Gene detail

Detailed information of XP_073237365.1 in Porites lutea

Genomic Location: chr3:3695780...3706625
NR annotation: no NCBI-NR hit recorded
Species Porites lutea · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

LOC140931451

ATGATTGGATGGCAGAATACGAGGAATGCTTTAGGAAAGCTCGAAGAATTGTTGACCTGTAAAATTTGTGCTAATTTGGTGTCTGATCCTTGTTCGCTTGAAGCTTGCGATCACATCTTCTGTCGTAACTGTATTAAGAAGTTGGTTGGTGCAGATTCTAAATGCCCAGAATGTGGAGCTTTCGCCTGGGTAAAGGATATGAAAACAAATCGTCAACTTGCAAATACTGTCAACATGTGTGCGAAGATCAGAATGTTAGTTGGATCTGATGATGAAAGTGACAACAATAGGAACAAGGCACATGCAACAACAGCGTGGGAAGAAACACAAGCAACAGATGATCAAGGGAGTGACTCCTATCAGTTCTCACCACTAGAAGAAACTACAGCAAAGTCAATTAACTGTGGCGTTGCTCTCCAAGAAAACTCCATTTGCAATGAAAGGGTTTTTAAGAAACCTGCCATGAAGACTTATGGTAAAACAAAGAAAGGAACACTGGAAAAGTACATGCAAAACAACTCCAAGGAACATGTTGACACCAGTTCTGTTGGAGACAAGCTGGAACAAAGTGATCAGAAGGTTTTGACATGTAAGGGTGGGAAACCCTCGAAAAGCAAGAAAGGAAAATCTGTTTTAACAAAGGGAAATGAAACAGTCTTGAGTGATACAACAGTACCTGAGAGAGTGGAAATCAAAGAGGAGTGCTTTGGGAGAAAACTGAAAAATAAAAAAGTGAAAGCAACAGCCTCATGTGTTGCAGTATCATCTTGTAATAATGAAGAGATTGAAAATGCAAAGGAAATTGAGAAGCAGTTGATGGAGAGTGAAGACAACTTACAGTTTGGAGTAAATAATGAAGATGACAATATTGAGATGGAAGAATATGCTGATACAGAATGCTTCACACAGGTTAAATCAAGAGATGAATGCAAGGAGAGTTCAGCACTAGAGGCCAACACAGGACCTTTAGATGAAGTTGAAGGGACTCCCGAAGATGTCAGGAGCATTCTCAGAACAAGAGCTCAGAGAAGAAAGTTGCAAGGACAGAGAGTGGGGACGCCACCTAAGGCAAAACCTCAGAAGGAACAAGTACATGTAACAGTCAGTAATATAGGAGATAAACAGACAAGCAGTGGAGAAAAGACAACCAAGCATAGCACAGAAACACCTGTCAAACAAGGGAGAAACAAGAGGAAGCTTCTAGAACAGAGTTTCTGCAGGCAACAGACTTCTATCTCCTTTTCTCCAGGCACAAAGAGAAATAAACGAGGAGAAACACCATTGCAAGTGGCAACCATAAAGGGCTGTCTGGAAACTGTGAAAAAATTACTTGGCGAAGGGGCAGATCCTAACACCAAAGACCACGCTGGCTGGACCCCTTTGCATGAAGCCTGTAACCATGGTTACCTAGCCATAGCTGAACTGCTATTGGACCATGGTGCCATGATTGACATTCCTGGAGGTTTTGATCATGACACGCCCTTGCACGATGCTGTCACCAACGGTAGAATGGAGATAGCAAGACTTTTACTCTCCAGAGGAGCTCCTCTTGATGTTAGAAACAAAAGAGGCCTGCTTCCAAAAGACTATGCAGCAACTGAGGAGATGAAGTCCGTTTTGTCCGGGACAACACCTATGAAGGATAGTGGATCCTCAAATCAGATGACCTCAGTACCTCTGGGCACAAAGTGTTCACAAGATTCTCCTAAAGTTCTCCTGGCAACTGGTCTTAGTTCGGGGCAAAAGACGAAGCTCCAAAGGTGCTCACAGATTCTCAATGCAAAGATCGTTAATGAGTTCTCTCTTTCTGTGACACACATTGTAACAGCAACAAACAGGAAAGGAGTTTGTCCAAGGACCATCAAGTATCTGAATGGCGTGGTGACTGGAAAATGGATAGTGAACTACGATTGGATAGAAAAATGCTTACGGCGGAAAGCCTGGATAGATGAGACTGCGTATGAGATAAAAGGAACAAATGATGCGACTGTCGAGGCGCCCAAAAGAGCCCGAATTAATTCAGTTAAGCAGCTTCCGGGTTTATTTGACGGTTGCCAGTTTTACTTCTATGGTGAATTCTGCCCACCCCACCCCCCAAAAGAAGACCTCATCCAGATGGTCAAGTTTGGCGGTGGAAAGATTCTTTCACGTGAGCCGAAACCAGACGTGGACGAGACTCTCTGCTTGCCCACGTCACAGAAAGCTAATGTGACCGCAGTCACTTTAGCACCTGTCGCTTACCACGCCAATCCAACCTCGAGAAATTATCGCTGCACACAGTACGTGATCTACGATTCTTTAGCGGACAAAAAGCCCCACATCTGGAGCACTGACTCTGTGTGTACTGTGCCTGTAACTTGGCTTATGGACTGCGCTTCGAACTTTGCAATCTTAGAATTAGATTTGGATTAA

