTATCTATCAGATCATGAAGCACTTCTACGCTCCAGCTCTGCTTTCAGATTTTGTCAGGCCATGCGTGATTGTTCTGTTTACTGGAATGTTATTCACAAGTATCGCCTTGACTCCACATATATCTGTTGGTTTGGATCAAGACATTGCACTTCCTAAGGATTCCTTCCTACTGGACTGGTTCAAGGACATGCGGCAATATCTACATGTTGGCCCTCCTGTGTACTTTGTTCTAGATGGCAAATACGACTTTGAGCACTCAAAGACCCAGAATCGAATCTGCGGCTCGGCAGGGTGTGATCCAGACTCACTTATCCAACAAGTCTTCACTGCTTCTCTCAGATCCAACAGGTCCAAGATTGCAATGCCAGCATCATCTTGGCTAGATGATTACTTCAATTGGATTGACCCAAGCACTACATGTTGTAGGATACTGTACGAGAACACCACATCTGGAGTTGTGCCCGCAAAGGGGCCAAATGGGGGCCTTGTCTTTTGTAATGCAACAGTAAAAAATGATCTTTGCATGCCATGCATGAACAAGTCACAGCAAGGGGAGAGACCAACACCAAGCGAGTTTGACATGTATTTGCCATTCTACCTCAAAGACAACCCTGAGTTGGTCTGCGCCAAAGGAGGACATGCCGCGTATGGCAAAGCATTACAGCTGAACAGTAACACATCGAAGTATCTAGTTAATTCATCGTACTTCATGTCCTATCATACCATCCTGAAAACCTCCGACGACTTCATAAGCGCTCTCAAAAATGCAAGAGAAATTGCTGACAACATGACAACAGCATTAGGTGACCCAGATATCAAGGTTTTCCCTTACTGCGTTTTCTATGTCTTCTATGAGCAATATCTAACAGCTGCCACCAATGCTTGGAAGAATCTTCTCTACTGCATAGCCGCTGTTTTCGTGGTGACATTCCTGTTGATGGGGTTCAACCTCAGCATTGCTCTGATTGTCACCTTTACCGTCGCCATGATCATAACTAATCTCCTAGGGCTGATGTATCTGTGGTCCATTAGTCTGAATGCCATCTCTATCGTCAATCTTGTGATGGCTGTAGGCATCTCTGTGGAGTTCTGCTCCCACATCGCCAGAGCGTTTGCCGTCAACACGCGAAACACCAAGCGTGAACGAGCTGAGGAGGCATTGATAGAAATGGGCAGTTCGGTTCTGAGCGGTATCACGTTAACAAAGTTTGGAGGAATCATCGTCTTAGCTTTCGCCAAATCACGGATATTTGAGGTTTTCTACTTCCGTATGTACCTCGGTATCGTGCTGTTTGGAGCTCTTCATGGACTCGTCTTCCTACCAGTCTTCCTCAGCTACATCGGTCCCAGGTCCACGCGGCAGAACAAGAGCGAGGAGGACTCGCTTCGAAACAGCTTCCTGAACGGCGAGTCGAAGCCGCTACTGAATGGATCACAACCCACATCTATACAGTGA

