Gene detail

Detailed information of XP_001632995.2 in Nematostella vectensis

Genomic Location: NC_064042.1:10414029...10425680
NR annotation: XP_001632995.2, F-box-like/WD repeat-containing protein TBL1XR1 isoform X1 [Nematostella vectensis]
Species Nematostella vectensis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_001632945.3

ACCTTTGGCGCTCAGTAAACATGGCGGCCGTGTGAAGTGGATAGAGTCCCTCATTCACTTACGTCTCATAGTCTGAATGCAGTTGAAAAACAACTGTATTTGTTGATAAATGTCCTCTAAAATTGCAGCAAGACACCATAGAGTGGTAGAATTTATATTTATGTGGACTTTTTTAGGGAAACAGTGAGTTTTTGCTTTGCCTGTTTCGCTTTTTCGGATTTCAAATCTCCGCGTGGTTTGAAACTTTAGAGTAAAAAATTGTTGAGATCGACCTCAACtgttaatatatatattatgagATATTTATCATGTCTATGAGCAGCGATGAAGTGAATTTTCTTGTGTATAGATACCTACAAGAATCAGGATTTCAACACTCTGCCTTCACCTTTGGAGTTGAAAGCCACATAGACCAGTCTAGTATAAATGGTTCAGTCGTCCCCCCTGGTGCCCTAGTAACAATTCTCCAAAAGGGAGTGCAATACGTTGAAGCAGAAGCAACTGTTACTGAGGATGGTGGACTTTTGGACGATGGTGAGCTGGACCAGTTATCGCTGATAGACGCTGCACTACCGGATATCataagtactaggcacaccCTTCTCAGCAATAAAGGAATCAAACCAGAAACACCCTACAAGAACGACAATGGATCAAATGAGATCTACATGCATAATAACTCAGTTTCAAATGCTGATAGTCTACAGATTGATGGCTCAGTCAATGATATTGCCAACCAAAAGGCTTTGGTTTTGAAAGGCCATCAATCAGAGGTTTTTGTGTGCTCTTGGAACCCCACACAAGATATCCTTGCATCAGGATCTGGGGATGGCACGGCACGGCTCTGGCCAATGACAGATTCTGGACTCGGGGTACCTGTGGTACTAGCCCATAATATCAAAGACCAAGAGAATCACAAAAACAACTCTTATGATGTAACCTCTTTAGAATGGAATAGTGAAGGTACTTATTTAGCTACTGGATGTTATGATGGCTGCGCAAGGATATGGGACCCAGAAGGTCAATTGGTGACTACCCTAAGAGAACACAAGGGACCATTATTTTCTGTGAAATGGAATAAGAAGGGAAACCATCTTTTAGGAGCCGGGGTAGACAAGGCTTGTATTATATGGGATGCCAACACATGGGATGTGAAGCAGCAGTTTGCATTTCATCAAGCTCCCACGTTAGATGTAGACTGGCAGAAcaacaacagttttgcttcaTGCTCTACCAACAAGCTGATCCATGTGTGCAGACTGGGGCTAGACAAGCCTATTAAATCATTTAGGGGGCATATGAGTGAAGTGAATGCAATAAGATGGGATCCGTCGGGCACACTTCTGGCATCCTGCTCAGATGACATGTCTGCAAAGGTTTGGAGTTTAAAGGAAGATATGTGTGTTCATGACTTACAAGGCCATAAAAAAGAGATATACACTATTACTTGGAGCCCAACTGGGCCTGGCTCAGCCAACCCATCGGCCCCTCTCTTACTAGCTAGTGCATCTTACGATACGACTGTCCGATTGTGGGACGTTGAGCGAGGCGGCTGTCTGCAGGTCCTCAGTAAACATCATGAGCCTGTGTACACCATATCCTTCAGCCCTGACGGCAGATACCTGGCATCTGGCTCGTTTGATAAGCGAGTACACATCTGGTCTACCCAGACTGGCAACTTAGTTCATTCCTTCCAAGGAAGCGGGGGGATATTCGAGGTTCAGTGGAGTCCGCGAGGAGATAAACTAGCTGCTTGCTTTTCTAATAATACACTATGTGTAATAGACGTGCGGACGCTATAACAgctgtgtgacgtcacacgtgacgtcatcgatgcgTGACGCGTCACGCTCGTGTGTCACGTAGTCAGCCACAAGCCGGTGGTACATGAACCCAAGACGGCATTAGAACGCATGCCAAGTGAAGGTGTTACCGCTGGTCAGGTTCTGGAAGAAAATAAGGCGTTTTACCGAGGCAGAAATGTTTTGGTTATATACCGTTCAAAGACCTAGTTGTTGGTCGTTCTCGCATGCGACAACCTTCAACTTCTCTGCTGAGGTGGTTGTGTTCCTGTTTCTCCAAATTTGCCGTCATCGAACGAAAAGAGTGATTTCTCGCGAAGTTCGGTACCATCAGTTCGCCGCGCGCAAGAATCCTTGCCGCATTTTAACTTAAGTAAACCTAACTTAAGTATATGTGTACATATGTAAGTAAGTAGATCCTATATGTCAAATCTACGCCCTATTGTGTACACGTCGTCTATACCATATTTGGCTCTACGCCCCATGTATGGTGTGCACGTCATGTATACCATATTTGGCTCTACGCCCCATGTAATGTGTACACGTCATCTATACCATATTTGACTCCATCCCTCCATACATTTTCATCAGCGGTTAGTGTCACCTTTTCGCATCGGTACAGCGTGCACAGTCTTCATCCTTGTACGAAGCATGACAGCATGAACCGGAAATGAGAACGCAGGTCCTAATAAGTAGTCATTTACTACCCACAGTTCTCTTTTCACATTATTCTAATAACACGACCCGCTAAAATTCTTGTACATGCGCAATGGTGACCTAACTTGGTGTGTCAATCAAAAATGTAAATTTGCGCAGTCGTTTTAGATACTTGCGTTGCGCTCTTCTTCAAAATACTTGCGCACACGTACTGAAAACTACTTATTACTTTTACGCAAAATTCTAGGTGCGCGCGAAACAGGCGTTTGACCGCTGATTTCTGTCTCATCATAAAGAGTTTTATTTGAATCTTTTTTATCCGATGTAGTGAAATAATATTACCTCCGTCATTAAAAACGACCTCCAACTGAACTGATAGTTAAGAGTGGACTATTTCCAATAATAAACTCTCTGGCTTTA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q8BHJ5	F-box-like/WD repeat-containing protein TBL1XR1 OS=Mus musculus OX=10090 GN=Tbl1xr1 PE=1 SV=1
Q9BZK7	F-box-like/WD repeat-containing protein TBL1XR1 OS=Homo sapiens OX=9606 GN=TBL1XR1 PE=1 SV=1
Q7SZM9	F-box-like/WD repeat-containing protein TBL1XR1-A OS=Xenopus laevis OX=8355 GN=tbl1xr1-a PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006285 (this species only)
Ubiquitin family	UBD\|Other\|Beta-prp · all ubiquitin genes in this species
Ubiquitin family	E3\|E3 adaptor Cullin RING\|CDC20 · all ubiquitin genes in this species
Ubiquitin family	E3\|E3 adaptor Cullin RING\|DWD · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00400 all species →	WD40	WD domain, G-beta repeat	Repeat	Interproscan
PF08513 all species →	LisH	LisH	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001680 all species →	Repeat	WD40 repeat	Interproscan
IPR019775 all species →	Conserved_site	WD40 repeat, conserved site	Interproscan
IPR020472 all species →	Repeat	G-protein beta WD-40 repeat	Interproscan
IPR036322 all species →	Homologous_superfamily	WD40-repeat-containing domain superfamily	Interproscan
IPR006594 all species →	Conserved_site	LIS1 homology motif	Interproscan
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	Interproscan
IPR045183 all species →	Family	F-box-like/WD repeat-containing protein Ebi-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR22846 all species →	WD40 REPEAT PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0000118 all species →	Cellular Component	histone deacetylase complex	Interproscan
GO:0003714 all species →	Molecular Function	transcription corepressor activity	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	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
K04508	TBL1; transducin (beta)-like 1	-	Chromosome and associated proteins	ko03036	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_001632995.2 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

