Gene detail

Detailed information of XP_001637680.2 in Nematostella vectensis

Genomic Location: NC_064038.1:10789786...10793220
NR annotation: XP_001637680.2, lysM and putative peptidoglycan-binding domain-containing protein 3 [Nematostella vectensis]
Species Nematostella vectensis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_001637630.3

gcAAGTACATATAAAATATGTAAGTCATTTATGGTTCAGAGATATAAGATTATTATTGTGTAAGGTTATAACAGTACTTATAAGCTTATAAAAACCTAGAATTAAAGAACATGTTAGCCTTTAGACCCCCGTTTAATAAGAACTAGTTTagtataataattataataatttattaatttatattgcgcttttttcatataatgATCAAAAGCGCATTACAATATAACTAAATGTTGAACtaatatatacaataaaatttacaattataatcgaaaataatatgaaataatAGATTCATaggaaaaatattgaataaaaaataaaataataaaaataaaaatatctttatattGATGATTATGTGATATCAAGTGTTAAAAGCTAATTTAAAAAGATGAGTCTTAAGTTGCGCTTTAAAATTAAAGATACTGCAATTGATGGTGCGAAGATTTGCAGGGAGAGCGTTCCATAATGTAGGTGCAGCAACACTAAACGATCTGTCACCGAAAGACTTCATCATTTTTCCTGGGGGATGCATTTAGCCTAAAATTTGAAACAGGTTCTTGCTAGTATTGACATTTCATCAATCTAGATACCCCACTTCTACCAGCCATTACTatataaacttttcttttaaattaagAACCTATTGAAGAACCTAAGAAGCCTTAAATTTAAAATAGTACCCGTTAAATAAGAACCTGTTTAGACTAACCTGGAAAAACCTAGGTTCTTATAAGTGGGTAAgtactttattattattgtaatcTAAAAAATGCTGTGATGATATAAAGTATACTGAGCCCGGTTTTTAAACCTTAGACAAAAACTTGTGTACTTCTTTCCATTAGTAATAATGTCTCGGTTATGATATTAGTCTAACTTGATAATTGGTTACAGTCCTGTTTGCTTTATTTCTTTAACGCTGacataaaatatttcttaaataCCTTTCTctccctttttttttagttttgcgAGACAAGTGGATGATTTTGTTGCTCAATGTCCAGGCCAGTTAGGCTTTTCGTTACAATAACCTTATGGACGCATGCCCCTAAAGCCCCATCTACAAtaacaatttttagttgacaactATGTTTGTCGGGATCTACACTAGCAATTTTTCATGTGTGACAATTTTGAATTGCCGAGAAAAAGCAAACCTGCTAGCTTTTGAGCAACTATAGTTGCCACATAAGGTTGTCCAATTTGCTCCAAATAAAAATTCTCACATAAAAATTGTCAACTAAAGCTTGTTAGTGTAGATGGGGCCTAAATAACTCCTAAGGTATGCCTATGGTGTTCACATTCTTTGAGGAACCCTGTATGGGACGAACCGGTAGAAAAgttagggggggaggggaaaaacaaaaaaagcgcaaggaaaaaatatagaaaataaaagacCGATCGAACATCAGTTTTCTACTTCAAGTCAAATTCTCATATCTGTTGATTGCTTCAAATTCCTGTCCCATGTTCACATTTTGGCAATCAAGTTATCATCTCCGCAAAAACAGGGCAAAATCTCATTGTTATGTGATGGTTTAAAACTTCCTTCACGTGATTTAAAGGAAGAACATATCGCACATTAAACAGGTTGTTCCACTGCTTATCGTTTTGCGTTATTTCCGTAACGGATTTGCGTAGCGTGACGCACAATTCCAAATATGGGCATTCACTTGGCCTGCGTACGCAACTAACCGCAAGAGTGACGTGTTACAAAATGGCGGAACTACTGCTGTTGCCGCATCGAAAACGATATCTTTAGAAATTCGCAGACTCCATCAAAAAATAAATCCGAGAGATCGATCTTGACAAGCGTACTGGTCGAGGATGTGAACTGTGTAAAGTGTGAGCCGAAATAGCATGAATAGACGTGGCAATTATACTAAGTATTCGGccttaaaatttgaaaatgaatcATTTGGAGAAGTTCAGAACAAAGCTGTTTCTAGAGTGTATGTCTTTGGGAATGATTCCTCCGAAGAGTTATCTTTGGATGACCAAGCAGTTGAGATGTCGGAGATACGGACTAGAGGAGGCAAGAAGGAATCAAAGCCTTACTCGGGGCAGGATCTCAAGAAAAGCTTTTTACTCGAGAGAGAAATACATGAGAACGACACACTACAATCTTTCGCGCTCAACTTTGGATGTACGATGGAAGAAATCAAAAGAGCCAACAATCTTTATTCCGAGCAGGACTTCCACGCACTACAGATGATAAAAATTCCTGTCCAACCCCATGGGCTTCTTGCTGAacaggaaaaagaaaacaaagagaagGGGAAAAAGACGAAGCAAAAACCACAACCCCTTGACCTAGAGGCAACAACAACTGCTAATGATAACAATGCAGAgtttgatgataatgatagccTCGTGAGAACAGTCAGTATTCGCTCTGCTCTGAACTCCCCATATAGTTTTCTTAAAAACATGGACGAAGacttaaaaaatatatgcaaAGGGTCATCACTACGCAAGGCAAATCTTGATCAAGTGGCACGGACATTAACAGTGAattgtatacaccccatacgATTGCAGACAGAAAAAAGGGACCTTGGGAATGTTTGGGGAATCGGATGGAAGTGGTTTGTGGTGCTCCTTGTTCTTGTTTGTATTGTCATTCCTGCGTTTATCGCTGCTTACTGGCTTTGGCCACATAAAAAGAGATAACAAATACAAAGACacagatttttaaaatttattatttcaatttCATTAGGTTGtctaaaatgtaaaaaagcaGAAACAATTCGCAGGGGGGGGGTAGTTGCATAAATAAGGGCATCGAGTTGAGATATCTTGTACAGTATCTTTTTAACAATTAAATTTTAGAATACTA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q7Z3D4	LysM and putative peptidoglycan-binding domain-containing protein 3 OS=Homo sapiens OX=9606 GN=LYSMD3 PE=1 SV=2
Q99LE3	LysM and putative peptidoglycan-binding domain-containing protein 3 OS=Mus musculus OX=10090 GN=Lysmd3 PE=2 SV=1
Q5M836	LysM and putative peptidoglycan-binding domain-containing protein 3 OS=Rattus norvegicus OX=10116 GN=Lysmd3 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0008427 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01476 all species →	LysM	LysM domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR018392 all species →	Domain	LysM domain	Interproscan
IPR045030 all species →	Family	LysM and putative peptidoglycan-binding domain-containing protein 1-4	Interproscan
IPR036779 all species →	Homologous_superfamily	LysM domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR20932 all species →	LYSM AND PUTATIVE PEPTIDOGLYCAN-BINDING DOMAIN-CONTAINING PROTEIN	Interproscan

