Gene detail

Detailed information of XP_001634252.2 in Nematostella vectensis

Genomic Location: NC_064035.1:12380020...12388502
NR annotation: XP_001634252.2, homeobox protein Hox-C5 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_001634202.3

TCAATACATTTGTGATTTGATTCTGTCCTTTGGTAGGGTTGCTCGCCTTGCGCCAGTTTTAACGCGAGGAAATTGCGCGATGGTAGAGGTAATTTTCTTGTTACAATAGTCTTTCTGACCAGAGGGTGTTCATTTTAAGCACATAAAAATACCAATAACAGGAAAATTACTTATAGAGCTTCTAAAAATACAAACGCGCACGATTTTCACCACAGAAAAACACGTTTATAAAAATGGAGATGTTGCtcaaaaagtaaacaagttatagATGGAGGTACAGAGATAAGAATAGATCTAGTCTTTTCACGACAGGCTATGCAAGTTATTTTCAGATTTAACTTTTGTTTGACACAAACAGTACTTGGTTTTGTTCTGATCGGCCCTTCGAAAAGTCTCTCTGTAGAGCACGGCGGAACCTTCAAAGACCTGCCACATGTTGATGGACTCAGCATGCTTCCTTGTTAATTTTTCGTCGCCGGACCCCTTTGAAGTTCTTTTTCACAACAAAAGCAGAGTTGTATATTCCGTCCCTTATTCCACTATTCCCTTAAATAAATCTGTCAATCGAATGCGTCTTATTATCCGTCGATTGGACCACGTAAACTACAGTTTTAATCTCATTTACCACCCTATGCCCGACTTGGATTAACGTTTGATGGAGACCGGGACAGTAAGCAAGACACATTTGGGCATGAGCGGCGGTGGCGAGTGGCGCTGTAGGATGTCCTTACCGCATTTAGGCATGGCCTCAAACTTGCAGCCACAACGCTACAGTAACAATTTGGACTTTGGGCAAACAGTCCCCCTTACGCACGCACCAGTTCCAACAAGCCCTGTTGTGGGCTCAGGAATTCCGAGACAAGGACTCTACTACCATTCATCCATCTCTGCTGCGCAGAAACCATCGACACAGCCTGAACAACAAATCTTCCAACACCAAACTTCCACCAAATGTCAGGCGCAAAAGAAAAACGCTCAGGCGGAGAAGAAGCGTTGGCAAACGGCCGACTTTCGATGGATATTCACCAAAAGAAAAGCTACAGGGCCAGCGTCCATCAACACGAAAATTCCTGAAGAGAAAGAGCAAAACCCTTCACCGAGTCAGAAGAAACGATTCACATTCACACAAAGGCAACTTGTCGAGCTAGAAAAAGAATTCCATTTCAGCAAATATCTCACGAGAACACGGCGAATCGAGATTGCTACAACTCTAAAACTCACTGAAATGCAAATCAAAATCTGGTTTCAAAATCGAAGAATGAAATGGAAAAGGGAGTTTAAGGATTCCTTGCAAAAACCAGCGAACGGCGAGCCTACGTACCAAAACTCAAGCTTTGTTCAGCCTTTCCACAATGCACCCTTCAACGGCAACCATTCAACTACGATGGCATTAAACGGACTTGCGTACTATCCAAGCTACATGTCTGGGTTTGGGTAACCCCAAACCTATCAAATAACTTATGATGGTTGCAAAAACGGTTTACTCAGAGAACGACTTAGAGCACGGTATAACCATCCAATCATCCAGAAATCAAAGCATGTTATTATAAGCTTTGCCTCCTTATTTATCTCCAAGACAAAACATGAAACCTTAACTTAATACTACAATGACTAAACAGGTTTAGTTCCCCCAGTAAGACTAGATCAAGTATAGCTAAAATAACTATAGATATACAGCATTGCATGGCTCGACAatagcctcgtccccaggctacTCTCGATCAGCTCTACTCATTCggattcaaaatggcggtttCAAAATGGCATTTTTCTGAGTTGCAAGAGAATCAAAAGGTGATGTCATAAAAAGGCCACGCAGCCATGAGACGCCTCCTGGGAACCAGCTAGAGGAACTTGTGCCAGCATTGATGCTGGGTGATGTTTGTGCTATTGCAAAAATACCTGTCTCAAATATCTGCTGGAATTatttaattatatttattattatcgtaTAATCATTATTTCCTTAATGAGCAGGAGCACTAGGGAGCGTAACTTCACTTCTGTAAGAGTTCAGAGTTGCAGAAGGTTCGAGAAAGACTTGAAAAAGCTAGACTTTCACAGCTTTTCTTTGGTATAATTTGGAAGGTTCCTATAATAGAAATAAGCAGTGTATACCCCGCCAAAGAGAACAGAGAAAATGAATGTCAACGTTACATTGTACCTTTCAAAATATACCAAAGCTTTCTGTAAAGATCTCTTACTGTAAAACAACAAGATTTCGAccattattttcttaaattgcCCGAAGTTCGAAAATAATCTGTCTCTGGAAAGACACAAAAGTGGATACTGGATTGGAAAATTTTTAAATCTTCAAGAAATGAACTATTGAGAATGCTCATTCTAGCATCGGTGCTGAGAAATAAGCAGTGTATACCCCGCCAAAGAGAACAGAGAAAATGAATGTCAACGTTACATTGTACCTTTCAAAATATACCAAAGCTTTCTGTAAAGATCTCTTACTGTAAAACAACAAGATTTCGAccattattttcttaaattgcCCGAAGTTCGAAAATAATCTGTCTCTGGAAAGACACAAAAGTGGATACTGGATTGGAAAATTTTTAAATCTTCAAGAAATGAACTATTGAGAATGCTCATTCTAGCATCGGTGCTGAGCTTTAAATcaatttaatttaaaaataatgtaTTTGCCCTTCGGAAGGTGGGCGTATTACTACTGTACAAAATAACAACTGCTGGTCACTGTACAAAATAACTGTTGGCtactgtacaaaaaaacaactgAGGCTA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P81192	Homeobox protein Hox-A4 (Fragment) OS=Lineus sanguineus OX=187800 GN=HOXA4 PE=3 SV=1
P09634	Homeobox protein Hox-A7 (Fragment) OS=Rattus norvegicus OX=10116 GN=Hoxa7 PE=3 SV=1
P02830	Homeobox protein Hox-A7 OS=Mus musculus OX=10090 GN=Hoxa7 PE=2 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000051 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00046 all species →	Homeodomain	Homeodomain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR017970 all species →	Conserved_site	Homeobox, conserved site	Interproscan
IPR009057 all species →	Homologous_superfamily	Homeobox-like domain superfamily	Interproscan
IPR001356 all species →	Domain	Homeobox domain	Interproscan
IPR020479 all species →	Domain	Homeobox domain, metazoa	Interproscan
IPR046327 all species →	Family	Homeobox protein Hox-A1/B1/D1	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45946 all species →	HOMEOBOX PROTEIN ROUGH-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000981 all species →	Molecular Function	DNA-binding transcription factor activity, RNA polymerase II-specific	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0000978 all species →	Molecular Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	Interproscan
GO:0003700 all species →	Molecular Function	DNA-binding transcription factor activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:0043565 all species →	Molecular Function	sequence-specific DNA 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

