Gene detail

Detailed information of ANN04181-RA in Leptoseris scabra

Genomic Location: Scaffold_5__1_contigs__length_58733080:12760851...12791811
NR annotation: XP_044173451.1, uncharacterized protein LOC114961836 [Acropora millepora]
Species Leptoseris scabra · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

ANN04181-RA

ATGCACTGGATTTTTCTTGGCGTTGCCCTCGCCTTGAGTTGGAACCTTGAGTTTTCACGCGGCTCAGAGGTTCGCGTTCGTCTTGTTGGGGGAAAGCACAGCTACGAAGGACGAATCGAGGTGTATTACAAGGACGAGTGGAGAGCAGTTTGTGATCACAAATGGGACAGGAGGGCAGCCAGAGTGGTTTGCCGAATGCTTGGATATCCTGATTTGTTACGTTTCACAAAAGGGCATCACGCATATGGTCGAGGAAATGGCAAATTCTGGCTGGATGACGTCAAATGTACTGGAGAGGAAGAATCAATTGACAAATGCTCTCACAGGCCTTGGGGCAAAAACAACTGCCTACCGTACAATCAAGCAGGAGTAGTCTGTAGAAGGCATTTGAGCGACCTGGCTATTGAACCGGAGCCTTCAGGAGCCAGCGGCGAGGTTCGAAAAGTCAATGTAAGGTTACTGGGCCCAGTTGTAGATGACTACATATCGGAGGGTATTGTCCAACTGGAACACGAAGGAAAGTGGGGTTACATTTGCCCTTCTAACTGGACACCTGTCAACTCCTACGTGTTGTGCGGTCAGCTTGGATTCCCAAACACAGAGGAACAGGATTCGTATTCAGAGACAATACAGGACGTGGAGCCCGTCTATTGGCTGGATCAAGTGACGTGTAAAGGATGGGCGTCGTCCATCGTGTCATGTGACCATGCGGGGTGGGGCCGTCACCAGTGCGATGATTCTCGCGTGTTGAAGATTAAATGCGTTCGGAGACAAATTCTAAAGCCTCTGGACGTAAGACTACGAAGCGGGGCCTTGGTGTCCGAGGGTCGAGTGGAGGTGGAATATCAAGGCTACTGGGGTACCATCTGTGACGATCACTGGACACTGAGAGAGGCTAATGTCGTCTGCAGGTCACTGGGTTATGGGTCAGCGGCTATGGCAGCCACAAACGCGTACTACGGGAGAGGAATGGGAAGGGTCTTCTTAGACGAAGTCACCTGCGAGGGAAGAGAGAAGGATATCAGGCAGTGCAAGCACAGCGGCTGGCGCAGATCAAACTGTAACAACCACGAAGATGCTAGTGTCAGATGTCACGTGCCACCGCTTCAGGGTCACCAGATTAGAATCCAGGGGGGTGCAAATCCCAGGGAGGGTCGAGTTGAAGTGTTTCATGATGGTAAATGGGGAACAGTCTGTGGGGATGGATGGGGAATCGAGGAAGCAATGACAGTCTGCCGACAGCTCAATCTTGGGTATGCGGGAAAAGCTGTTACACAAAAGAACTTCAGCGAAACAGATCTCGAGGTGATGATGTCTGGCGTACGATGCCGCGTCGACGAGATCTCCCTTTACAACTGTCGCCATGACGAATGGACAAATGCCACATGTAGCAGTATGGACAACTTAGCCGGGGTTGTTTGCGTTAATGCTTTACCTGATCTTGTACTCGACACCGATATGCTCAAACGCTACATGGAGATGAATAGAGTTGCCTTACGCTACCTGCAATGTGCTTTTGAGGAGAACTGTCTGTCTGCTAGTGCTGCAGAGGAGATGAGGCATTCAGTATGGCATCAACGGCGACTACTTCGTTTTAGCGTTAAGGTTGAGAATCGGGGGTTAGATCATTTCAGACCATCTGCAGACAAGTCGAGCTGGGAATGGCACAGCTGCCACAAGCACTTCCACTCCATGGAGTCTTTCTCCACTTATGATCTTATTCGTCAAAGGAGCGGCAAAAAGGTCGCCGAGGGTCATAAGGCCAGTTTCTGTCTGGAGGACACCAAGTGTGATCCTGGATTTGAACAGGTTTGGAACTGTACTGATAAAGGAGATCAAGGAATATCACCCGGATGTTTTGATATTTATCATTACAATATCGACTGCCAGTGGGTTGATGCTTCGGACTTCATGCATGGCTCGTTTGTTCTCAGGGTGCACGTTAACCCTGGGAATCAAGTGGCCGAGTCGGACTTCAAGAACAACGTTGGAAAGTGCTCTTTGTATGATTACGGACGCTACGTTATTGTCATCAGGTGTTGGATTGATAACTGCGACAGTGGAATAGAAACGCGTGGCGGAAACGCTGGTGCAAATTGCTGCGTTTTTCCGTTTCTGTACAATGGCAAGCTCTATCACGACTGTACCACAGATGGTTACAAAGGTCAAGATTTGTCACGGGCGAAAAGACTGAGTGGCATTCTAGAGTTTTGGATCCCGGTGGAAACAAATCGCATCTTAATGCTGCGCTTTCTCCTACCTGTTGCTCTTTTGCTGGGCATGCGTATCACAAGTGGTTCAGAGGTTCGACTCGTCGGAGGAAAGCACTATTATGAAGGGAGAGTCGAAGTGAAATATGACGGCGAATGGAGAGCGATTTGTGATCACAGATGGAATTTGAAAGCAGCCAATGTTATTTGTCGCATGTTAGGATTCCCCGATGCTCTTCGCTATACCACTGGACATAAACCATTTGGTCGAGGAAACGGTAAATTTTGGTTAGATGATGTCAGGTGCGGAGGCAGAGAATACGACATTGAGCGCTGCTCCCATAGAGACTGGGGCCGACACAACTGCCATTCAATCAATCAGGCTGGAGTCATCTGCAAGCTGCACCGGAGTGACGTCGTCTGTGAGCCTGAGCCATCACGAGCCAGCGGTGAGGTTATTAAGGCGAACTTAAGGTTACTTGGTACGATTAAAGATGACTACATATCGGAGGGTATTGTCCAAGTGAAACACGAAGGAACTTGGGGTTACATTTGCCCTACTAACTGGATAGCAATGAACTCCTACGTTTTGTGTGGTCAGCTTGGATTCCCAAACACAGAGGAACTGGAGTCGTATTCAGAAACAATACGTGACGTGAGAGCCGTCTATTGGCTGGATCAAGTGACGTGTAAAGGATGGGAATCATCCATCGTGTCATGTGACCATGCGGGGTGGGGCCGTCAACAGTGCGAGGGTGGAAAAGCTGTGAGGATAAAATGTACGCGCAAGGAAAAGACACAAATGCCTTCAGAGGTAAGACTCCGCAGTGGAGCCTTGGTATCTGAAGGGCGAGTGGAGGTAAAGCAGCAGGACACCTGGGGTACCATATGTGATGATCACTGGACCCTGAGAGAGGCTAATGTCGTCTGCAGGTCACTGGGGTATGGGTCAGCGGGTATGGCAGCAAAGAATGCGTACTTCGGAAGAGGGGTTGGAGAGGTCATGTTACATGACGTGCGTTGTCAAGGTTCTGAAAGAAGTATCGGTCAATGTACACACAAAGGATGGCGAAGTTCTGGCTGCAATCATTACGAAGACGCTTCAGTTAGATGTCATGTACCACAGTTACAAGGCCATAAGATTCGTCTCAGCGGTGGTGCAAATGACTACGAGGGCCGAGTTGAAGTGTTTCACGATGGCAGATGGGGAACAGTTTGCGCTGATAGCTGGGGAATAGAGAATGCCATGGTGGTGTGTCGACAGTTGAACCTTGGATATGCCAGCCATGCTGTCATGCAGAACTACTTCGGTGGAACAAACCTTAGGGTTGTCATGTCGGGTGTGACATGCCGGGTAGATGAGATCTCCATCTTCAACTGTCAACGCGATATATGGGAGAATGCCACGTGCAGCAGCAGGCATAAGTTAGCTGGAGTTATTTGTGATGATGCATTGCCGGACCTGATTATTGACACCGCTGCACTTCGGAAAGAAATTCAACTGGAGAACAAGATGCTGCACGACCTGAGATGCGCGTACGAAGAAAAGTGTCTCGCAAAAAGCGCAGATGTGCTCTTCAAGTCTCGTAGATCAAGACATTATTACCGAAAACTGTTGAGGTTTACAACAAAGATTGAAAACAGAGGATGGGACGACTTCCGGCCGAACTCTCCCAGACCAAGCTGGAATTACCACAGGTGTCATGCGCATTACCATTCTATGGAGACTTTTGCTAGCTATGATTTGCTCCAAAAAGATTACTCGGTTATTCGGGCAGAAGGTCACAAGGCCAGCTTCTGTTTGGAGGACACAAAGTGTGATCCGGGGTTTGAGAAGAGGTGGAATTGCACCAGAGGAGGTGACCAAGGCATATCTCCCGGATGTTTCGATATCTACAGCTCTAAGATTGATTGCCAGTGGATTGATTTTACCGACATCCGAAGACTTGACTCATTTGTCCTTCGTGTCCACCTCAATCCTGGGAACCAAGTCAGCGAGTCTGATTTCAGGAACAACATTGCTAAGTGCAGAGTGATTTACTACGGGAGATTTGTAATTTCTGACGCATGCTGGATCGAACTTAGGGCCTGCTTACAAGGAGGGAGGAGAACTGCGAGAGTGGGGTGGATACTCATGGTGGAAATTCTACCGGGGCATGCTGCGTGTTTCCGTTCAAGTACAATGGCAAACTGTATCATTCCTGTACCACCGATGGATATGAAAAGAAATGGTGCTCAACAACAGACAATTTCTCCAAAGATAAGAAGTGGGGACTTTGTTTTGATTAGCTCAGTGCGTGAGCCGTGGTCAGGGTTTTGTTTTAGCAACTTTGGGATGATGCCTCAGATACGGCAGAGCCTTAGGGGCTGTTCACATGGAGGGAGAAAGATCCTAGCACTAGGAAGATCCTAG

