Gene detail

Detailed information of XP_032220007.1 in Nematostella vectensis

Genomic Location: NC_064043.1:10888353...10898942
NR annotation: XP_032220007.1, paired box protein Pax-6 isoform X2 [Nematostella vectensis]
Species Nematostella vectensis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_032364116.2

CACGAAACACCCTTCGTAACAAATGCACTGGAAAGCACCGCCAGCTAGCAACAAAATCGCACTCAAGACAACTTCGTATGTTGTTAGCAATAATTTCTAGATTTGCTTGAATGTTTTCCAAGTCTATCGTGCCTACGCTATCGAGACAAGATTGGCAGGCCATAGCTCGGGGGTAGAGACATAAGCAAAGTGTATTAACGTATGAATGATAGCCAAATTAGCATGAGAATAGTGACGCAGTACTCTGGACTCTATTTagaacacaccaagtacttaGTGGTGCTCAACTCGCATACCGCTACAGAATCACAACATCGCCTCTCTATTAAGTTTTGGCTGGCGACCAGGGGTGACAGTGTTTAGTAACGCCTCAGTGATCTTAGGAAGCGCCTGAGTGATTTTTCAACAGTCAACTCCGTGCTCACTCAAACTGCTAGTATGTCCCATAGTAAACAAGGCCATGGCGGAGTTAACCAGCTCGGAGGTGTTTTTGTCAACGGAAGACCGCTACCTGATGTGGTCCGGCAAAGAATCGTGGAGCTTGCACAGAGCGGAGTCCGTCCATGTGATATTTCGCGCCAATTACGAGTGTCCCATGGCTGTGTCAGTAAAATCCTCTGTAGGTTCTACGAGACGGGCTCCATAAAACCTGGAGTTATTGGAGGCAGCAAGCCTAAAGTTGCAACCGGGAATGTGGTGACTAAGATAGCAGAGTACAAACTTGCAAACCCGACCATGTTCGCGTGGGAAATAAGGGATCGACTTCTCAGTGAAGGGGTCTGCACGAGTGATAATGTCCCCAGTGTTAGCTCGATCAACCGAATCGTCCGTAACCGCATCAATAGCCAGGATAAAATGAGCAACCCTAAAGGAAACCCTGGAGACAACTCTCCAATGGACATGGCACTAAAATCAGATCGAGACATGCAGGCGATAAATGTACCGAGGTCTTCGTATTCCATTAGTGGGTTGTTGGGGATTCCAATGCCACATCAACAGGTTGCTCAACACACCTCGCCTAGCAAGCGCAAATACTCAGTGGATAGCGCCGACAGCACAGGCAGTCATTCAGGTGATGAGGGTGACGACCCTAATTCACAGAGAAGCAAGATGTCTCGCCGCCAACGCACAAACTTCACTGATGAACAAATCGAAAAGCTTGAGAAAGTTTTTGAGAAGACTCACTATCCGGATGTATTCACAAGAGAGGAACTGGCTCAACAAGTGAACCTGTCAGAGGTGTGGTACTCTAACCGCCGAGCAAAGTGGAGAAAGGAGGGCAAAGACGGGCCACAAGACCCCCAGGGTCCCATCCAGACGACTTACATCTCTTCCAATGGTTATAGTCACCCATCAGTCATCAGCCCATCTAACATGCAAATGAACCCCATACACGTGGAGGCAGACCACACCCAAGTTCACTATCCACCCTCAAGTGACCAGAATATCCATGTCAAGAGAGAATTGACTGAGTTAAAGCCCATTTCTGAGAACTCTCTGGGCATGGGAATGCCGACCATCCAGCAAAACCAACAATTCACAAGCTACTCCTCTCCCAGTCCCACCACCTACATATCAGTGCCGACTACCGGGAGTGGAGGGCATCAGTACCAACTGCAGCCCATTTTCAGTAACATCTCAGGACAGTACCAAATGCAAAACCCTATTACAACTATCGCAGACAGCGAAACAACACAGATCATACATGGAAACCCTGCCTCAAGCCAGGCACTTTCACCGCCAGCAGCCAACACGGCACCAGGCTATGTCCTTCCTCCTGTCAGCACCCTAACCAACAAGGGCCATGACAGCACCCAGTATCAATCAGCGCAGTTTGCTCAAATTCCACCAGGCGCCTATCCTTCATCGGACCAGTGGATACCTGCATACCCACAGGGTTTCATCGGCCGACCGGCTACAGTGTTTGCTGTTCCCGCTCAATGGGCAGCCCCTCCTCCTTCGTCATCAAGAATTCAGAGCTCAAAGCTCACAACATCAGCTTAGGTAAAAATCCCACATGGCACAAGGACGAAAGGAAGTCCTGGTCCATTGCTGACGTCTAGGGGGAACTTCATAGTCAaactcaaataaataaattcaaaGATGTGATCACTCATACAACTCTCTTCAAGTCAAGTTTATTTGGATTTTAAAATTACATTTTGGCAATTACTGTCAATAAAATAATGTATAATCGATAACTGCACATGCTAAATATCGTTTAATAGTTTAACGCTTTTGTAAAAAATTTGAATACTTGAGTTTAGTTGAGCCCTTGAGATGTTTATAGACAGTAGCATAGGTGTGGTTATAGTGGGTCCTTATTTTGATATTGAAATTTTATCAAATTAAGGATTTCCTGAATTGTTTAGATTCTTAGCTAagctattttttcttttaggcTATAGATATTTTAGAAGAATTACCCCCTTTTTATACAAGGGAAAATAGGTTTGTGAACTGTTTCCTTGTCCCTTATTTTGAATGATAAAGTATTTTCTTGTTCTGCTCAATGGCTCAATTAAATATTTATCAATAAGATGGTGTTTATTAACACTTcattattttttgaaaatctgACTAGACATTTAgtcaaatatattttcattcaTCCACATTCTGATGCGATTGTGACATAAATTTTCTTGTAATAATCTTGCATTTGGACAAACAACCCAGATATATCATGGGAAAACAGTATTTTTGTACATATTTTTCTATCTCATGCACATGCAACATTAGAATATACAGGTTTTTTGGAATGTTCACTTTTTCAAAACCAATAGACAAGACTTGCTTTTGGTCACTAATTCTAAAGGTTTACCATGACAGCTACAGATCTGAACTCCTGTAAATTTAGAGAAATGCACAAGGACAAGATGTTTCAAATTTAATGGATAGTACATACTATATGAACATTTCCTAAACAAATTTTAATCCTGTATTAGTGATgtctggattttttttacaatcgAGTTTTagaagtaattaggtaaataaACACAGAGTGAGGTAAATATGTTTTTCCACATGGACTCTACGTGTGATATTACACATGGTATTTAATGATAGTGGATCATCGGCTTTATTTAATGGCGATATATGCTTTCATACAAGGTGATATTGTTCTCAAGGTATATTTAGTAACATGTCACAGCAGCATTTGAATTAGTCACAAAATAAAAGGTTGTATATTTTTTCTGA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
O57685	Paired box protein Pax-2-A OS=Xenopus laevis OX=8355 GN=pax2-a PE=2 SV=2
Q90268	Paired box protein Pax-2a OS=Danio rerio OX=7955 GN=pax2a PE=2 SV=2
Q02962	Paired box protein Pax-2 OS=Homo sapiens OX=9606 GN=PAX2 PE=1 SV=4