No KEGG orthology assignment for XP_001634252.2.

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

Expression pattern (RNA-seq)

Transcript abundance of XP_001634252.2 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

27TPM > 0

16Conditions

1.3Max TPM

0.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole 6 week old aboral regenerate · regenerate 96hpa	3	1	0.16	0.48
whole 6 week old aboral regenerate · regenerate 144hpa	3	3	0.43	0.52
whole 6 week old aboral regenerate · regenerate 0hpa	3	2	0.14	0.23
whole 6 week old aboral regenerate · regenerate 2hpa	3	1	0.14	0.42
whole 6 week old aboral regenerate · regenerate uncut	3	3	0.24	0.40
whole 6 week old aboral regenerate · regenerate 4hpa	3	1	0.04	0.12
whole 6 week old aboral regenerate · regenerate 120hpa	3	2	0.41	0.72
whole 6 week old aboral regenerate · regenerate 36hpa	3	2	0.22	0.46
whole 6 week old aboral regenerate · regenerate 24hpa	3	1	0.10	0.29
whole 6 week old aboral regenerate · regenerate 20hpa	3	1	0.03	0.09
whole 6 week old aboral regenerate · regenerate 16hpa	3	2	0.16	0.24
whole 6 week old aboral regenerate · regenerate 72hpa	3	2	0.40	0.86
whole 6 week old aboral regenerate · regenerate 60hpa	3	3	0.87	1.26
whole 6 week old aboral regenerate · regenerate 48hpa	3	1	0.20	0.59
whole 6 week old aboral regenerate · regenerate 8hpa	3	1	0.04	0.13
whole 6 week old aboral regenerate · regenerate 12hpa	3	1	0.03	0.10

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	0.48
SRR6320837	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	0.00
SRR6320863	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	0.00
SRR6320847	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	0.52
SRR6320838	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	0.43
SRR6320841	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	0.34
SRR6320840	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	0.23
SRR6320846	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	0.19
SRR6320839	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	0.00
SRR6320861	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	0.42
SRR6320842	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	0.00
SRR6320848	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	0.00
SRR6320844	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	0.40
SRR6320843	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	0.25
SRR6320845	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	0.08
SRR6320872	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	0.12
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	0.72
SRR6320883	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	0.50
SRR6320850	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	0.00
SRR6320851	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	0.46
SRR6320852	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	0.21
SRR6320855	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	0.00
SRR6320854	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	0.29
SRR6320853	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	0.00
SRR6320856	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	0.00
SRR6320857	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	0.09
SRR6320859	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	0.00
SRR6320860	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	0.24
SRR6320880	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	0.23
SRR6320858	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	0.00
SRR6320865	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	0.86
SRR6320862	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	0.35
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	1.26
SRR6320866	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	0.74
SRR6320867	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	0.62
SRR6320870	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	0.59
SRR6320868	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	0.00
SRR6320871	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	0.13
SRR6320875	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	0.00
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	0.10
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.