Gene detail

Detailed information of ANN35059-RA in Leptoseris scabra

Genomic Location: Scaffold_218__1_contigs__length_43989:10378...16436
NR annotation: WP_054552507.1, family 20 glycosylhydrolase [Pseudoalteromonas lipolytica]
Species Leptoseris scabra · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

ANN35059-RA

ATGCTTGCAACTGCCCCTTTAATGGCAAGTGCAGCATTAACTCAATCGCAAGTTGATCAGTTTGCGAAAGGCACCGAACTGCTGTTTTCGGTTGAAGATAACTTTCGTAATAAAGATGCGGGCTTTTTAGGAAAAATTACCCTTAATAATGGCTCTGATGTGGCGTTACCTACGGGCGAAAGTGACTGGCAGCTTTATATTCACTCAGTTCGTAAAATCTCAACTGAGTATGTTGCGGGGCTAAACATTGAGCACGTTAATGGTGACCTCCATCGCATCGTACCAACGAGCGAATTTAAAGGTTTAGCTGCAGGTGAAAGCTTAGAGTTGCCGTTCGATGCGCAAGTGTGGATTGTTGCTTACAGTGACTTTATGCCACGGGCATTTTTTGTTTCGGGTAAGAATAAACCAGCCGTATTTGCTAATACCGACACAGAAGACTTTAAACAGTTTGTGACGCCATTTACCCGTGAGAATCAGTTACGCCGTTACAATGAGCCAAAAGATTTATCGGTTTTAGCAACGGCAAAAGTACGCTTCGAGCGTAATAGCACAGATAAGGTGTCGATCAGTAAAGAGGATGCTTTAAAGCGTATTATTCCTAAGCCTCGTAAAGTCGATTTTAATCGTGGTAGCGCAACGTTAAACAATAATTGGCAAATCAGTTATCAAGGCCAGCTTAAGCACGAAGTTATGGTGTTTATGCAAGACTTACAAGATGACTATGGCATTAGCCTTAAAGCACAGCCTGATCATATCAATGTCGGCAAAGACAAAGTAATACGCTTAAAAGTTGACCCTAAACTCAATAATGCAAAAGCTGAAAGCTACACTCTAGAGATTGATGATGAAGTGATCACCATTGTAGGTAGCGATAACGCCGGTGTGTTTTATGCGATGCAAAGCTTATTAAACCTCATTCCTGCAAATAGCCAAGGCAGTGCCAGCTTACCGCAGTTAGAACTTGAAGACTCACCGCGCTATGGTTGGCGTGGTATGCATTACGATAATGGTCGTAACTATCATGGCAAAGAAGCAATGTTCAAGCTGGTTGAGCAAATGGCTCGCTATAAAATGAATAAGCTACACTGGCACTTTTCAGAAGATGAAGGTTGGCGACTTGAGATCCCAGGTCTACCAGAGCTTACCGACGTTGGCGGCTATCGCTGCTTTGATTTAGAAGAGCGCGAGTGCTTATTAACTCAGCTTGGCACAGGGCCATTTAAATCAGGCTCTGGCAACGGTTATTTGAAACGTGATGAGTTTGTTGAGCTATTAAAGTTTGCGAAAGACCGCCACATTCAAATCATCCCTGAAGTTGAAGGGCCAGGCCATGCGCGTGCCTCAATCAAAGCGATGGAAGCGCGTTATCACAACATGTTAGAAGAAGCTGAGAAAGCCGCTAAAAACAACATTAAAACGCGCTCTGCAAACAAAGAAATTCAACACATAGATATGGGACCAGCAACGCAATACTTGCTTACCGATCCTAAAGATACCTCTGTGTACATGACGGTACAAAACTACAAAGATAACTCAATGAATGTGTGTATGGACTCTACCTACGCATTTTTAGATAAAGTAACTTATGAACTTCAGCAGATGTACCGCGAAGCAGGTGTGCAGTTAAAGAACTTGCATATTGGTGGTGATGAAGTTGGTGCTGGTTCGTGGATAGGCTCGCCAATCTGTCAGGCGTTATTTGCTGATCCTAATAACGGTGTAGCTGGCCCGGCTGATTTAAAACCTTATTTCACACAACGTGTTGCTACCTTACTTGAAAAACGCGGTATTTCTCCGGGTATTTGGGAAGATGGCATCATGTATGACCGCGAAAATTCGTTTAAACGTGATGAGTTCCCTAATAAAACCTTTACCGTTAATACTTGGGATAACATTTGGGAATGGGGCGTTGCCGATAGAGCATACCGCCTAGCAAATGCCGGTTACCAAGTGGTGTTATCACACGGTACGCATTTGTACTTTGACCACCCATACGAAGCAAGCCCTGAAGAGCGCGGTTATTACTGGGCAACTCGTTACACAGATACTAAAAAGGCCTTTAACTATATGCCTGATGACGTGTATGCCAATGCTGATTACACCCGCACTCGTGAGCCAATTGTTAATTTAGAAGCGTTGGTGGGCCGCCCGTTACCTAAACTTGAAAAGCCAGAGAACATTCTGGGTATGCAAGGACAGGTATGGTCAGAAACAATCCGTACTGAAGAGCAAGTATTAGCAATGATCTTCCCGCGTATTTTGTCAGTGGCAGAGCGTGCTTGGCATAAAGCCGATTGGGAAGGCGAAAGTGTCGATATTAAAAAACAAGCAAAAGACTGGGCTGAGTTCTCAAGTGCAGTCGGTTTAAAAGAGCTTGAGAAACTAGCTAAAGATGGCATCAATCTGCATTTACCAGTACCTGGCGGTGTGATTGAAAATGGTAAGTTGTATGCCAACAGCGCATTTGCTTATTTGAGCATTGAATACAGTCTAGACAACGGCCAAAGCTGGCAAACTTATGCCGAGCCTGTGAAGGTTGATAACAATACAAAAGTTGCGCTACGCACCCGCTTAAACGCACAGCAAACCAGCCGCGTGACCGTTGTGGACATATTGAACCACAGAGAACACAGAGGCGCTGCGCGCTACACAGAGAAACCAAATTATCACAATGAGGCTATCACCTTTTCAGGCATCGCTGATTATTTTCTCGTTTTATATCGCGGTAACTTTTACGGCTTTACCTTCGGCGATGATCATCAGAAAGGTAAAGAGCTTAGCCAAACTGATATTGATGCCATGGCTAATGGCTTAATTTTACCGTATTTAGGGATGGCTATTTTTATTGGTATACTCGGCTTTGCGGTAACTAAAATGCCATTGCCAGAGTTAATTGATGACGACGTTGATGAACAGAAACCGGGGCAGGTAAAAGAAGCATTAAGCCATCCGAGTCTTGCCTTAGGGATAGTGGCACTTTTTGTTTATGTAGCTGTTGAAGTAATTGCCGGCGATACCATTGGTAGCTTTGCGTTGTCGTTAGGTATTGAAAAATACAGTGTTATGACATCGTACACCATGGGGTGTATGGTACTAGGTTACTTTTTAGGGATTTTACTTATCCCTCGTGTGTTATCACAACAAACAGCACTAACTATTTCAGCGGTATTGGGCTGTGTGTTAACGCTAGCGATAGTTACAGGTAGCAATGAAACTGTATTTATATCAACATTGTTTGGCCTAAAATCGGTACTGCCTGATACCTTATTGCTCATTGCTGTGCTAGGCTTTGCTAATGCGATTGTTTGGCCTGCAGTTTGGCCGTTAGCATTATCTGGTTTAGGAGAGAATATGGATACTATAATGAACTGGATCAATGAGAATTCAGGTTTAATCATACATTACGCCGTTCAGGCTGTTCTTGCGCTAATCATTTTCTTCATCGGTGGTCGTATCGCAAAATTTTGCGAAGGGATGACTGAAAAAGCATTTGATAAAAAGAAAGTAGACAAAGCCGTAGGTTCATTTGTAGCAAGCATTGTTTATGCTATTGTTTTTGCAGCAACTATCTTAATGGCACTATCTCAACTTGGCATTGAGACAACATCATTCATTGCTATTTTAGGTGCGGCTGGTTTAGCTGTAGGTCTAGCACTTCAAGGTTCACTGTCTAACTTTGCTTCAGGTGTTTTAATCATCCTACTTCGCCCTTTCAAATCAGGTGACTATGTAGAAGCCGGTGGTAAAGCGGGTACTGTTAAGAAAATCGAAATTTTCTCTACAGAATTACGTACACCAGATAATAAAGTAATTATCATGCCTAACTCATCAATCATGGGCAGCCCAATTACAAACTTCTCTCGTGAATCAACTCGTCGTATCGATTTAGTAATTGGTGTGGGTTACGATGCAGACCTTAAAGAAGCAAAAGCAGTTCTTAAATCAGTATTAGATAAAGAAACTCGTTTATTAAAAGATCCAGCATACACAGTCGCTGTATCTGAGCTTGCAGATTCAAGTGTGAACTTTGTAGTTCGCCCGTGGGTTAATTCATCAGATTATTGGCCAACGTATTTCGATCTAATGGAAAACATTAAGATCGCATTAGATGACGCAAATATCACGATCCCATTCCCGCAAATGGATGTTCATTTGCATAAAGAAGATTAA