Transcript

rna-XM_048734688.1

ACCCTTCAACAACACCCCTCAGATTTCTTTACTGGATTGTCTCTCAAACGTTGAACTTTAGTTTGCGTTTCAACCGGATTTGTCGCAGGAATCAGCATTAGATCTTTCTAGCAGCGTTTAGGAGAGGACGTGGAACTAGAAAagtattgatttttttatagaatttgacgaaaaaaatgcaattcGCAGCGTTTGTTTTAGTAGTGGTTTCTCTGTGCACGTCAACTACCGAGGCGGAAGAATATGCACCGATCCACAAAGAAGGGTACTGTGTTTGGTACGGCCAGTGCACGGAGCCAGGCCAAACGCCGGCGTTGAATTGCCTTTATAACGAACCGGCAAAAGAATTGAACGACACCAAAGCAatgaatattttgaaaaacctCTGTCCAAAGATAGCCCAAGGTGGGAAGACTTGTTGTGACCTGAGGCAATTGGAAGCATTAGACTCAAATTTGAACACGCTGCGCCAGTTTACAAGCCGCTGTCCTGCTTGTTGGCAAAACATGCTTGATATGTACTGCGAGTCAACTTGTAGCCCGGACCAATCACTGTTTATGGACCCAACAAGCGTTGTAGGTTTTCCCCCGTACAccccctacatgattaacACGATCAACTACTATATTGCCCCTGAATACAAAGATCAGCTTTTCAAATCCTGTAAGGATGTTATTTTTCCTGGGAACAATGAGAAAATCCTGAATTTGCTGTGTGGTCAAAGTGCAGAGACTTGCAGCCCACAAAAGTTGTTGGAGTATATGGGGAGTACATCTAACGGACAAGCACCCTTTGACATTCATTACCCTGAAATTATTCGCCCTAACATGACGTGGATGAACCAAACTGCTTATAAATGTAGTGAAAGCTTCATTAATCCACTCACGAACCGCACATCAGCGAAGTGTAGTTGTCAAGATTGCCATGGGTCTTGTCCAGTTCTTCCTCCAGAACCTCCCACCCCAAAACAGAAAACCATCATTGGCTTGAGCATCCTCAGTTTTGTCTTACTGGTGGTCTTTATTGGGTTTTTCATTCTCTTCATGGGCATCTCATGCTACAAGATCTTAAGCAAGCCGGCTTACATGCGTTTACCAGACAATGTCGTTGCAAGGGGAGTAGTCTACACTGAGGAACGCCCTCCATCTAATGTCATCAATGTTGAAATCGCACGAAAGCCTGGTTGCTTTGAGGTTATGGGCGTAGCTATGGAACAAAAGCTCCGCAAGATCTTCTCTTTGTGGGGACTATGGTGCAGTAATCATCCATATACTGTTATAGTTGGCTGTATTGTTTTTGTTGGCATACTTGCTGGGGGAGTCGGTTACTATTCAATCATCAAAGACCCAGTCAAGTTGTGGTCTGCTCCCCAGAGCCGTGCAAGACAAGAAAAGGACCTTTTTGATAGCAAGTTCTCACCGTTTTATCGTACAGAACAACTGATCATCACAGTTAACCAAAATTATCCCCAGAATCACACAGGCTACAAGCAGTATCCTGATGATAAATTCATCCCTTTTGGACCTATCTTCCACTTGGACTTACTGAATCAGGCATTAGATCTCCAGAACTATCTCACTGATATGGTAGTGCCACACACAGAGAATGGCAAAACCACCAACATCACACTTGAGGATGTATGCTTTAAGCCGCTGGCACCCCTGAACACCAAGTGCACCATACAAAGTGTATTTCAGTATTTTCAGAACAGCAAAGAGTTGCTGAACAAGTGTAGGACAAGTTTGGGATATGACTGTTACAAACCTCACCCAGCTGACTACTTCCATGACGATTTTCACGATCACATTCTCTACTGCACCAGTGCTCCAACATCTCTTGAAGATTTCAAGTGGGGTGGAGGCCCATGCCTTGGTGAAAACGGTGTTCCAGTCAACCCAAACATCGCCCTAGGAGGCTTTGAAGGGACTGACTACAACAACGCCTCTGCCCTCATCATCACGTTCGTCGTGGAAAACCACAGGGATGAGAAGAAGAATGCCAAGGCAGAGTCATGGGAGAAGGCGTTTATTGACCACATGAAGAGCTATGTCGAACATCCTGAGAACAGTAACTTGACCATCAGTTTCTCGTCAGAGAGGTCGATTCAGGACGAGTTAGACCGTGAGAGTGAGACTGACATTGCCACCATCTTGGTCAGCTATACCATCATGTTTGTTTACATTACCATCGCTCTTGGTCAGATCAACTCCTGTGAGAGAATCATGATTGACTCCAAGTTCACCCTTGGCTTCTGTGGTATCATAATCGTCCTGTGCTCTGTCATCTGCTCCATCGGCTTCTGGAGTTATGTGGGCGTGCCTGCCACCTTAATCATCATTGAGGTTATCCCGTTCCTCGTACTAGCTGTCGGGGTGGATAACTTCTTCATCATGGTCCAGGCTTACCAGAGGATCAATCGTTACAGCAATGAGCCTGTCTCAAAAAAGATCAGTTGTGCCCTTGGTGAAGTTGCACCCAGTATGCTACTTTCATCACTCTCAGAATCTGTTGCTTTTGGATTTGGTGCGATGTCCGACATGCCTGCAGTTAAGGTTTTCTCTCTCTATGCCTCCTTCGCTGTCGCCGTTGACTTCATCCTCCAGATCACATGGTTTGTGGCTCTTATGTCACTTGACGCCAAGCGACAGGAAACCAATCGCTGGGACATCATGTGCTGTGTCAAGCAGAAGAAGACAGAGCATCGTGAGCAAGATGGCTTTATCTATCAGATCATGAAGCACTTCTACGCTCCAGCTCTGCTTTCAGATTTTGTCAGGCCATGCGTGATTGTTCTGTTTACTGGAATGTTATTCACAAGTATCGCCTTGACTCCACATATATCTGTTGGTTTGGATCAAGACATTGCACTTCCTAAGGATTCCTTCCTACTGGACTGGTTCAAGGACATGCGGCAATATCTACATGTTGGCCCTCCTGTGTACTTTGTTCTAGATGGCAAATACGACTTTGAGCACTCAAAGACCCAGAATCGAATCTGCGGCTCGGCAGGGTGTGATCCAGACTCACTTATCCAACAAGTCTTCACTGCTTCTCTCAGATCCAACAGGTCCAAGATTGCAATGCCAGCATCATCTTGGCTAGATGATTACTTCAATTGGATTGACCCAAGCACTACATGTTGTAGGATACTGTACGAGAACACCACATCTGGAGTTGTGCCCGCAAAGGGGCCAAATGGGGGCCTTGTCTTTTGTAATGCAACAGTAAAAAATGATCTTTGCATGCCATGCATGAACAAGTCACAGCAAGGGGAGAGACCAACACCAAGCGAGTTTGACATGTATTTGCCATTCTACCTCAAAGACAACCCTGAGTTGGTCTGCGCCAAAGGaGGACATGCCGCGTATGGCAAAGCATTACAGCTGAACAGTAACACATCGAAGTATCTAGTTAATTCATCGTACTTCATGTCCTATCATACCATCCTGAAAACCTCCGACGACTTCATAAGCGCTCTCAAAAATGCAAGAGAAATTGCTGACAACATGACAACAGCATTAGGTGACCCAGATATCAAGGTTTTCCCTTACTGCGTTTTCTATGTCTTCTATGAGCAATATCTAACAGCTGCCACCAATGCTTGGAAGAATCTTCTCTACTGCATAGCCGCTGTTTTCGTGGTGACATTCCTGTTGATGGGGTTCAACCTCAGCATTGCTCTGATTGTCACCTTTACCGTCGCCATGATCATAACTAATCTCCTAGGGCTGATGTATCTGTGGTCCATTAGTCTGAATGCCATCTCTATCGTCAATCTTGTGATGGCTGTAGGCATCTCTGTGGAGTTCTGCTCCCACATCGCCAGAGCGTTTGCCGTCAACACGCGAAACACCAAGCGTGAACGAGCTGAGGAGGCATTGATAGAAATGGGCAGTTCGGTTCTGAGCGGTATCACGTTAACAAAGTTTGGAGGAATCATCGTCTTAGCTTTCGCCAAATCACGGATATTTGAGGTTTTCTACTTCCGTATGTACCTCGGTATCGTGCTGTTTGGAGCTCTTCATGGACTCGTCTTCCTACCAGTCTTCCTCAGCTACATCGGTCCCAGGTCCACGCGGCAGAACAAGAGCGAGGAGGACTCGCTTCGAAACAGCTTCCTGAACGGCGAGTCGAAGCCGCTACTGAATGGATCACAACCCACATCTATACAGTGAttatcgttgattgacaataATGTTACCATAATTACTGCGATGTGATTGGAAGGAGGGCGGCAACGTGTAACAATTGCGGTGAAATCATTGTCACGCATACGTTGCCATCGCAACTACATATTGCTTGGCAGAGACGAGTCACGTGGTACACACGGACGAAGAAAACGCTTTCCAAGatgcctttgttattaaaggtCCAAGTCGTGTCGTTCTTTCTGAGAAAGCTTCCTGCCGCCGCGACGACATACTGAACCAGTTATGAGAATGAAAAACAGATAAAGATATTTGGTATTATGACAATTAtatgaaaattttaaaatcagGGGTATATAGTGGTAATTGTGATGGTTAACTTTAAGCAGGagtatattttgttattttattttatttttacgttTTGTTCACTTCTAGGTCTAGACGTAATGTTGGTTTCTCCTAATTTGTTTGCCTCCCCTCTCATATTATTCTAACGAGCTCTCTCCCCCTGCCAAAGAGTGCGTGACACATGACGTGACACATACGTCACTCACTATACTACCTAGCCATACCTGCACGCGGATTTTGTTAATAAACACGTCATTTATA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
O15118	NPC intracellular cholesterol transporter 1 OS=Homo sapiens OX=9606 GN=NPC1 PE=1 SV=2
P56941	NPC intracellular cholesterol transporter 1 OS=Sus scrofa OX=9823 GN=NPC1 PE=2 SV=1
O35604	NPC intracellular cholesterol transporter 1 OS=Mus musculus OX=10090 GN=Npc1 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001584 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF16414 all species →	NPC1_N	Niemann-Pick C1 N terminus	Domain	Interproscan
PF12349 all species →	Sterol-sensing	Sterol-sensing domain of SREBP cleavage-activation	Family	Interproscan
PF02460 all species →	Patched	Patched family	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR032190 all species →	Domain	Niemann-Pick C1, N-terminal	Interproscan
IPR000731 all species →	Domain	Sterol-sensing domain	Interproscan
IPR003392 all species →	Family	Protein patched/dispatched	Interproscan
IPR004765 all species →	Family	NPC1-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45727 all species →	NPC INTRACELLULAR CHOLESTEROL TRANSPORTER 1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0015918 all species →	Biological Process	sterol transport	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0032934 all species →	Molecular Function	sterol binding	Interproscan
GO:0005319 all species →	Molecular Function	lipid transporter 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
K12385	NPC1; Niemann-Pick C1 protein	-	Transporters	ko02000	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_048590645.1 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