Transcript

ANN04181-RA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P58022	Lysyl oxidase homolog 2 OS=Mus musculus OX=10090 GN=Loxl2 PE=1 SV=2
B5DF27	Lysyl oxidase homolog 2 OS=Rattus norvegicus OX=10116 GN=Loxl2 PE=2 SV=2
Q5RFQ6	Lysyl oxidase homolog 2 OS=Pongo abelii OX=9601 GN=LOXL2 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000074 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01186 all species →	Lysyl_oxidase	Lysyl oxidase	Family	Interproscan
PF00530 all species →	SRCR	Scavenger receptor cysteine-rich domain	Domain	Interproscan
PF00040 all species →	fn2	Fibronectin type II domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001190 all species →	Domain	SRCR domain	Interproscan
IPR036772 all species →	Homologous_superfamily	SRCR-like domain superfamily	Interproscan
IPR050912 all species →	Family	Lysyl oxidase-like protein	Interproscan
IPR036943 all species →	Homologous_superfamily	Fibronectin type II domain superfamily	Interproscan
IPR017448 all species →	Domain	SRCR-like domain	Interproscan
IPR013806 all species →	Homologous_superfamily	Kringle-like fold	Interproscan
IPR000562 all species →	Domain	Fibronectin type II domain	Interproscan
IPR001695 all species →	Family	Lysyl oxidase	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45817 all species →	LYSYL OXIDASE-LIKE-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0004720 all species →	Molecular Function	protein-lysine 6-oxidase activity	Interproscan
GO:0005615 all species →	Cellular Component	extracellular space	Interproscan
GO:0018057 all species →	Biological Process	peptidyl-lysine oxidation	Interproscan
GO:0005507 all species →	Molecular Function	copper ion binding	Interproscan
GO:0016641 all species →	Molecular Function	oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor	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 ANN04181-RA.

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

Co-expression network

Genes whose expression across the transcriptome samples of Leptoseris scabra tracks this one. Counts are over the whole network; the network view itself draws at most 100 partners per query gene (CNIDO_NET_TOP_K), so a hub gene can show fewer edges than the number below.

No co-expression network has been built for this species, so this gene has no partners to show. Networks are available for the species listed on the Network Analysis page.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Leptoseris scabra, and in which cell types it is a marker. Expression is stored per cell, so the violin plot and the cell-type means are computed in the viewer — open a dataset to see them.

No single-cell dataset has been published for this species. The atlases that do exist are listed in the Cell Atlas.

Epigenetic marks

Chromatin and DNA-methylation data covering this gene. Peak calls are listed per sample with the genomic region the peak falls in; DNA methylation is listed as sample availability only, because those tables are queried by the DNA Methylation page itself.

No epigenomic data has been deposited for this species. The assays that exist across the site are described in the Epigenomic Data module.

What you can do with this gene

Every tool below opens with this gene already entered, so you land on the analysis rather than on an empty form. Links open in a new tab.

Analysis	What it does	Status
Primer design	Design PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.	template found	open →
BLAST	Search this gene’s sequence against the CnidoSite BLAST databases. The query is filled in and the species’ database is preselected — press Run to start.	template found	open →
Expression heatmap	Draw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it.	no expression matrix	–
Gene family / orthogroup	Look this gene up in the single-copy orthogroups built from the high-quality cnidarian genomes, and see which other species carry an orthologue.		open →
Gene set analysis	Start a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.		open →