Gene Ontology

No Gene Ontology signature was recorded for XP_001637680.2 in Nematostella vectensis.

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_001637680.2.

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

Expression pattern (RNA-seq)

Transcript abundance of XP_001637680.2 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

40TPM > 0

16Conditions

9.7Max TPM

3.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole 6 week old aboral regenerate · regenerate 96hpa	3	3	5.02	5.89
whole 6 week old aboral regenerate · regenerate 144hpa	3	3	3.29	4.10
whole 6 week old aboral regenerate · regenerate 0hpa	3	3	4.60	5.90
whole 6 week old aboral regenerate · regenerate 2hpa	3	3	4.73	5.71
whole 6 week old aboral regenerate · regenerate uncut	3	3	3.34	4.61
whole 6 week old aboral regenerate · regenerate 4hpa	3	1	1.74	5.22
whole 6 week old aboral regenerate · regenerate 120hpa	3	2	2.38	4.02
whole 6 week old aboral regenerate · regenerate 36hpa	3	3	4.46	5.15
whole 6 week old aboral regenerate · regenerate 24hpa	3	2	3.05	5.21
whole 6 week old aboral regenerate · regenerate 20hpa	3	3	5.35	6.75
whole 6 week old aboral regenerate · regenerate 16hpa	3	3	4.79	5.23
whole 6 week old aboral regenerate · regenerate 72hpa	3	2	2.97	5.07
whole 6 week old aboral regenerate · regenerate 60hpa	3	3	6.31	9.68
whole 6 week old aboral regenerate · regenerate 48hpa	3	2	2.93	4.81
whole 6 week old aboral regenerate · regenerate 8hpa	3	3	3.46	3.84
whole 6 week old aboral regenerate · regenerate 12hpa	3	1	1.49	4.47

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	5.89
SRR6320836	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	5.34
SRR6320837	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	3.82
SRR6320847	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	4.10
SRR6320841	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	2.96
SRR6320838	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	2.80
SRR6320846	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	5.90
SRR6320840	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	4.47
SRR6320839	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	3.43
SRR6320861	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	5.71
SRR6320848	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	4.52
SRR6320842	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	3.96
SRR6320843	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	4.61
SRR6320844	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	3.26
SRR6320845	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	2.14
SRR6320872	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	5.22
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	4.02
SRR6320883	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	3.13
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	5.15
SRR6320855	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	4.59
SRR6320852	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	3.66
SRR6320854	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	5.21
SRR6320853	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	3.92
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	6.75
SRR6320860	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	5.11
SRR6320857	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	4.20
SRR6320880	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	5.23
SRR6320858	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	4.93
SRR6320881	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	4.21
SRR6320862	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	5.07
SRR6320865	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	3.84
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	9.68
SRR6320867	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	4.66
SRR6320866	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	4.60
SRR6320870	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	4.81
SRR6320871	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	3.98
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	3.84
SRR6320875	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	3.35
SRR6320876	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	3.18
SRR6320877	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	4.47
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.