Gene detail

Detailed information of XP_032229778.2 in Nematostella vectensis

Genomic Location: NC_064043.1:16462233...16490750
NR annotation: XP_032229778.2, sodium channel and clathrin linker 1 isoform X1 [Nematostella vectensis]
Species Nematostella vectensis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

LOC116613230

ATGGAGTCAAGTGGAAGCGATTCAAGCTACGTGAACTTTCTGCAAGACCAAGTGAGGAGGCTTAATGCAGTTCTCAAAGAGTACCAGAAGAAATACCTTCCTGTCAAAGATCCTGAGATTAAGGGTAATGAGCCACTTCCACCATGGATGACAAATCAAGGGATTCTGTCCCCTTTACTTGTTGAGTATGATGAGACCATCACAGTACTTCAGGACCAGCTCAAGTTCTACAAGAATGAACTGTTAACACTGAAACAGAGAACAGACCGGATAGTAGAGGAAAATAAAAGATTACATGAAGAGCTTCGGCAGAGTATTGAGAACCACATGGGTTCAGTGAGCCAAAATGATGCATTCGGAGTACCTGATCTCCAGAACAAAATCCTTGAGAATGTCCAGCGGCAGTTGCAGCTTGTCACTCAGGAAAAGGATAGCTATATAGAGATGTGGGAGAATGCTACCTCAGAGCTGGAGAAACTGCAGCAAATAGACAGGGAGAGGGCAGCAGAGTTGCGCCACAGATCCACTGATGTTGCAGCATTACAGAGTGACCTTAAAAAAGCCAGACGCTTTGCAGAAGATATTCAAATGCAAAGCAAACGACTGAAGGTGGAAAATAATGAACTTCTAAAAGCTGCTCAAACGCAAGATCAAGAGATTGAAAGCCTTCGTGCAGAGTTAAGAAAGAGCAAAGCTGAGCTAAAAGCTGGAAGATCTCAAAATGAAGACTACAAGAAAACATTAGAGCTTTTACAAGACCGAATAAAAGCAAGGGCTCGTGCTGCTGGCCAGGGCGAGGATGACGCAGAGAGAAGTCTAAAGTCAGACAACTTACAAAAAGAGCAATTGCAGACCCACAATATGGCTCTAGAGACCCGCCTGGCAGCGTTAATAAAGGAACTAGGCAAGCTTCGCTCCGAAAAATCAGATTTGGAAGAACGATTGCAGTCAATGCAAAAAAGAAACGCGGACCAGGAGGAGCGTGAATTAGAGGCCATTGCGCATGTGCGAGACAGTGTACAGATGGTCGAGAATGCCGTTCTGGAGCGAGACCAGGCGGTGATCCGCGAAAAACAGAAGACGCAGGAGGCTAATAGGTTACAAGAGGTCGTCAACCGCTTGCTCAGAGAAGCTGGCAAACGCACCAGGGAAGAGGTTGACGCGGTGCGGAACCAGTGCAACAAAAACATGCAGAAGTTAATGGAGGAGATGCATTATCTTGAGATGGAGGGTGCAGAGAAGCAAGCACAGCTGGAGCGAGTGTACCGAGAGAAAGACGCTGTCGAGAAAGAGCTGGAAAAGGTTTACCAAGAGGGTCCCTGTGAGATAGAGCGCGTGGGAATGACGTTTGAGGAGTTACAGAAGCGAGTAAGCATAGCCGAGATGGCCCGGGATGAGGCCTCAGTCAAGACTGACACACTTAACTCGGTTGTCAAACGACAGGAACACAGATTTGAACAAGAGAAAGCCCAGATAATGTCAGAAAATGAACAGCTTCGCCGAAGACTTAAGTCTATAGAAACTGAGTGTGAAGAAATGTCGGAAAACTCTCTAAATCTGACAGATGAAATCGACAAGCTAAAGCGGGAACTCCTTGCTGCCAAGCAAGCCCAAGAAAGCGCAGAGCACGAGATGGCCACCGAGGTCGCAGCGTTAAAACAAAAGAATGAATATGCACAGAAAGACTTCGAGATCAAACTTCGCAGCGTTGAGGAGATGAACCGCCAGTCTGTGAATGAACTCAGAGAGCTGCTCAGTACACAGCAACGCGTCGGTGTCCAGTGGAAAGAGGAATCAAAGGCGGTAACTCAACGCTTCGAGCAGACGGTAGTAGAATTAAGACAAGAAATCAATAAACAGCGCAAGCGAAACGACGAGTTGAACAGCCATCTTGTTGACGAACGACAAAGGGCAGACCAGCTCGAGTCAAAACTAGAGACTTCGAAGCAGGCCATTTCTAAGTTGCAGAAGATGGCTTCAGACGCAGAAACCCGAGCAGACGCAGCAAGCGTGCAGGTATCAACTCTGTTAGATCGCGAACGGCAACTCCTGCACGAGCGAAAGCTTTTAAACCGCGAGCTTGAGAAACTAAAACTCGAGAAGAGTAGGCCTGGGAACAACAGAAACCGGGAACCACCACAGCGCCTTTCGGATCTGCAGAACAACCCAAACGTGGGCTCAGCAAATGGTTATGAGCCGTCAGTTCGCCTCGACTTGATGTCTCCGCGAGACGAAAGGCTCATTGGGGATTTGGATGGTTTCGGACGTAGACCACATTCTGGTGAATATGGCGCTTCAAGAAATAGGGTGATTCTTTAG