Transcript

rna-XM_073381264.1

TTTCATCAATGTCTCGTTGATTTCAGCGTCGATTTCTCGTTCATCTGTTActtttattcaactttaaaaaggaTTTCCTTAAGATGATTGGATGGCAGAATACGAGGAATGCTTTAGGAAAGCTCGAAGAATTGTTGACCTGTAAAATTTGTGCTAATTTGGTGTCTGATCCTTGTTCGCTTGAAGCTTGCGATCACATCTTCTGTCGTAACTGTATTAAGAAGTTGGTTGGTGCAGATTCTAAATGCCCAGAATGTGGAGCTTTCGCCTGGGTAAAGGATATGAAAACAAATCGTCAACTTGCAAATACTGTCAACATGTGTGCGAAGATCAGAATGTTAGTTGGATCTGATGATGAAAGTGACAACAATAGGAACAAGGCACATGCAACAACAGCGTGGGAAGAAACACAAGCAACAGATGATCAAGGGAGTGACTCCTATCAGTTCTCACCACTAGAAGAAACTACAGCAAAGTCAATTAACTGTGGCGTTGCTCTCCAAGAAAACTCCATTTGCAATGAAAGGGTTTTTAAGAAACCTGCCATGAAGACTTAtggtaaaacaaagaaaggaaCACTGGAAAAGTACATGCAAAACAACTCCAAGGAACATGTTGACACCAGTTCTGTTGGAGACAAGCTGGAACAAAGTGATCAGAAGGTTTTGACATGTAAGGGTGGGAAACCCTCGAAaagcaagaaaggaaaatctgtTTTAACAAAGGGAAATGAAACAGTCTTGAGTGATACAACAGTACCTGAGAGAGTGGAAATCAAAGAGGAGTGCTTTGggagaaaactgaaaaataaaaaagtgaaagcAACAGCCTCATGTGTTGCAGTATCATCTTGTAATAATGAAGAGATTGAAAatgcaaaggaaattgagaagcAGTTGATGGAGAGTGAAGACAACTTACAGTTTGGAGTAAATAATGAAGATGACAATATTGAGATGGAAGAATATGCTGATACAGAATGCTTCACACAGGTTAAATCAAGAGATGAATGCAAGGAGAGTTCAGCACTAGAGGCCAACACAGGACCTTTAGATGAAGTTGAAGGGACTCCCGAAGATGTCAGGAGCATTCTCAGAACAAGAGCTCAGAGAAGAAAGTTGCAAGGACAGAGAGTGGGGACGCCACCTAAGGCAAAACCTCAGAAGGAACAAGTACATGTAACAGTCAGTAATATAGGAGATAAACAGACAAGCAGTGGAGAAAAGACAACCAAGCATAGCACAGAAACACCTGTCAAACAAGGGAGAAACAAGAGGAAGCTTCTAGAACAGAGTTTCTGCAGGCAACAGACTTCTATCTCCTTTTCTCCAGGCacaaagagaaataaacgaGGAGAAACACCATTGCAAGTGGCAACCATAAAGGGCTGTCTGGAAACTGTGAAAAAATTACTTGGCGAAGGGGCAGATCCTAACACCAAAGACCACGCTGGCTGGACCCCTTTGCATGAAGCCTGTAACCATGGTTACCTAGCCATAGCTGAACTGCTATTGGACCATGGTGCCATGATTGACATTCCTGGAGGTTTTGATCATGACACGCCCTTGCACGATGCTGTCACCAACGGTAGAATGGAGATAGCAAGACTTTTACTCTCCAGAGGAGCTCCTCTTGATGTTAGaaacaaaagaggCCTGCTTCCAAAAGACTATGCAGCAACTGAGGAGATGAAGTCCGTTTTGTCCGGGACAACACCTATGAAGGATAGTGGATCCTCAAATCAGATGACCTCAGTACCTCTGGGCACAAAGTGTTCACAAGATTCTCCTAAAGTTCTCCTGGCAACTGGTCTTAGTTCGGGGCAAAAGACGAAGCTCCAAAGGTGCTCACAGATTCTCAATGCAAAGATCGTTAATGAGTTCTCTCTTTCTGTGACACACATTGTAACAGCAACAAACAGGAAAGGAGTTTGTCCAAGGACCATCAAGTATCTGAATGGCGTGGTGACTGGAAAATGGATAGTGAACTACGATTGGATAGAAAAATGCTTACGGCGGAAAGCCTGGATAGATGAGACTGCGTATGAGATAAAAGGAACAAATGATGCGACTGTCGAGGCGCCCAAAAGAGCCCGAATTAATTCAGTTAAGCAGCTTCCGGGTTTATTTGACGGTTGCCAGTTTTACTTCTATGGTGAATTctgcccaccccaccccccaaaagAAGACCTCATCCAGATGGTCAAGTTTGGCGGTGGAAAGATTCTTTCACGTGAGCCGAAACCAGACGTGGACGAGACTCTCTGCTTGCCCACGTCACAGAAAGCTAATGTGACCGCAGTCACTTTAGCACCTGTCGCTTACCACGCCAATCCAACCTCGAGAAATTATCGCTGCACACAGTACGTGATCTACGATTCTTTAGCGGACAAAAAGCCCCACATCTGGAGCACTGACTCTGTGTGTACTGTGCCTGTAACTTGGCTTATGGACTGCGCTTCGAACTTTGCAATCTTAGAATTAGATTTGGATTAATTTTATGgtctttgttgtcttttttaacATTCTGCGCTCCTGTAAAACAAATCTTTACGAACGGTCATACGGTCAAGTCTACTTTGGAGTCT

