Gene detail

Detailed information of alor_g11150.t1 in Acropora loripes

Genomic Location: Acropora_loripes_36:1693750...1710417
NR annotation: CAH3151628.1, unnamed protein product [Pocillopora meandrina]
Species Acropora loripes · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

alor_g11150.t1

ATGTCCTGTACAGGGACACCAAAGCCTTTCGTTTGTAATGTGAAGAGGGACACGTTAGTGGATACTCGAAAGCTGGTTTTGCCACGTCATGACGTCAACACTCCCGGGGCCCTGGTCATGCCTCGACCCAGTGCTGCTCACCAGTTGGAACGTAATAAAGAAGGACTTGGAGTAGTAGACGTGATAGTGGACCCACACTTGTCACAGCACCTGAGGCCTCACCAGAAGGAAGGTGTTAAGTTCCTGTATGAGTGTGTCATGGGGCTCAGGAATTTCAACGGCAACGGCGCTATTCTTGCGACTCTTCATAAACAAGGCATGTATGGGGGGCGTCCCTCCGTCAAGAGAACCCTGATCATTACTCCAGGAAGTCTGGTCACGAACTGGAGCAGCGAGTTCCGCAAGTGGCTTGGTAGTGAACGGCTGAAGGTGTACACTGTTACATCGGAGAAAAGAGTCAAGGGATTTGTTGACAGTCCTCTTTATCCTGTGATGATAATCAGTTACGAGATGTTTTTGCGGTCAGTGGAGGAGATCAGGAGCATCAACTTTGGACTTGTCATCTGCGATGAGGCACATCGCTTGAAAAATACCAACATTAAAACCGCAACAATGATTTCCGGACTTAAAACTAAGCGTCGTATCCTTCTGACGGGCACACCAGTGCAGAATGATCTTAAAGAATTTCACTCGCTCATCGACTTGTGTAATCCAGAAATTCTTGGTACTCAAGCTTCTTTTCGCCGATTATACGAGGAGCCCATAGTCCGCGGACAACAACCTGATGCCAGCGGTGAGGAAAAACTCTTGGGACAAACAAGAGCTAATGAGGGCAATTCTCCCGACTTGACATCTATAGACAAAGAAACAGTAAGCCGAGAAAAAAGCAGCAACTACAGAAATCGTGCTAAACAGGTTGACGAGTTTGTTCTTCTTAAGACGGACGTCAGAAATAAACAGCCGGTATCTTCCTCCAAAGGTTCTCTGCAGCTTTCTCTGTACCGCCATCTTCTCATGTCGCGTGTTTTGAGGTCATGTCTGACGTCGTATGTCTCAGGTGGCTCTCGTCACCTGGTGTGCATAAGCGCATTAAAAAGGCTTTGCAATGATCCAAGTCTCATTTACTCGCAATGCCAAGACGCAAATGATGTGTCGGAAGGTTGGGATGTCGAAGAGGAATCGTCATTATATGAAGGGCTTGACCGTTGCTTTCCACAAGGGTTCAACCCAGACACTTTTACGCTGGACAACTCAGGCAAACTGCAAGTGCTTGGAAAAATGTTGACACAAATGCAGCGTGCAGGCGCAAGAGTGGTTCTTGTGTCAAACTACACGCAGACTCTCGACTTACTTCAAAAGCTCTGTGAAACGAGAGGCTATCAGTTCTTTCGACTTGATGGTAAAACACCAACAAGCAAACGCCAATCACTGGTGGATCGCTTTAATGACAAATATTGTAAAATATTCGTCTTTCTGTTGAGTTCTAAAGCTGGTGGAGTGGGCTTAAATTTAATTGGTGCTTCAAGACTTATACTCTTCGATATTGATTGGAACCCAGCCAATGACATTCAGGGAACAATAGAAGAGAAGATCTACCAGCGTCAATGCGTCAAGCAAGGTTTGAGTGGAACAGTAGCTGACGCAAAGGAAACTGTGAAAATTGAGTTCTCAAGGGAAGAACTAAAGGACTTGTTTACACTTCACGAAAACACTTTGTGTTTAACGCATGATCTGTTACAATGTACATGTCTGAATTCGGAGGATGATAACAGCAACAACGAATGTGGTTCAGATAGAAGAGACAGCGAACAGTCAAAAGCAACTAGACCGTGCCAGTTGGGATTTTACGACACCAACCAAAACCAAAATAATTTGTCATTAGCTGAGCTGGTAAACTGGCAACATTTTCCACGCCCTAGTGTTCCTGGGTCTGACTTTGAGGATGAAGCTGTGAAGGAAGCAGGAAGTACAGTGTCTTTTATTTTGGCCACTTTCAAGTCACTTTTGTCTGCGTTTAATGATGACGATGATGACAATCCTGATGTTGAGGCCGATGAAGCTGCTACTGAGGCCAGGTCTCGCCCCACAGTTCATACACCAGGGCCCTGGTTTGACCGCATTTTGGAGGTGAAGAAATGGGTGAATGTGAAAATTGTGAACCAAGTTGGTTCCCAGGTTAAAATAAAAGCCAACAAGATCCTGCCCAGTGCCGTATTAAGCAGTGGTGAAATCTTCGTTTATCATCGGCTTCTCAATGGAACTGACCGAAAGTCTACGATCACTCTTAAAGCAATCGATGAATACACGGATAAACCACTGATCATAAATGGAGAAAAGGAGTTTAGTGTAATGCCAACTACGTATGATGAGACACAAGAAGCGTATATTGCTCGTGAAGGAAGCGGTAACCGATGGTTTTACGTGAAACTGATAAACCATGCTGGAGGCCAGGCCAGAATTGTCTCTGACCAGATTCTCCCCGCCACAACACTTGAGGTGGATGAATCTCAGGTGGAGTACGCTCGTTTGGAACCTGGTGATGAGTATAAGAGAATTGTTTTGAGAGCAGTGGACGTGAGGAATGGGGAACCTCTCAAGCTAAATGGGGAATACACGCTGGGCTTAAGGCCTGATGACTCGGGCGATGTTGCTAGAGTGAAAATTACACGTGGAGATACAATTTATGCCAAATGCGACAACTTCGAGCCAATGCAAGAAAGTTCCTTTGAATATCAAATATCAACAGGCGATACAAAGAGTTGGTTTGATGCTGTTAGAGCTTGCAAGCTCTGTAATTCGGAATTGCTGAGCGTCCATACGAGAGAAGAAAACGACTTCATCACAGGACAACTGCGCAAGTCAACTGAAGTGAATAAGCTATGGATAGGAATGACATACAAAGAAGAAAAACGAATGTGGACCTGGATTGATGGCTCACGCTACAGATTCCAGAATTGGAAAGAGGGTCAGCACTACGATGGTAAAGATGAACAGTGTGGTATTGTGTATCAGCGTTATGACTGGGGAAGATGGGATGACGATAACTGTTACAAACCATTCGGTTTCATCTGCAAAAGACATCGAACTAGAGACGCAGTGGAGTCGAAGAATAATACACATTCATCAACAGAGAAACGAGGGTGTTCGTCTGTTGAATCAGAGTGCCCATCCCTGTGTCGTATTGTGCGCTCTCCCGGAAACTGTCCAAAGTGTGACTGTGGACTACTTGTCAAAGGTTTCGATACTATGACAGCTAGGGAACAGGCCAAAGTTCGCGGTCTCTTCTCAGACGCCTCTCATCAGATGCACCAAGCCAGTCTTGCGCAAATTGAACAGGCTCGTGCAATGCGTCGCTTCACGATCATGCAAGAGGCTGGTCGATTGATGGCCGAGTCACGCAATCTTCAGCAGGCAGCCGAACAAGAAGGAATCCCTTTGAATCTGCCGTACTCTCAGGGATTCCAGCAGAGGCAGCAGATTTCTACACCGGACAAAAGCACCAATGAAATAGCCAGCGAGATAGTTGGTTTGATCAACAATATAGAAAAATCTGAAGAGAGTGGAAAAGAGACAGACAAGAAAGCTAATTAA

