Gene detail

Detailed information of aflo_s0060.g53.t1 in Acropora florida

Genomic Location: sc0000060_pilon:1309920...1325233
NR annotation: XP_044168803.1, lethal(3)malignant brain tumor-like protein 3 [Acropora millepora]
Species Acropora florida · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

aflo_s0060.g53.t1

ATGCCTCCACCAGTCCAGGATGGGCCTTTGATGGGCAAATTTAAACTCAAAGGGAAAGGAGAAAAATATAAAGTTAAAGCAGCCAAACAGTTCATTGCATTAGAACCAGCTGACCTAATGAATGGCGAAGAAGTTCCATACGACTCCACCAAGCCATTTGTTTGGTCAGAATACCTCGCGGCTTGTGGGGCGAAAGCAGTTCCTAACATTGTTTTCAAACAGGAGAATCCATCATTGGACGTATTTCCCAAGCCAAACCACGCTTTTAGAAAGGATTACAAACTAGAATGCATTGACCCAAAGCACCCCTCCTACATCTGCGTGTGCACTATTGTGAAGGTGAAAGGAGCCCGACTTAGGATGCACTTTGATGGCTGGTCTGAGAGCTATGATTTCTGGACAAACTGGGATTCGCCTTTTATCTTTCCAATGGGCTGGTGCGAGAAGAACGGACAAGTCCTACATCCCCCGAGAAGTTTCAACAAACAAGAATTTAACTGGGAAAAGTATTTGAAGAAATGCGGCGCAAAGGCGGTTCCAGAACATTTATTCAAACCGGTTCATGTCACAGAGCACGGATTTAAAGTCGGCATGAAACTTGAAGCAGTGGATCGTAAAAACCCCGATCTAATATGTGTTGCCACGGTGACAAATGTGATTGGCAACCATTTCCTTGTTCACTTTGATGAATGGGATGATTCCTATGACTACTGGTGTCAGGACGATTGTCCTTATATCCACCCAGTGGGCTGGTGTGCAGAAAATGGAAAGAAACTGAACCCACCAAACGATGACGAGGTGTATACTTTTCAATGGGAGCAGTATCTGCGGGACACTGGAACCGTAGCGGCATCTCCTGATTTGTTTAAGAAGCGCCCCATGCCAAGTTTCAAGGCTGGAGAAAAATTAGAAGCTGTGGACAAGAGAAACCCCTCCCTTGTGCGTGCAGCCCGTGTCGCGAGCGTTGAGGAGTACAGAGTGAAGATACACTTTGATGGATGGGATGATATCTATGACGATTGGTTTGATGCAGACTCAAATGATTTGCACCCTGTGGGGTGGTGTGAGAAAACAGGACATCCTTTGGAGACCCCACTCACAACACGTGAGAAAATCTCCAGCGCGGCTTGTCCAACTCCTGGCTGTAAAGGAATCGGTCATGTGAAGGGTGCTAAGTATTCCACACATCACAGTACATTTGGCTGTCCTTACTCGCTACAAAACCTGAACAAAGACTCATGTCTTGTGGATCGACTCTCCAACAACTCTATGACTGAGGAATCTGATTGGTCCTACGCTTCCAAACAAAAGGCTACTGGGGGCAAGGAAGTAAAACCTGAAATTTTGCCCAGTCAAACAGTGGAGGGCGTGTGTCCCACCCCGGGATGTGATGGTTTGGGTCATGTGACGGGGCATTGGAAAACTCATTACACTTTGTCAGGTTGTCCAAACAACGAAGCAAACCAAGCCAAGGTTTTTTCAAAACACTCCTCCAAGTCACCTGTCGCAAAGAAAACCCCACACCTCTCCCCATTATCCTCTAGTCCTCCCTCCGTCAGTGGATCGCTGAAGAGCCCTGTTAGTGGCAGTATTATATCCACGAGGAGCTCAGTCAGGAAAGGATTTTTCAAGGAAGACAGACATTCTGGAGGTCCAAACAAATACGCAGACAAGGCAGTTCAACATGTCACACCCTTTGCATTTCCTTGGCCGCTGGGAAGTCAGTTTTCAATGATGGGTCTTAGTGAACTCAAAGCCGCCATTAATTCAGAAAACGATGGCGTTGCTTCCAGCGAGCGCCAGCGGATCATGAAATGGACCATTGATGACGTCATGAGTCACGTGAAATCCTTAGGATGCGTGGATCAGGCGAAAGTGTTCGGGGAAGAGCTTATTGATGGCGAAGCGTTTCTCCTCCTGACACAGAATGACATTGTTAACTTACTCAAAATCAAGCTTGGACCAGCCCTTAAGATATTTCACACCATCCCAAAGCATTGA