Protein

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005511 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00533 all species →	BRCT	BRCA1 C Terminus (BRCT) domain	Family	Interproscan
PF14835 all species →	zf-RING_6	zf-RING of BARD1-type protein	Domain	Interproscan
PF12796 all species →	Ank_2	Ankyrin repeats (3 copies)	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR017907 all species →	Conserved_site	Zinc finger, RING-type, conserved site	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR036420 all species →	Homologous_superfamily	BRCT domain superfamily	Interproscan
IPR002110 all species →	Repeat	Ankyrin repeat	Interproscan
IPR001357 all species →	Domain	BRCT domain	Interproscan
IPR036770 all species →	Homologous_superfamily	Ankyrin repeat-containing domain superfamily	Interproscan
IPR039503 all species →	Domain	BARD1, Zinc finger, RING-type	Interproscan
IPR001841 all species →	Domain	Zinc finger, RING-type	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR24171 all species →	ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 39-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0004842 all species →	Molecular Function	ubiquitin-protein transferase activity	Interproscan
GO:0031436 all species →	Cellular Component	BRCA1-BARD1 complex	Interproscan
GO:0070531 all species →	Cellular Component	BRCA1-A complex	Interproscan
GO:0085020 all species →	Biological Process	protein K6-linked ubiquitination	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
K10683	BARD1; BRCA1-associated RING domain protein 1	-	DNA repair and recombination proteins	ko03400	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 Porites lutea 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 Porites lutea, 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 →