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000410 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00046 all species →	Homeodomain	Homeodomain	Domain	Interproscan
PF00292 all species →	PAX	'Paired box' domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036388 all species →	Homologous_superfamily	Winged helix-like DNA-binding domain superfamily	Interproscan
IPR001356 all species →	Domain	Homeobox domain	Interproscan
IPR009057 all species →	Homologous_superfamily	Homeobox-like domain superfamily	Interproscan
IPR001523 all species →	Domain	Paired domain	Interproscan
IPR043565 all species →	Family	PAX family	Interproscan
IPR043182 all species →	Domain	Paired DNA-binding domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45636 all species →	PAIRED BOX PROTEIN PAX-6-RELATED-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0000978 all species →	Molecular Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	Interproscan
GO:0000981 all species →	Molecular Function	DNA-binding transcription factor activity, RNA polymerase II-specific	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:0048856 all species →	Biological Process	anatomical structure development	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_032220007.1.

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

Expression pattern (RNA-seq)

Transcript abundance of XP_032220007.1 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

76.7Max TPM

51.5Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole 6 week old aboral regenerate · regenerate 96hpa	3	3	61.44	76.71
whole 6 week old aboral regenerate · regenerate 144hpa	3	3	39.62	58.38
whole 6 week old aboral regenerate · regenerate 0hpa	3	3	53.60	61.18
whole 6 week old aboral regenerate · regenerate 2hpa	3	3	64.62	65.15
whole 6 week old aboral regenerate · regenerate uncut	3	3	48.14	57.28
whole 6 week old aboral regenerate · regenerate 4hpa	3	3	42.36	43.13
whole 6 week old aboral regenerate · regenerate 120hpa	3	3	60.09	70.95
whole 6 week old aboral regenerate · regenerate 36hpa	3	3	60.71	64.66
whole 6 week old aboral regenerate · regenerate 24hpa	3	3	38.95	49.88
whole 6 week old aboral regenerate · regenerate 20hpa	3	3	32.35	46.14
whole 6 week old aboral regenerate · regenerate 16hpa	3	3	31.11	35.93
whole 6 week old aboral regenerate · regenerate 72hpa	3	3	62.55	70.05
whole 6 week old aboral regenerate · regenerate 60hpa	3	3	64.17	72.18
whole 6 week old aboral regenerate · regenerate 48hpa	3	3	71.26	73.42
whole 6 week old aboral regenerate · regenerate 8hpa	3	3	46.64	56.98
whole 6 week old aboral regenerate · regenerate 12hpa	3	3	45.65	67.49

Per sample · hover a bar for the full sample record · show / hide the sample table

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	76.71
SRR6320836	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	59.25
SRR6320837	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	48.36
SRR6320847	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	58.38
SRR6320841	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	36.90
SRR6320838	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	23.58
SRR6320840	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	61.18
SRR6320846	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	58.41
SRR6320839	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	41.19
SRR6320842	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	65.15
SRR6320861	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	64.75
SRR6320848	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	63.96
SRR6320843	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	57.28
SRR6320844	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	50.42
SRR6320845	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	36.72
SRR6320873	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	43.13
SRR6320849	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	42.18
SRR6320872	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	41.77
SRR6320850	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	70.95
SRR6320882	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	60.24
SRR6320883	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	49.08
SRR6320855	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	64.66
SRR6320851	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	60.79
SRR6320852	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	56.67
SRR6320854	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	49.88
SRR6320853	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	34.40
SRR6320856	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	32.56
SRR6320857	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	46.14
SRR6320860	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	26.34
SRR6320859	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	24.59
SRR6320881	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	35.93
SRR6320880	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	33.79
SRR6320858	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	23.62
SRR6320862	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	70.05
SRR6320864	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	65.46
SRR6320865	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	52.15
SRR6320869	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	72.18
SRR6320867	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	62.33
SRR6320866	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	57.99
SRR6320868	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	73.42
SRR6320870	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	70.84
SRR6320871	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	69.52
SRR6320874	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	56.98
SRR6320875	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	47.41
SRR6320876	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	35.53
SRR6320878	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	67.49
SRR6320877	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	45.45
SRR6320879	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	24.01

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.