Transcript

alor_g11150.t1

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9DG67	DNA repair and recombination protein RAD54B OS=Gallus gallus OX=9031 GN=RAD54B PE=2 SV=1
Q9Y620	DNA repair and recombination protein RAD54B OS=Homo sapiens OX=9606 GN=RAD54B PE=1 SV=1
Q6PFE3	DNA repair and recombination protein RAD54B OS=Mus musculus OX=10090 GN=Rad54b PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001215 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00271 all species →	Helicase_C	Helicase conserved C-terminal domain	Domain	Interproscan
PF00176 all species →	SNF2-rel_dom	SNF2-related domain	Domain	Interproscan
PF00059 all species →	Lectin_C	Lectin C-type domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR049730 all species →	Domain	SNF2/RAD5-like, C-terminal helicase domain	Interproscan
IPR001650 all species →	Domain	Helicase, C-terminal domain-like	Interproscan
IPR016187 all species →	Homologous_superfamily	C-type lectin fold	Interproscan
IPR001304 all species →	Domain	C-type lectin-like	Interproscan
IPR000330 all species →	Domain	SNF2, N-terminal	Interproscan
IPR038718 all species →	Homologous_superfamily	SNF2-like, N-terminal domain superfamily	Interproscan
IPR014001 all species →	Domain	Helicase superfamily 1/2, ATP-binding domain	Interproscan
IPR018378 all species →	Conserved_site	C-type lectin, conserved site	Interproscan
IPR016186 all species →	Homologous_superfamily	C-type lectin-like/link domain superfamily	Interproscan
IPR050496 all species →	Family	SNF2/RAD54 Helicase and DNA Repair	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45629 all species →	SNF2/RAD54 FAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0140658 all species →	Molecular Function	ATP-dependent chromatin remodeler activity	Interproscan
GO:0000724 all species →	Biological Process	double-strand break repair via homologous recombination	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0007131 all species →	Biological Process	reciprocal meiotic recombination	Interproscan
GO:0015616 all species →	Molecular Function	DNA translocase activity	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
K11654	SMARCA5, SNF2H, ISWI; SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5	EC:5.6.2.-	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 loripes 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 loripes, 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 →