Transcript

aflo_s0060.g53.t1

CTGGGTGAAGAAGTGTAGTCTTCCATCTCATAAGTGAAAGCCATGAATGGACTGCTGCAGGAAGGTGGGTCCCTTGTTACGAGTACAATGGAGGAAAGCTATGAGCCGCAATCAAAGAGACACAAAGTGGAAAGTGATGGAGATGAACATCTAAATTCTCAAAGTCAGATTCCATCTGACAACATCGAGTTCGCTCCTGGTGAAATTACTATTGGGAATAACAGAGAGATTGAATCTGCAATGATGAATCACACTAATCCAAGCTCCAGTAATGACTTAAAATCGAGTGGTAAGGGTGTTGCTGCAAACCCAAGTGAGGCAGTAATTGCTATGGAGACCTCCGATACAGATGCAAAAACAAACAAACTGAAACAAACTAATAATAATATTGAAGACAGTAAAGATACTTCTGTAGATTCAACAGAGGCAACAGGTTTGAAGATCAAGAAAGAAAAGAAACCCCAATTTGAAGATGATGACCCATTTGCAGCTTTGGATTGGAATAATGGAATTGCCACTCTGCCAGGGAGCAACCTGAAATTCAAGTTGACAGAGTTTGGTACACTAGAGATAATAAGCACTGTGGAAACAGAGAAGGGTGAGATTACTTGGAGCACCCCAACTGAACATGGATGCAAATCTGCAAATGATGACACAAATAGCATTGTAAAGGAGTCACCAGGCATTGTTCTCACTAAGAAGGATGAAGGCAGAAGGAACAAGGGCAGAGAGTTTGTGCGCAAAGTCAAAACTTCAAGCGGCAAAATTATGAAAAAGAAAAAGAAAGGAAAAGGGAAGAAAATTTCAATGGCAGGAAAGACGGCCGGGTTGATAAGCAGTTCTATGCCTCCACCAGTCCAGGATGGGCCTTTGATGGGCAAATTTAAACTCAAAGGGAAAGGAGAAAAATATAAAGTTAAAGCAGCCAAACAGTTCATTGCATTAGAACCAGCTGACCTAATGAATGGCGAAGAAGTTCCATACGACTCCACCAAGCCATTTGTTTGGTCAGAATACCTCGCGGCTTGTGGGGCGAAAGCAGTTCCTAACATTGTTTTCAAACAGGAGAATCCATCATTGGACGTATTTCCCAAGCCAAACCACGCTTTTAGAAAGGATTACAAACTAGAATGCATTGACCCAAAGCACCCCTCCTACATCTGCGTGTGCACTATTGTGAAGGTGAAAGGAGCCCGACTTAGGATGCACTTTGATGGCTGGTCTGAGAGCTATGATTTCTGGACAAACTGGGATTCGCCTTTTATCTTTCCAATGGGCTGGTGCGAGAAGAACGGACAAGTCCTACATCCCCCGAGAAGTTTCAACAAACAAGAATTTAACTGGGAAAAGTATTTGAAGAAATGCGGCGCAAAGGCGGTTCCAGAACATTTATTCAAACCGGTTCATGTCACAGAGCACGGATTTAAAGTCGGCATGAAACTTGAAGCAGTGGATCGTAAAAACCCCGATCTAATATGTGTTGCCACGGTGACAAATGTGATTGGCAACCATTTCCTTGTTCACTTTGATGAATGGGATGATTCCTATGACTACTGGTGTCAGGACGATTGTCCTTATATCCACCCAGTGGGCTGGTGTGCAGAAAATGGAAAGAAACTGAACCCACCAAACGATGACGAGGTGTATACTTTTCAATGGGAGCAGTATCTGCGGGACACTGGAACCGTAGCGGCATCTCCTGATTTGTTTAAGAAGCGCCCCATGCCAAGTTTCAAGGCTGGAGAAAAATTAGAAGCTGTGGACAAGAGAAACCCCTCCCTTGTGCGTGCAGCCCGTGTCGCGAGCGTTGAGGAGTACAGAGTGAAGATACACTTTGATGGATGGGATGATATCTATGACGATTGGTTTGATGCAGACTCAAATGATTTGCACCCTGTGGGGTGGTGTGAGAAAACAGGACATCCTTTGGAGACCCCACTCACAACACGTGAGAAAATCTCCAGCGCGGCTTGTCCAACTCCTGGCTGTAAAGGAATCGGTCATGTGAAGGGTGCTAAGTATTCCACACATCACAGTACATTTGGCTGTCCTTACTCGCTACAAAACCTGAACAAAGACTCATGTCTTGTGGATCGACTCTCCAACAACTCTATGACTGAGGAATCTGATTGGTCCTACGCTTCCAAACAAAAGGCTACTGGGGGCAAGGAAGTAAAACCTGAAATTTTGCCCAGTCAAACAGTGGAGGGCGTGTGTCCCACCCCGGGATGTGATGGTTTGGGTCATGTGACGGGGCATTGGAAAACTCATTACACTTTGTCAGGTTGTCCAAACAACGAAGCAAACCAAGCCAAGGTTTTTTCAAAACACTCCTCCAAGTCACCTGTCGCAAAGAAAACCCCACACCTCTCCCCATTATCCTCTAGTCCTCCCTCCGTCAGTGGATCGCTGAAGAGCCCTGTTAGTGGCAGTATTATATCCACGAGGAGCTCAGTCAGGAAAGGATTTTTCAAGGAAGACAGACATTCTGGAGGTCCAAACAAATACGCAGACAAGGCAGTTCAACATGTCACACCCTTTGCATTTCCTTGGCCGCTGGGAAGTCAGTTTTCAATGATGGGTCTTAGTGAACTCAAAGCCGCCATTAATTCAGAAAACGATGGCGTTGCTTCCAGCGAGCGCCAGCGGATCATGAAATGGACCATTGATGACGTCATGAGTCACGTGAAATCCTTAGGATGCGTGGATCAGGCGAAAGTGTTCGGGGAAGAGCTTATTGATGGCGAAGCGTTTCTCCTCCTGACACAGAATGACATTGTTAACTTACTCAAAATCAAGCTTGGACCAGCCCTTAAGATATTTCACACCATCCCAAAGCATTGATGCCAGTAACAACTTTACCACTGTCGAATGGATAAGAATTTCAGTTTGGAAACTTTTAACTAATTTTTGGTCATTAACCTGAGTAATTAGCCAAAAGGTTGGGACGAACAAACCGAGAATTTGCTATGCAATGAGTTTCTATAGTTATATACCTGTAGGCGTCATGGAATCTTTTTTGTTAAAACTAGTTAAAAATCTTAATTTGGTAGCGCGCGCTTCCGAAATTCCTTGCATTCTAAAAAAGGTGAATTTGGTGAATTTCTGAGCTGTGTTGAAAAAAACGTATACAAAATTGAAGGAAAAAAAAAACAATGGCCATGTTCTTAGAAAGCAACAACTACGGCGTCGGATATACTGTTGCAGCAACTTAGTCGTGGTAAAATTTCATTCTCTTTCTCTCTATCCTTAGTttaaggacggtgcctactattgttattgcgcatacgttctgcgcatctccagacactcggatttcctatcgccaatgcttactaataaagggatatttttccg