Transcript

ANN35059-RA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q04786	Beta-hexosaminidase OS=Vibrio vulnificus OX=672 GN=hex PE=3 SV=1
P13670	N,N'-diacetylchitobiase OS=Vibrio harveyi OX=669 GN=chb PE=1 SV=1
Q54468	Chitobiase OS=Serratia marcescens OX=615 GN=chb PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000971 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF21082 all species →	MS_channel_3rd	Mechanosensitive ion channel MscS, C-terminal	Domain	Interproscan
PF03174 all species →	CHB_HEX_C	Chitobiase/beta-hexosaminidase C-terminal domain	Domain	Interproscan
PF00924 all species →	MS_channel_2nd	Mechanosensitive ion channel, beta-domain	Domain	Interproscan
PF02838 all species →	Glyco_hydro_20b	Glycosyl hydrolase family 20, domain 2	Domain	Interproscan
PF21088 all species →	MS_channel_1st	Mechanosensitive ion channel, transmembrane helices 2/3	Domain	Interproscan
PF05552 all species →	MS_channel_1st_1	Mechanosensitive ion channel, conserved TM helix	Family	Interproscan
PF00728 all species →	Glyco_hydro_20	Glycosyl hydrolase family 20, catalytic domain	Domain	Interproscan
PF03173 all species →	CHB_HEX	Putative carbohydrate binding domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR049278 all species →	Domain	Mechanosensitive ion channel MscS, C-terminal domain	Interproscan
IPR025705 all species →	Family	Beta-hexosaminidase	Interproscan
IPR004867 all species →	Domain	Chitobiase C-terminal domain	Interproscan
IPR008965 all species →	Homologous_superfamily	CBM2/CBM3, carbohydrate-binding domain superfamily	Interproscan
IPR011066 all species →	Homologous_superfamily	Mechanosensitive ion channel MscS, C-terminal domain superfamily	Interproscan
IPR029018 all species →	Homologous_superfamily	Beta-hexosaminidase-like, domain 2	Interproscan
IPR023408 all species →	Homologous_superfamily	Mechanosensitive ion channel MscS, beta-domain superfamily	Interproscan
IPR013783 all species →	Homologous_superfamily	Immunoglobulin-like fold	Interproscan
IPR006685 all species →	Domain	Mechanosensitive ion channel MscS	Interproscan
IPR015882 all species →	Domain	Beta-hexosaminidase, bacterial type, N-terminal	Interproscan
IPR049142 all species →	Domain	Mechanosensitive ion channel, transmembrane helices 2/3	Interproscan
IPR010920 all species →	Homologous_superfamily	LSM domain superfamily	Interproscan
IPR036259 all species →	Homologous_superfamily	MFS transporter superfamily	Interproscan
IPR011014 all species →	Homologous_superfamily	Mechanosensitive ion channel MscS, transmembrane-2	Interproscan
IPR004866 all species →	Domain	Chitobiase/beta-hexosaminidases, N-terminal domain	Interproscan
IPR008910 all species →	Repeat	Mechanosensitive ion channel, conserved TM helix	Interproscan
IPR014756 all species →	Homologous_superfamily	Immunoglobulin E-set	Interproscan
IPR012291 all species →	Homologous_superfamily	CBM2, carbohydrate-binding domain superfamily	Interproscan
IPR017853 all species →	Homologous_superfamily	Glycoside hydrolase superfamily	Interproscan
IPR015883 all species →	Domain	Glycoside hydrolase family 20, catalytic domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR22600 all species →	BETA-HEXOSAMINIDASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004563 all species →	Molecular Function	beta-N-acetylhexosaminidase activity	Interproscan
GO:0005975 all species →	Biological Process	carbohydrate metabolic process	Interproscan
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0030203 all species →	Biological Process	glycosaminoglycan metabolic process	Interproscan
GO:0030246 all species →	Molecular Function	carbohydrate binding	Interproscan
GO:0055085 all species →	Biological Process	transmembrane transport	Interproscan
GO:0004553 all species →	Molecular Function	hydrolase activity, hydrolyzing O-glycosyl compounds	Interproscan
GO:0030247 all species →	Molecular Function	polysaccharide 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 ANN35059-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 →