Gene detail

Detailed information of XP_001637641.2 in Nematostella vectensis

Genomic Location: NC_064038.1:11499849...11503605
NR annotation: XP_001637641.2, la-related protein 6 [Nematostella vectensis]
Species Nematostella vectensis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_001637591.3

CAACTGTTTGACACATCAGACATTAGCCGTGGTTGAACGAGGAGGTGGTAGCGGGAAAGCCTAGCTCGTTCGGAAGCCTTTTTTAGAGATTTTTCGCTTGTGGCGTAGCTCAAAGATGGCCGAAGAAATAGCAGTTGTCTGTGATCTCGATAAAAAAACGGAGAATTCGCCGAAATTGTTGATTAACGGTGAGGAGTGCGCCGCTTGTTCCGATCATGACATCGCTGCGTCTTCAAACTCCGAGGAAGAGAATGACCAAAAATTGAGCTTCCGATCGAATAGTCCTTGCGATTCTCACTCGGAAAACGAGGCTAAGGGACACCACGGAGAGTTCCAACCTCCCAACGATGAGCTGAAAGCGAGAATCAAATCCCAAGTCGAGTTTTATCTTAGCGATGATAACCTGGCTCGCGATGCATTTTTGCTCAAACACGTTCGTCGCAACAAGGAAGGCTATGTCAACCTCAAGCTCATAACGTCCTTTAAAAAGGTCAAATCACTCACTAAGGACTACAGAGTTGTCGCTGAGTCATTGAAGGATTCTACTATGTTGAGTATGAACGACGAAAACACGAAAGTCAAGAGAAACGAGCCGCTAAGAGCTGAGTTGATGGACCGGAATCCGGGTCGAACTGTAGTAGCGACCAATATCGAAAACCCATCCTTCGAGCACGTAAGTGAAATGTTCTCAAAGTGTGGAGAGATTGTATTGATCAGGATTATTCGTGGGGGAAAGACCATACCGCCTGATTTGAAGGAATACGAATCGAAGTTTCCAGAGAATGAGACCTTCGCTGTAATCGAATTTGAGACCATGGCAGCGGCCGCACGTGCGTGCTCCGAACTGACACAAGATGGCGGCATTCGAGTCATAGAACTAGGGAAAggagcgaagaaaaaagacaagaaaCTAAGGTCTAGAGAGTTAGATAACGACTCAGTACCGGAATCAGACGAAGAAcacgaagaaaaaaagaaaaagaaaagaaatcgaggaaaaaagaacaaaaacaagagatTGTCTGAATTAGCAGGTACTTCTGACGACAGTCATAACAGCTCATGCTCCGAATCTGACAGCTCAACTCACAACTCCTTCAGCAGTTGCAGACGCCGGTATCATAGCAACCCCGGACTGTCATCAAACTCCCACAACCGCACTGAGCCCCCAGGCATCAATGGCCAGTGGAGGTCACCGCAGAGTAGCCCAGAACCCCAGAGACGGCACTTTAACAGCCCTAGTCCAAACAAGGAGGCAAGTAGTAGTGCACCAAATAGTCCATGGTCCCAAAGACGCAAGACCACATCCTCTAAACCTGGTGGACACTCCCCATTGGTTGATAGAGAGCCAGTTAAACATCGCATGGTACAGTTGGAGGGTGTTGAACGGTTGCCACGGGGGCCTGATGGTACTAAAGGTTTTCATGGCTTTGGTAGGGGTCAACCTATGATTGCTGTAGCCTAATTTCCAGCATAAATTTGTATCATAGGGAATATTATTTTGGCATGATgtcattttgatttttttaagtagTACCATTATCAAGGAATAATAGCATAGTTTAAATGGCACTCAAAGGGAGCTCTACTATTTCCAAAGAAAACATAGCAATTTAGAACTTTCCAAATTAACATATTCTCCCATTtttcagggcttctggaattacgcggaaaaaactcaaaattatgcGGGAATCTTGGCTAAATTATGCGCTACATTACGccgaaaatcaatcattacgcaggattttgcaatacatgttgtttaaaaatcaaaattttgcaggattctTTACTTAATTACGCGCTCagttacacggaatatcaactgttgcgcccaaactacattttgtaccaaaagaaagcacaaaataacttgaaaaggttaatttttttgcgcgaaaatattttaggcgagttttcattggcttctagccaccagccaattaaaaaaggtattttattgttagtcctaggccttcgcggtttagcaaagaaattcagttcgaaatattgCACTCTTACCAAGAatatatctctttttttacaagaaatagaggtaaaaaccctaaaagaacacatcaacTGTGCActtaatgttttgtctttcaaaatttagccaaattacacgGGATTAtgcggaaatttgtggtttacgcggattacgcgaagaaagccaaattacgcgcttcctcACAAgagcgtaattccagaagccctgatttTTATGTCACCACCTCTGTGTAATTTGATGTAAAAAGCTAATGATAATTCAAAAGGCCTCTTGCATATAGACCTATTTTTTCAATCATTGAAACTAAAAAAAGAGGAATTATATTGGAACATAACTAAAGCAATACATTTATTAAGGATTGTTTGCCATATACTTCATGAAATCATCAGCTTTTCTAAGTTCCTCTGAACAAATTAAAACAATACAAGTGAACATTGTTGTATAATATATTCATCCAAACAGAAATGTTAATCATTTGAGAACACCTGGTTTACTTATTCCAAGTTATTATTTTAACAGCCTAGTCTGTTTATTTCATAATTCAAATAATTCGAAATTTTCAAGTTTACCTGTGTACATTTTTACATATTTAATATAGACTAGCAAGTGTGCTCTTTAGGGTTGCAGAAGAGAAGAATGTTAATACATTGAGTTATAAGTTATAGTTCTTCAGCTCTACAATCTACAGTTTTTTaaactgaaaacaaaatatttatatagtgGTTAAAATTGTGTAGTAGGTTAAGATAAtgatatataaaacaaaaaagtacatTTGTCCTTCAGCCTAAATAGTTTGCAATACAAGGCTTCCTTTAGAGTAAAAGCTACCTTAGTTTGTAGTTTTAACACACTGTGGCAAACATCCGACTAAATACAGTCTACATAGTGCTATAGTATACATAGTGCATATGATATATAGTTCATATATTTCTATAAAGATTTTGCTTTTATATTTACTTTAGCAAAAATTTGTCTTGACTGATTAAAAATTTTAAATGTTTCCAACATGCAACAAACATTTTTGTTAGCATAATTAGTTAGCTGCTACGGAGTTTGATTTTCCaagtatattttattttgataaagaataaaaattaaCAGGCATGTACCCTGGATAGGATGTGCAGAGGGGTGCGCAGTTAGGTATTGTATGAAGGATAGTATTTTTGATGATCCTTCAGTGAGAGATGACCCAGGTCTTGTCAGGCAAGGAAGGGTGTATATTCCCCCATGCCTAGCCCTTGTGGTTGAGGTTCTTTCATGTTGTGGGATGGTTCTTAGACTTAATAATTTTACAATGTTAGCTGAGCTATACTATCAACTGATTAATGAGTTACAAAGTGTCAGCTGAGCTATAAAAGAAAGTCGCTTATTAAGATTATATATAAGTTAAAGTTTGAGTAGTATACATATAATAGCCCCAAATTGGGACATTGCATAGAAAATACACTCACACATTTACTAAAGAACTCCAGCTATGAATTTTGTACTTCTTTTGGTATATCGTGAAACAAAGTAAGTACTTGAATTAGACTGTTTTTTATTGGCTTATATCTCGATTGAAGCTTTCATTTTGTGTGTGCTAATTGCTTTTTTATCCTGAACATTAGGTTTTTCTGGTACTTAGAATGTATGtagcattttctttctctataCATGCATGCCTAGCTACTAATTCCTACTACAGTGTTGTATATACTTATATGAAAGTCTTGCAATAAATTTGAAATTTCAGTGTGA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9BRS8	La-related protein 6 OS=Homo sapiens OX=9606 GN=LARP6 PE=1 SV=1
Q8BN59	La-related protein 6 OS=Mus musculus OX=10090 GN=Larp6 PE=1 SV=1
Q7ZWE3	La-related protein 7 OS=Danio rerio OX=7955 GN=larp7 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0008358 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF05383 all species →	La	La domain	Domain	Interproscan
PF12901 all species →	SUZ-C	SUZ-C motif	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002344 all species →	Family	Lupus La protein	Interproscan
IPR036390 all species →	Homologous_superfamily	Winged helix DNA-binding domain superfamily	Interproscan
IPR036388 all species →	Homologous_superfamily	Winged helix-like DNA-binding domain superfamily	Interproscan
IPR006630 all species →	Domain	La-type HTH domain	Interproscan
IPR034880 all species →	Domain	La-related protein 6, RNA recognition motif	Interproscan
IPR024642 all species →	Domain	SUZ-C domain	Interproscan
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan
IPR045180 all species →	Family	La domain containing protein	Interproscan
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR22792 all species →	LUPUS LA PROTEIN-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006396 all species →	Biological Process	RNA processing	Interproscan
GO:1990904 all species →	Cellular Component	ribonucleoprotein complex	Interproscan
GO:0003729 all species →	Molecular Function	mRNA binding	Interproscan
GO:0005844 all species →	Cellular Component	obsolete polysome	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	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
K15191	LARP7; La-related protein 7	-	Transcription machinery	ko03021	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_001637641.2 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

