Gene detail

Detailed information of PcrG020491.mRNA1 in Podabacia crustacea

Genomic Location: scaffold_32:2599960...2603445
NR annotation: no NCBI-NR hit recorded
Species Podabacia crustacea · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

PcrG020491.mRNA1

ATGGATCATCTGAAGGAACTGTTGCTCCCTAATACCTTTAACAAATGCGGTTACGTAGGAGTTTTTCTTTGGGCAGTAATCGGAGTTATCCTGCTTGGCGTCTTTGCCGAAATGGATAATGGTGAACGGAGTGATTTTCGCTGTAAGGCGAAGCTGCAGGAGATGGACTTCGTGCGAGCAAAGTGTTTCGAAGAGTACGATAAGCGGCACAACAAATATCGTTTTCCCGTCTATGGTTTCGTGCTCATTAATTTCTTATTTATTGGAATTGTTAGTGCGGTTTACTCCCAAGTAATGAAGTCAACAGTTGAGGATCATCAGAAGGAATCCAGAGACGCCGCATCAGTGGACGCCGAGAGACAGCGCCCAACTGAAACACGCACACTAGACGCCGAGAGACAGCGCCCACCTGAAGCACGCACACTAGACGCAGAGAGACAGCGCCCACCTGAAACACACAGACTGTTCGTGGCGTACTGTTGTCAACTTATGGTGAGATTTGCTTTAGGAATTGTTGCTATAGTTCTACAAACTCAATTGCTTTATCCCTCCATCTTTCCCTCGGATTTCAACTGTGATTTAAGCAGTCCTGCAGCCAATGAGTCAGCCGGCAAGAACTCGACCACATACCAATGCCATAATCAGAGAGCACGGCAGAAAACCGTCTCCATGCACGCAGTGATTGCAGTGAACGGAGTTTTTGCAGTTCTCATTTTCATTGAGTTTATGGCTATCTTGATATTACGGGTAAAACGAGGGAAAACGTTCCTCAAAGACTCGCAGTTTCTGAAATATTATCTTAACTGCGGCCGTACACGCGTTCCTGAAGAACATCCTAGTCTACCGCTACAAGAACAACTGCCTTCGTCTTTTATCAAAAGGCTGAAGGAAAGTATCATTAAAGACACTGAGACACTTCCAGATCTTGAGGCACTGATGCAAGCTACTCCAGGTGAAGGCGAAAGAATTGAAGATCTAAAGCTCGACAGTATTTACACGAATTTGGTTCTCGTACCAAACAGAGCGAATTACGACTTCAGCGGAAATAGACAGGAACAACTCAAACAATATCCCATGCCAGAAGAAAATTTGGAGCCAAAGAGACGAGAAGATATCATCGATGTTGAAAACAAAAAAGTGTTAATTGTCGGCCGACCCGGAATCGGCAAAACAGTATTTTGTACAAAGTTTCTACGAGACTGGGCTAAAAATGAGACACAAGATACTATGAAATATGAGCTCGCTTTCCTCATTAAGTTCAGACGGTTCAATTCGCAAGAGAAGCCGTTTAGTCTTCGTGAATTACTAACTTGTTCTGAACATGCAAAGACAGAACATCTTCCTGATCAAGGCTGGAGCTTCATTCTTAAAAACCCCGAGAAAGTCCTGATCCTTTTCGACGGCTTGGACGAATATTTAGATATCTCAAGTATCGCTAACACGGACGTTAACAACAGCTACAACGACAGTGTTGAACAGACGATGCCTTTTGCCGCTCTCTACTCCAAACTAGCCAATGGAAAACTTCTTCCGGAAACAACAGTTCTAACGACTACAAGACCCACCGCGGTGTCAAAAGTCAGGCAAGTTCGATTCAATAGAACTTTTGAAATCATTGGCTTTACTTCCATGCAAGTTGAAGAATATGTAGAAAACTTTACGGAAGAACATGTGAAAGATGGAGCGGAACATTTGAAGAGGGCAGCAGGAAAAATGCGGGAACACATCAAAACAAATATAAACATATTTTCATTGTGCTACGTTCCTGTCAATTGTTTCATCATTTGCTCTTGCCTAATTCAAATACTAAAGGACTTCACGGAGAAAGGAATGGATTTAGCTGCTGTTGGTCTACCAACAAAACTTACCCAGATTTACAAGATGGCCACGAAGCTGTTTTTCTTCAAGCACAACAAGCAATACAAAGATAAACCACTTAGCTGGGAAGTGATTGACGAAGATACTGAGTTGCCTCCTGAAGTAGAAGAAAAATTCAAACGACTTGGAAAAGTGGCATTCGATGGTATAAAGGAAAGAAGACTTATCTTCAAAAAAAGCGAAGTCCAGGGATTGGAGGACAGTGCACTGTTCCACCAACTGCCTGATCGTAAAATTGACGCTTTCAAGCACGAAGCTCAATTCTGTTTCCTTCATCTGACGATGCAGGAATTCCTCGCAGCGAAGCACATAGTAGATACCATGAATGAAGCACAATTGAGTAAATTTGTTTCCGACCACATCAACAAAGATGAATGGCATGTCGTCCTGCAGTTTGTCGCTGGCCTGCTCGGTGAACGAAAGCGACCGATTGAAATCTTTACAAACCTGCTTCCTGTGGAAACAGTAAAGAGAGGTGATGGATTTACCTGTTGGCCGACTTGGAGCGATCAACATTCAGCACTGACAATACTCAAATGTTTATTTGAGTCAGGCGAGAGCGAACAATCACATTCCGTTGTAAAAAGCAAACTAGAAGAGATTGGTTTTAATGATGTAAATTTTAGTTCGTGTAACCTCGCTCCTTCTGACTGCACAGCAGTGGTTCATGCGCTGAAAAATGTTCCACAAATTTCGTGCATAAATTTGTCCGCTAATCCCATTGGTTCGTTGGGTTTTGTAGAGATTAGAAAGTTGTTAGACAATGGTAATTGTCAGATAACACAGTTAAGACTCGGCGCCAATAACATAGGTGATAATGGTGTGTTAGAGTTGTGTAATGTAATTACTAACAGTAAATTAACCGAGTTACACCTCAGTAACAATAATATAACAGATGTAGGTGTGTTAGAGTTGTGTAAAGTAATTACTAACAGTAAATTAACCAAGTTAGACCTCAGGAACAATAAAATAACAGATGTAGGTGTGTTAGAGTTGTGTAAAGCAATTACTAACAGTAAATTAACCGAGTTAGGCCTCAGTAGCAATAAAATAACAGATGTAGGTGTGTTAGAGTTGTGTAAAGTAATTACTAACAGTAAATTAACCAAGTTAGACCTCAGGAACAATAAAATAACAGATGTAGGTGTGTTAGAGTTGTGTAAAGTAATTACTAACAGTAAATTAACCGTGTTATACCTCAGTAGCAATAAAATAACAGATGTAGGTGTGTTAGAGTTGTGTAAAGTAATTACTAACGGTAAATTAACCGAGTTATACCTCAGTAGCAATAAAATAACAGATGTAGGTGTGTTAGAGTTGTGTAAAGTAATTACTAACAGTAAATTAACCGAGTTATACCTCAGTAGCAATAAAATAACAGATGTAGATGTGTTAGAGTTGTGTAAAGTAATTACTAACGGTAAATTAACCAAGTTATACCTCAGTAACAATAAAATAACAGATGTAGGTGTGAATAATTTGTGTGATGTGTTAACTAATTCTAATTGTAAATTAACCTTGCTAGTCCTCTGGGGCAATGAAGCAATAACAGCTGAAGCTAAAAAGCGAATAACAAACGCTAATCCTAATTGCGAGGTCCGCTTTTAA