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
E1C2V1	Lethal(3)malignant brain tumor-like protein 1 OS=Gallus gallus OX=9031 GN=L3MBTL1 PE=3 SV=1
D3ZWK4	Lethal(3)malignant brain tumor-like protein 1 OS=Rattus norvegicus OX=10116 GN=L3mbtl1 PE=3 SV=1
Q96JM7	Lethal(3)malignant brain tumor-like protein 3 OS=Homo sapiens OX=9606 GN=L3MBTL3 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002002 (this species only) · gene tree & orthology
Transcription factor family	zf-C2HC · all TF in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00536 all species →	SAM_1	SAM domain (Sterile alpha motif)	Domain	Interproscan
PF02820 all species →	MBT	mbt repeat	Domain	Interproscan
PF01530 all species →	zf-C2HC	Zinc finger, C2HC type	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036060 all species →	Homologous_superfamily	Zinc finger, C2H2C-type superfamily	Interproscan
IPR013761 all species →	Homologous_superfamily	Sterile alpha motif/pointed domain superfamily	Interproscan
IPR002515 all species →	Repeat	Zinc finger, C2H2C-type	Interproscan
IPR001660 all species →	Domain	Sterile alpha motif domain	Interproscan
IPR004092 all species →	Repeat	Mbt repeat	Interproscan
IPR050548 all species →	Family	Polycomb group and chromatin remodeling factors	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12247 all species →	POLYCOMB GROUP PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0005515 all species →	Molecular Function	protein 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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K24387	L3MBTL; lethal(3)malignant brain tumor-like protein	-	Chromosome and associated proteins	ko03036	deepkoala

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 Acropora florida 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 Acropora florida, 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 →