48TPM > 0

16Conditions

934.5Max TPM

672.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole 6 week old aboral regenerate · regenerate 96hpa	3	3	585.26	712.02
whole 6 week old aboral regenerate · regenerate 144hpa	3	3	465.62	618.87
whole 6 week old aboral regenerate · regenerate 0hpa	3	3	820.57	846.38
whole 6 week old aboral regenerate · regenerate 2hpa	3	3	800.22	863.64
whole 6 week old aboral regenerate · regenerate uncut	3	3	630.47	653.30
whole 6 week old aboral regenerate · regenerate 4hpa	3	3	765.16	865.44
whole 6 week old aboral regenerate · regenerate 120hpa	3	3	592.34	628.00
whole 6 week old aboral regenerate · regenerate 36hpa	3	3	617.64	699.83
whole 6 week old aboral regenerate · regenerate 24hpa	3	3	640.48	717.19
whole 6 week old aboral regenerate · regenerate 20hpa	3	3	722.69	824.51
whole 6 week old aboral regenerate · regenerate 16hpa	3	3	748.80	896.56
whole 6 week old aboral regenerate · regenerate 72hpa	3	3	608.90	695.30
whole 6 week old aboral regenerate · regenerate 60hpa	3	3	547.39	574.62
whole 6 week old aboral regenerate · regenerate 48hpa	3	3	598.10	649.80
whole 6 week old aboral regenerate · regenerate 8hpa	3	3	827.04	902.26
whole 6 week old aboral regenerate · regenerate 12hpa	3	3	786.89	934.52

Per sample · hover a bar for the full sample record

Show the sample table (48 samples)

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	712.02
SRR6320836	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	579.38
SRR6320837	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	464.36
SRR6320847	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	618.87
SRR6320841	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	426.25
SRR6320838	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	351.75
SRR6320846	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	846.38
SRR6320839	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	827.72
SRR6320840	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	787.61
SRR6320842	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	863.64
SRR6320861	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	782.40
SRR6320848	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	754.62
SRR6320844	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	653.30
SRR6320843	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	646.42
SRR6320845	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	591.69
SRR6320849	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	865.44
SRR6320872	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	772.68
SRR6320873	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	657.38
SRR6320882	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	628.00
SRR6320850	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	614.73
SRR6320883	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	534.30
SRR6320855	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	699.83
SRR6320851	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	644.59
SRR6320852	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	508.48
SRR6320854	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	717.19
SRR6320853	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	653.76
SRR6320856	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	550.51
SRR6320860	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	824.51
SRR6320859	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	698.59
SRR6320857	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	644.96
SRR6320881	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	896.56
SRR6320880	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	711.99
SRR6320858	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	637.84
SRR6320864	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	695.30
SRR6320862	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	613.07
SRR6320865	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	518.34
SRR6320869	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	574.62
SRR6320866	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	569.22
SRR6320867	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	498.32
SRR6320868	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	649.80
SRR6320870	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	587.96
SRR6320871	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	556.54
SRR6320875	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	902.26
SRR6320876	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	797.78
SRR6320874	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	781.06
SRR6320878	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	934.52
SRR6320877	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	741.80
SRR6320879	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	684.35

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.

Co-expression network

Genes whose expression across the transcriptome samples of Nematostella vectensis tracks this one. Counts are over the whole network; the network view itself draws at most 100 partners per query gene (CNIDO_NET_TOP_K), so a hub gene can show fewer edges than the number below.