Transcript

PcrG020491.mRNA1

Protein

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000079 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF12799 all species →	LRR_4	Leucine Rich repeats (2 copies)	Repeat	Interproscan
PF13516 all species →	LRR_6	Leucine Rich repeat	Repeat	Interproscan
PF00029 all species →	Connexin	Connexin	Domain	Interproscan
PF05729 all species →	NACHT	NACHT domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR051261 all species →	Family	NOD-like receptor (NLR)	Interproscan
IPR032675 all species →	Homologous_superfamily	Leucine-rich repeat domain superfamily	Interproscan
IPR025875 all species →	Repeat	Leucine rich repeat 4	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR001611 all species →	Repeat	Leucine-rich repeat	Interproscan
IPR006553 all species →	Repeat	Leucine-rich repeat, cysteine-containing subtype	Interproscan
IPR038359 all species →	Homologous_superfamily	Connexin, N-terminal domain superfamily	Interproscan
IPR013092 all species →	Domain	Connexin, N-terminal	Interproscan
IPR007111 all species →	Domain	NACHT nucleoside triphosphatase	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR24106 all species →	NACHT, LRR AND CARD DOMAINS-CONTAINING	Interproscan

Gene Ontology

GO term	Category	Description	Source
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

No KEGG orthology assignment for PcrG020491.mRNA1.

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 Podabacia crustacea 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 Podabacia crustacea, 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 →