Gene detail

Detailed information of HK74SY85_g10789 in Paraphelliactis xishaensis sp. nov.

Genomic Location: ctg72:282481...286328
NR annotation: KXJ18452.1, Retinoblastoma-like protein 1 [Exaiptasia diaphana]
Species Paraphelliactis xishaensis sp. nov. · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

HK74SY85_g10789

ATGGCCTCCAATATAAACAGGGAAGATGATTCTGATCCGAGAGAAAGGTTCGACAGTGTATGTCGAGAACTTAACATGGACGAGGGAACGTCAGAAGAAGCTTGGAGATCGTATGAAAGGATCAGAACGAACTATACACTCGAGGTTTGAACACTGTTACCGATATGAACGAACTCAGTCAGTCTTCTTTGCAATCGAACATTTTGTACGCGTTCTAAACGCCTGCTTTTCAGCATTATTAAGGCTTGATTCTTTGACTTAACTAATGTAGCGTTTGTTTTACTGTAGGGGAAAAGCATTCACTGGCTAGCTTGCGCTTTGTACGTTGCTTGTAGACGAAGCGTTGTGCCAACGGTTGATAGTTCTGGTACTGTAGAAGGAAACTGCGTCTCGTTAACCAGACTTATTCGCGCCTCTGGTTTAAGGTAAGCTGAATTTATTTTCATTAAAACCTTATTCTGAGAGAGTACTAAGCGATCAGAAAAACTAACTCTGATTTTTGATGTGTTTTTAGTCTGATAGATTTCTTCAACAAGATGAAGAAATGGCTTGATATGTCGAACGCATCCAGTGAATTTCGAAGGAAGATCGAACATCTAGAACGAAATTTCCACGTCTCAACAGTTATATTCAAAAAATATCGTCCAATTTTCCTCGATCTGTTCCGAGATCCCAATGAAGAAGTCCCTAAAAGCCGAACAGGGAGAAAGGCGAGGTAAGTTTGGACATATTTTACTGCGTATTTTAGAAATGTAAGCCAAAATGTAAGTTTCACCAGTCAGGAGACGATGCGTGAAGGCGGTTTCGTGAAGGCCAAGTAGATTTTAAAGCGCTCGAACCAATTCAAAATATTCAGCTTTTGGTCTTTCTGCTTACATGTCTAATTGAACTCCTGAAAGGTCTTAGCAATAAAATTATCGAGCTCCACGCGTTTTTAAAAGACATAATTAATGCTTTTGATTGCTTTGTTCGACTGGTTCTTTGCAAAACATGTGAGTGAAAATTGGTGTCTTTGTTGATTTTTGTTGAAACAGAAAACATCCCTGTACTACAGCAGAAGTGTTTGCATTTGGATGGACTCTCTACGTACAAGCAAAAGGTAAAATCGATATTGGAGATCAATCGACCTTAGCTTGGACCCGGGCTTGGAAGGTCATGAAACAATTTTTGAATCCCATCATCTGATCAGTAAAAGTTCCTCTGCTATTCGAATTGAGAAGTAAAGTTTGGACTGTGCCATCGTTTCATCTTTGATGAAAAATTGAAATTCACAGCAATTAGGAGGCTCGGCTCTGCTCTTCCGCTCTCCTAGGCTATTAAATACTGTTATTCAGAACCTGGGATTTTTTAATGAGGGATATTTCCTATTGAAATAAGTTGATTGACCTGCGAAACTGAAACTTGATATTCTACATGTATAGCAAAAGCGGCAGCGTTTTATAAGCAACATTTCTGCAACTTGTGTTCCAAACTCGCAATGTATTGGTAGCATTGACTTCAGATAAAGCAATTTGTTTACAATCTGCAGATTTTAAATCATATTGAAATGTGATCACATTGTGATCCGTCACTCAAATAGGAGCAAATATTATGATTGTACACATATTCTTCTAAATCTACCATAACAGATCTAGTCTTGAATAAAAAAAAGTTATTGCAAGCTGCTTGTTCCCTGTGGAGATTGCTAAAGCTTAGATTTTATCCTTGTACACGAAACATGAGCTTAAATTATAATTTCTTGCCTAAAGGAGTAAAGCCAATAAGTCGATTGCTGCCTCACAAAACTTTAAACCCAATGTTTTGCTCTAATCTTTTTCACTGCTTAAAATACACACTCTTATACCTAAAAGTCTTAGAATTACTTTCTATTACATGAAAAAGTACTGTACTGTTTCCTCTTACAATATTTTGCATTTGGAATTCAGCACTTATGCAAATACACAGCGATGTTGTAGCTGTGAAATTTTTTCCTTGTAATAATGCTTAGTCAGTCATCCATAAACATTATAATCATATAATTGTTCAAGCTGGGCCCTTGGATTGTGCTTGGATTTGTACTGTCGCTAAAGACTGCATGCGAGTTTGGACTTGCCGATTTCTAATATTAAAAACAGTAATTGTGTAAAAGTTAATGAGCAAATATGTTTTTGTTTGGGTGCCAAAGATCGCGATCATGTTCAGACATGTTTTTTTATCCTTCATTAAACAAATCACATATGTCTCAATTACTAACAAGTTGCAAAATGGAGAAATGGAAttattactcgggctacttccggaggaaacccgagtaataaaataagctttctttttattatttttatttttcgttggccacaaacggacataattaattccgaacgcctatcgaactaaatccgaaagtatgattcgctcaaacgggtcaaatagtttccgagcgcataatgaattaaatccgaagtattgttggctctacgaacgcagtaaatgccgagaacagagcatttatcgagcttatcgaccacatgcatgggagtttcaatccaactcgaaggaaagaaatacgctcatctcacatataaacacaactgaacgctgttcatagtaagccccacactaaaacatatcgttgttagggttccgaatgattttggacacatgcagggatcgaaattagacaaaggagacagcagcttcgtcgattcgtcacatcatagtctggatgttaaaatacgaagttcgtggatgattttcaagtatttttatttgaccgattttcctctgcatttgcctggacattcttgaataatcattgttttacatgtccaaagctagagagcgagggatttgattttccagaagattttggtgagattttcgcctcagctgacccatgctggagtcgcttcgcaggctagccttcacgctgttgttgcatattctaatagtctccctcgcagctgtcacgcaggcatttactttaatttgctccaaataaagtaaataatgccgtcatgtgtcttggctaagtcggcttgaatcatgaatttatgtgtgatattcgaactttttaaagtaaaaaaaaaaaaacccagcagctaataatctaataatctgcttcactcagcaaaactactgagcaaaaactccgaaggcttcaaaaacagtcctgtcatcgctgatcgcaaaacagcacataaaaaaaacgtaaaaacgtatcggacaataaaatgaatcatatttctgagaaatataatgattgaagtttattttattccacgtttgaataacattcaagtaaataattttaagtcggtcgattaagccgtcacaaggtcaaacagtgacgtgtaattcaaaatgacatacagtataagactttcaagttgcgtcacgccacatttacagtacatcagatattcattagaagttcagtttacaatgcgatttatatatctagttttttaaactcaatttatagttcttgtatttacaaagtaactgcttaactacttcatagcccgagtgaatgctcatagagcgtcttgttTAAATAAATATCAGTGAAAATTTAATATAATCTGGTTTTACCATCTTtataaataaaaatctaggttatcaatataaattaaTTTATACTAATATTGGCTACTCTCTCAGCTACTTTTGCTAGCTCCAGTTTGTTGGTAAAATGCTGCATAGTTTGGAACCATTTAGTTATGGGCCCCTAACATTTACTTTACTTACATTGAACTACTTTATTATAAAAACTTATAACCATTTCTACTCTTTTAGGCAATTTCCCAGCCATAAGTGATGACTTGGTGAATTCTTATCATCTGCTTCTATGCTGTCTTGACTTAATCATGGCCTCCAATATAAACAGGGAAGATGATTCTGATCCGAGAGAAAGGTTCGACAGTGTATGTCGAGAACTTAACATGGACGAGGGAACGTCAGAAGAAGCTTGGAGATCGTATGAAAGGATCAGAACGAACTATACACTCGAGGGGAAAAGCATTCACTGGCTAGCTTGCGCTTTGTACGTTGCTTGTAGACGAAGCGTTGTGCCAACGGTTGATAGTTCTGGTACTGTAGAAGGAAACTGCGTCTCGTTAACCAGACTTATTCGCGCCTCTGGTTTAAGTCTGATAGATTTCTTCAACAAGATGAAGAAATGGCTTGATATGTCGAACGCATCCAGTGAATTTCGAAGGAAGATCGAACATCTAGAACGAAATTTCCACGTCTCAACAGTTATATTCAAAAAATATCGTCCAATTTTCCTCGATCTGTTCCGAGATCCCAATGAAGAAGTCCCTAAAAGCCGAACAGGGAGAAAGGCGAGAAACAGAAAACATCCCTGTACTACAGCAGAAGTGTTTGCATTTGGATGGACTCTCTACGTACAAGCAAAAGGCAATTTCCCAGCCATAAGTGATGACTTGGTGAATTCTTATCATCTGCTTCTATGCTGTCTTGACTTAATC