Direction	Partners	Most correlated partner	PCC
Positively correlated	39	XP_001622423.1	0.894971731213903
Negatively correlated	10	XP_048584933.1	-0.662154103283334

Open this gene in Network Analysis → The network opens with the gene already entered and both directions selected. There you can add up to 9 more genes, switch between the positive and negative network, and export the edge list.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Nematostella vectensis, and in which cell types it is a marker. Expression is stored per cell, so the violin plot and the cell-type means are computed in the viewer — open a dataset to see them.

Dataset	Tissue / stage	Cells	Cell types	This gene	Marker of
NVECT_2month	2 month animal · Adult tissues/organs	1,614	23	not in this dataset	–
NVECT_bodywall	body wall with mesenteries · 6-8 weeks adults	11,742	13	in viewer open ↗	Gastrodermis (2.994, 0.943%)
NVECT_embryo	embryos · 8, 10 and 12 h after fertilisation (deposit labels 8h/10h/12h)	9,711	17	not in this dataset	–
NVECT_gastrula	Blastula-gastrula intermediate · Developmental stages	49,166	27	not in this dataset	–
NVECT_gastruloid	dissociated and reaggregated embryos · 4-48 hpa	36,550	8	not in this dataset	–
NVECT_neoplasm	neoplasm · Adult tissues/organs	2,532	16	not in this dataset	–
NVECT_nervous	Gastrula Cells · nervous system	16,590	27	unmapped	–
NVECT_notch48h	embryos treated 24-48 hpf (DMSO vs LY411575) · 48 hpf	19,044	7	not in this dataset	–
NVECT_tentacle	tentacle · Adult tissues/organs	7,977	19	not in this dataset	–

Opening a dataset shows the UMAP with this gene coloured and the violin plot of its expression per cell type. A gene is in viewer when the dataset ships a per-cell expression vector for it; marker only means it is in the dataset’s ranked marker table but no vector was exported, so the atlas cannot draw it; not in this dataset means the dataset’s own gene-ID table does not list it, so no expression claim can be made for that dataset. unmapped is deliberately weaker still: the dataset has no gene-ID table on CnidoSite yet, so nothing is claimed in either direction. Where markers are listed, the numbers are log2 fold change and the percentage of cells of that type in which the gene was detected.

Epigenetic marks

Chromatin and DNA-methylation data covering this gene. Peak calls are listed per sample with the genomic region the peak falls in; DNA methylation is listed as sample availability only, because those tables are queried by the DNA Methylation page itself.

Peak calls overlapping this gene

Assay	Sample	Peaks	Region
ChIP-seq	H3K27ac_gastrulae_24h	3	Promoter (<=1kb) 2 · Promoter (1-2kb) 1
	H3K27ac_planulae_4days	2	Promoter (<=1kb) 2
	H3K4me2_gastrulae_24h	2	Promoter (<=1kb) 2
	H3K4me2_planulae_4days	2	Promoter (<=1kb) 2
	H3K4me2_polyps	4	Promoter (<=1kb) 4
	H3K4me3_gastrulae_24h	2	Promoter (<=1kb) 2
	H3K4me3_planulae_4days	1	Promoter (<=1kb) 1
	H3K4me3_polyps	2	Promoter (<=1kb) 2
	H3K27ac_Ncol3_negative	1	Promoter (<=1kb) 1
	H3K27ac_Ncol3_positive	1	Promoter (<=1kb) 1
	H3K27ac_Nep3_negative	1	Promoter (<=1kb) 1
	H3K27ac_Nep3_positive	1	Promoter (<=1kb) 1
	H3K36me3_gastrulae_24h	4	Exon 2 · Promoter (2-3kb) 1 · Promoter (1-2kb) 1
	H3K36me3_planulae_4days	1	Promoter (<=1kb) 1
	H3K36me3_polyps	1	Promoter (<=1kb) 1

5 further sample(s) also have peaks at this gene; open the assay page below to see them all.

Browse the full epigenomic landscape of this species: ChIP-seq · ATAC-seq.

DNA methylation (bisulphite samples)

Sample	Methylation profile
Whole_adults	open

The DNA Methylation page locates this gene by scanning the bisulphite table, which holds one row per cytosine. For the largest datasets that scan takes a while to return; it does not mean the link is broken.

What you can do with this gene

Every tool below opens with this gene already entered, so you land on the analysis rather than on an empty form. Links open in a new tab.

Analysis	What it does	Status
Primer design	Design PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.	template found	open →
BLAST	Search this gene’s sequence against the CnidoSite BLAST databases. The query is filled in and the species’ database is preselected — press Run to start.	template found	open →
Expression heatmap	Draw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it.	ready	open →
Gene family / orthogroup	Look this gene up in the single-copy orthogroups built from the high-quality cnidarian genomes, and see which other species carry an orthologue.		open →
Gene set analysis	Start a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.		open →