Transcript

rna-XM_032373887.2

GggtaattatatttttttgaagATGGCGTCCTTTGGATAAGTTTTGTTGTGTCTGCATCTGGTGTTTTGAGTTACGTTAAACCCTGTAGAATGCTAAATATATTTGCCTATGGCGAGTGTAATAAGGGGTCCGTAATTAGTTAaaagagacttggatgtgctAGAAAGATTCTCATTTAGGATGGAGTCAAGTGGAAGCGATTCAAGCTACGTGAACTTTCTGCAAGACCAAGTGAGGAGGCTTAATGCAGTTCTCAAAGAGTACCAGAAGAAATACCTTCCTGTCAAAGATCCTGAGATTAAGGGTAATGAGCCACTTCCACCATGGATGACAAATCAAGGGATTCTGTCCCCTTTACTTGTTGAGTATGATGAGACCATCACAGTACTTCAGGACCAGCTCAAGTTCTACAAGAATGAACTGTTAACACTGAAACAGAGAACAGACCGGATAGTAGAGGAAAATAAAAGATTACATGAAGAGCTTCGGCAGAGTATTGAGAACCACATGGGTTCAGTGAGCCAAAATGATGCATTCGGAGTACCTGATCTCCAGAACAAAATCCTTGAGAATGTCCAGCGGCAGTTGCAGCTTGTCACTCAGGAAAAGGATAGCTATATAGAGATGTGGGAGAATGCTACCTCAGAGCTGGAGAAACTGCAGCAAATAGACAGGGAGAGGGCAGCAGAGTTGCGCCACAGATCCACTGATGTTGCAGCATTACAGAGTGACCTTAAAAAAGCCAGACGCTTTGCAGAAGATATTCAAATGCAAAGCAAACGACTGAAGGTGGAAAATAATGAACTTCTAAAAGCTGCTCAAACGCAAGATCAAGAGATTGAAAGCCTTCGTGCAGAGTTAAGAAAGAGCAAAGCTGAGCTAAAAGCTGGAAGATCTCAAAATGAAGACTACAAGAAAACATTAGAGCTTTTACAAGACCGAATAAAAGCAAGGGCTCGTGCTGCTGGCCAGGGCGAGGATGACGCAGAGAGAAGTCTAAAGTCAGACAACTTACAAAAAGAGCAATTGCAGACCCACAATATGGCTCTAGAGACCCGcctgGCAGCGTTAATAAAGGAACTAGGCAAGCTTCGCTCCGAAAAATCAGATTTGGAAGAACGATTGCAGTCAAtgcaaaaaagaaaCGCGGACCAGGAGGAGCGTGAATTAGAGGCCATTGCGCATGTGCGAGACAGTGTACAGATGGTCGAGAATGCCGTTCTGGAGCGAGACCAGGCGGTGATCCGCGAAAAACAGAAGACGCAGGAGGCTAATAGGTTACAAGAGGTCGTCAACCGCTTGCTCAGAGAAGCTGGCAAACGCACCAGGGAAGAGGTTGACGCGGTGCGGAACCAGTGCAACAAAAACATGCAGAAGTTAATGGAGGAGATGCATTATCTTGAGATGGAGGGTGCAGAGAAGCAAGCACAGCTGGAGCGAGTGTACCGAGAGAAAGACGCTGTCGAGAAAGAGCTGGAAAAGGTTTACCAAGAGGGTCCCTGTGAGATAGAGCGCGTGGGAATGACGTTTGAGGAGTTACAGAAGCGAGTAAGCATAGCCGAGATGGCCCGGGATGAGGCCTCAGTCAAGACTGACACACTTAACTCGGTTGTCAAACGACAGGAACACAGATTTGAACAAGAGAAAGCCCAGATAATGTCAGAAAATGAACAGCTTCGCCGAAGACTTAAGTCTATAGAAACTGAGTGTGAAGAAATGTCGGAAAACTCTCTAAATCTGACAGATGAAATCGACAAGCTAAAGCGGGAACTCCTTGCTGCCAAGCAAGCCCAAGAAAGCGCAGAGCACGAGATGGCCACCGAGGTCGCAGcgttaaaacaaaagaatgaaTATGCACAGAAAGACTTCGAGATCAAACTTCGCAGCGTTGAGGAGATGAACCGCCAGTCTGTGAATGAACTCAGAGAGCTGCTCAGTACACAGCAACGCGTCGGTGTCCAGTGGAAAGAGGAATCAAAGGCGGTAACTCAACGCTTCGAGCAGACGGTAGTAGAATTAAGACAAGAAATCAATAAACAGCGCAAGCGAAACGACGAGTTGAACAGCCATCTTGTTGACGAACGACAAAGGGCAGACCAGCTCGAGTCAAAACTAGAGACTTCGAAGCAGGCCATTTCTAAGTTGCAGAAGATGGCTTCAGACGCAGAAACCCGAGCAGACGCAGCAAGCGTGCAGGTATCAACTCTGTTAGATCGCGAACGGCAACTCCTGCACGAGCGAAAGCTTTTAAACCGCGAGCTTGAGAAACTAAAACTCGAGAAGAGTAGGCCTGGGAACAACAGAAACCGGGAACCACCACAGCGCCTTTCGGATCTGCAGAACAACCCAAACGTGGGCTCAGCAAATGGTTATGAGCCGTCAGTTCGCCTCGACTTGATGTCTCCGCGAGACGAAAGGCTCATTGGGGATTTGGATGGTTTCGGACGTAGACCACATTCTGGTGAATATGGCGCTTCAAGAAATAGGGTGATTCTTTAGATACCGCTCATCGCGTGTACAATTGGATGAACATGATTCTTTGACCAACTCAACATAAGCATATCAACATCGTCAATATTACGTGTGAAGATACTGAACTATTGCTCAATGTACATTTTATTTCTATCCATAATAAAAGTGGGAAGAATTTAAA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q96NL6	Sodium channel and clathrin linker 1 OS=Homo sapiens OX=9606 GN=SCLT1 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003174 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF15964 all species →	CCCAP	Centrosomal colon cancer autoantigen protein family	Coiled-coil	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR038911 all species →	Family	Sodium channel and clathrin linker 1	Interproscan
IPR031887 all species →	Family	Serologically defined colon cancer antigen 8	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR35970 all species →	SODIUM CHANNEL AND CLATHRIN LINKER 1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005814 all species →	Cellular Component	centriole	Interproscan
GO:0045162 all species →	Biological Process	clustering of voltage-gated sodium channels	Interproscan
GO:0060271 all species →	Biological Process	cilium assembly	Interproscan
GO:0005813 all species →	Cellular Component	centrosome	Interproscan
GO:0007098 all species →	Biological Process	centrosome cycle	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
K25400	SCLT1; sodium channel and clathrin linker 1	-	Cilium and associated proteins	ko03037	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_032229778.2 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