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
D3ZS28	Retinoblastoma-like protein 1 OS=Rattus norvegicus OX=10116 GN=Rbl1 PE=1 SV=4
Q64701	Retinoblastoma-like protein 1 OS=Mus musculus OX=10090 GN=Rbl1 PE=1 SV=3
P28749	Retinoblastoma-like protein 1 OS=Homo sapiens OX=9606 GN=RBL1 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004503 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF11934 all species →	DUF3452	Domain of unknown function (DUF3452)	Family	Interproscan
PF00382 all species →	TFIIB	Transcription factor TFIIB repeat	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR024599 all species →	Domain	Retinoblastoma-associated protein, N-terminal	Interproscan
IPR013150 all species →	Domain	Transcription factor TFIIB, cyclin-like domain	Interproscan
IPR028309 all species →	Family	Retinoblastoma protein family	Interproscan
IPR036915 all species →	Homologous_superfamily	Cyclin-like superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13742 all species →	RETINOBLASTOMA-ASSOCIATED PROTEIN RB -RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0017025 all species →	Molecular Function	TBP-class protein binding	Interproscan
GO:0000785 all species →	Cellular Component	chromatin	Interproscan
GO:0000977 all species →	Molecular Function	RNA polymerase II transcription regulatory region sequence-specific DNA binding	Interproscan
GO:0005667 all species →	Cellular Component	transcription regulator complex	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:0030154 all species →	Biological Process	cell differentiation	Interproscan
GO:0051726 all species →	Biological Process	regulation of cell cycle	Interproscan
GO:2000134 all species →	Biological Process	negative regulation of G1/S transition of mitotic cell cycle	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 HK74SY85_g10789.

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 Paraphelliactis xishaensis sp. nov. 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 Paraphelliactis xishaensis sp. nov., 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 →