46TPM > 0

16Conditions

44.5Max TPM

25.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole 6 week old aboral regenerate · regenerate 96hpa	3	3	22.91	28.17
whole 6 week old aboral regenerate · regenerate 144hpa	3	3	19.58	25.42
whole 6 week old aboral regenerate · regenerate 0hpa	3	3	23.83	27.62
whole 6 week old aboral regenerate · regenerate 2hpa	3	3	27.78	30.35
whole 6 week old aboral regenerate · regenerate uncut	3	3	20.45	23.19
whole 6 week old aboral regenerate · regenerate 4hpa	3	3	23.88	25.97
whole 6 week old aboral regenerate · regenerate 120hpa	3	3	22.46	23.74
whole 6 week old aboral regenerate · regenerate 36hpa	3	3	27.46	33.55
whole 6 week old aboral regenerate · regenerate 24hpa	3	2	20.70	32.24
whole 6 week old aboral regenerate · regenerate 20hpa	3	3	31.45	33.32
whole 6 week old aboral regenerate · regenerate 16hpa	3	3	28.20	31.45
whole 6 week old aboral regenerate · regenerate 72hpa	3	3	27.31	28.39
whole 6 week old aboral regenerate · regenerate 60hpa	3	3	29.69	33.88
whole 6 week old aboral regenerate · regenerate 48hpa	3	3	32.23	44.52
whole 6 week old aboral regenerate · regenerate 8hpa	3	3	24.36	25.42
whole 6 week old aboral regenerate · regenerate 12hpa	3	2	17.34	29.64

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	28.17
SRR6320863	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	24.17
SRR6320837	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	16.39
SRR6320847	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	25.42
SRR6320838	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	18.73
SRR6320841	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	14.60
SRR6320846	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	27.62
SRR6320840	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	23.86
SRR6320839	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	20.02
SRR6320861	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	30.35
SRR6320842	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	27.23
SRR6320848	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	25.75
SRR6320843	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	23.19
SRR6320844	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	20.45
SRR6320845	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	17.71
SRR6320872	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	25.97
SRR6320849	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	24.98
SRR6320873	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	20.69
SRR6320882	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	23.74
SRR6320850	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	23.49
SRR6320883	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	20.15
SRR6320851	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	33.55
SRR6320852	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	25.87
SRR6320855	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	22.96
SRR6320854	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	32.24
SRR6320853	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	29.85
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	33.32
SRR6320860	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	31.98
SRR6320857	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	29.06
SRR6320880	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	31.45
SRR6320881	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	27.93
SRR6320858	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	25.22
SRR6320862	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	28.39
SRR6320865	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	26.90
SRR6320864	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	26.64
SRR6320869	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	33.88
SRR6320866	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	28.64
SRR6320867	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	26.55
SRR6320868	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	44.52
SRR6320870	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	31.67
SRR6320871	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	20.50
SRR6320874	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	25.42
SRR6320876	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	23.99
SRR6320875	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	23.66
SRR6320877	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	29.64
SRR6320879	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	22.39
SRR6320878	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.