38TPM > 0

16Conditions

19.2Max TPM

8.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole 6 week old aboral regenerate · regenerate 96hpa	3	3	13.48	16.07
whole 6 week old aboral regenerate · regenerate 144hpa	3	3	12.19	14.52
whole 6 week old aboral regenerate · regenerate 0hpa	3	3	8.66	9.73
whole 6 week old aboral regenerate · regenerate 2hpa	3	3	6.90	8.14
whole 6 week old aboral regenerate · regenerate uncut	3	3	9.57	10.83
whole 6 week old aboral regenerate · regenerate 4hpa	3	1	2.12	6.36
whole 6 week old aboral regenerate · regenerate 120hpa	3	2	10.57	16.90
whole 6 week old aboral regenerate · regenerate 36hpa	3	3	9.94	11.48
whole 6 week old aboral regenerate · regenerate 24hpa	3	2	4.76	7.26
whole 6 week old aboral regenerate · regenerate 20hpa	3	2	4.83	7.83
whole 6 week old aboral regenerate · regenerate 16hpa	3	3	7.74	8.36
whole 6 week old aboral regenerate · regenerate 72hpa	3	2	8.86	13.69
whole 6 week old aboral regenerate · regenerate 60hpa	3	3	14.86	19.25
whole 6 week old aboral regenerate · regenerate 48hpa	3	2	7.00	11.49
whole 6 week old aboral regenerate · regenerate 8hpa	3	2	6.31	9.64
whole 6 week old aboral regenerate · regenerate 12hpa	3	1	3.01	9.04

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	16.07
SRR6320863	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	13.38
SRR6320837	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	11.00
SRR6320847	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	14.52
SRR6320838	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	11.65
SRR6320841	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	10.41
SRR6320839	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	9.73
SRR6320846	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	8.50
SRR6320840	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	7.76
SRR6320848	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	8.14
SRR6320842	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	6.49
SRR6320861	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	6.07
SRR6320843	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	10.83
SRR6320845	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	9.32
SRR6320844	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	8.55
SRR6320872	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	6.36
SRR6320849	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	16.90
SRR6320883	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	14.80
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	11.48
SRR6320851	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	10.57
SRR6320852	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	7.77
SRR6320854	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	7.26
SRR6320853	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	7.03
SRR6320856	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	0.00
SRR6320860	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	7.83
SRR6320857	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	6.65
SRR6320859	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	0.00
SRR6320881	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	8.36
SRR6320880	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	7.67
SRR6320858	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	7.20
SRR6320862	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	13.69
SRR6320865	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	12.90
SRR6320864	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	0.00
SRR6320869	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	19.25
SRR6320866	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	12.79
SRR6320867	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	12.53
SRR6320870	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	11.49
SRR6320871	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	9.51
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	9.64
SRR6320875	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	9.29
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	9.04
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.