48TPM > 0

16Conditions

443.9Max TPM

138.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole 6 week old aboral regenerate · regenerate 96hpa	3	3	35.87	46.40
whole 6 week old aboral regenerate · regenerate 144hpa	3	3	18.77	24.42
whole 6 week old aboral regenerate · regenerate 0hpa	3	3	62.78	84.79
whole 6 week old aboral regenerate · regenerate 2hpa	3	3	327.97	372.05
whole 6 week old aboral regenerate · regenerate uncut	3	3	35.18	73.96
whole 6 week old aboral regenerate · regenerate 4hpa	3	3	243.10	271.90
whole 6 week old aboral regenerate · regenerate 120hpa	3	3	26.14	30.52
whole 6 week old aboral regenerate · regenerate 36hpa	3	3	109.33	178.02
whole 6 week old aboral regenerate · regenerate 24hpa	3	3	177.33	291.67
whole 6 week old aboral regenerate · regenerate 20hpa	3	3	306.54	366.05
whole 6 week old aboral regenerate · regenerate 16hpa	3	3	324.65	443.86
whole 6 week old aboral regenerate · regenerate 72hpa	3	3	51.84	59.40
whole 6 week old aboral regenerate · regenerate 60hpa	3	3	44.53	55.70
whole 6 week old aboral regenerate · regenerate 48hpa	3	3	95.22	125.55
whole 6 week old aboral regenerate · regenerate 8hpa	3	3	54.09	74.88
whole 6 week old aboral regenerate · regenerate 12hpa	3	3	300.48	425.46

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	46.40
SRR6320863	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	34.10
SRR6320837	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	27.10
SRR6320847	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	24.42
SRR6320841	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	18.02
SRR6320838	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	13.88
SRR6320846	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	84.79
SRR6320840	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	63.68
SRR6320839	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	39.88
SRR6320842	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	372.05
SRR6320861	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	348.84
SRR6320848	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	263.00
SRR6320843	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	73.96
SRR6320844	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	17.50
SRR6320845	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	14.09
SRR6320873	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	271.90
SRR6320872	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	271.29
SRR6320849	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	186.11
SRR6320850	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	30.52
SRR6320882	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	28.13
SRR6320883	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	19.77
SRR6320855	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	178.02
SRR6320851	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	105.71
SRR6320852	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	44.28
SRR6320854	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	291.67
SRR6320853	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	154.34
SRR6320856	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	85.99
SRR6320857	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	366.05
SRR6320860	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	335.07
SRR6320859	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	218.49
SRR6320880	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	443.86
SRR6320858	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	281.15
SRR6320881	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	248.95
SRR6320864	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	59.40
SRR6320865	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	59.12
SRR6320862	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	37.00
SRR6320869	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	55.70
SRR6320867	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	42.31
SRR6320866	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	35.56
SRR6320868	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	125.55
SRR6320870	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	109.42
SRR6320871	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	50.69
SRR6320874	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	74.88
SRR6320875	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	50.15
SRR6320876	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	37.23
SRR6320877	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	425.46
SRR6320878	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	307.78
SRR6320879	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	168.21

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.