Gene detail

Detailed information of gene23827.t2 in Actinoscyphia liui

Genomic Location: chr7:3280085...3305952
NR annotation: XP_028405452.1, uncharacterized protein LOC114528075 [Dendronephthya gigantea]
Species Actinoscyphia liui · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

gene23827.t2

ATGTTGACATTGTTATTAGATCCTACATGGTTGTCCACCAATCTTGGGGTGTTGACGTGTATCGAGTGTTCAGGAATACATCGTGATATGGGAGTACATGTATCTAGAGTACGATCACTAACCCTGGATAATCTAGGGACATCAGAACTACTGCTGGCAAAGTTTATCGGTAATGGTGGATTTAATGAAATTATGGAAGCAACTTTAGACTATAACCGCAAGCCAACAGCGACAAGCAATATGGAAGAGAAGAAAGAATTTATCAGAGCAAAGTACATGAAGCATCAGTTTGCACAAAAGTCTGGCGAGGGACCTGAAAAGATTCTACAGGAGCTTTATCTGGCCGTCAAATCACGTGACATTCTCACTGTTCTACAAGGGTTCGCAGAAGGAGTGGAATTAACCCGCCATTTGCCAGACAGTACATCACAAAATACAGCGTTGCACATGGCCGTTCAACAAGAAGATCTCACATCGCTACACATTGTGGACTTCCTGGCACAGAATGGAAAAGGAATAAACATAGTTAACGCCAGTGGGGATACTGCCCTACATATTGCTGCACGTAGTGGGAAAACCGAAGTGGCCAAGGTCCTTCTACGATCTGGAGCAACTGAAAGTATTTCACTAGCCAACTTAGACGGTAAAAGCCCGCTGGACCTAGCAAGGGACAATGAGCATACAGAGGCCGCTGACTTGCTTAAAAAGTGTTCTTCGGGCAAGCTTAACTTTTGTGACCATGTTAAAATAGACTGGGGATTACATCAGGCTGATGGGATTTATGACGCACCTGCCGACATCATAGATATCAAGGTTGTTTTGAATCATGACGACGAATCTATCCAGGATAAGCCTCGGAGCGGTCCCCCCACCCCGCCCCGCCATCGTCGTGTTTTGCCCACTAGACCAGTCAGTCAATTTGTAACACCATCTAGTTCCCGTACACCAAGCCAACAAGATGCTGACGCTGTGAGCGCGCTGATCTCTGGTCTCACTCTACACAACAATGACAGCGGCCATTATATACCGATGGATACTGGGGACAAGAGCGGCAACCCGAATGGGTCGCCGGTGATCTTGAGAAGGAAGCCACCGCCTCCACCTAAAACTAGCGGCGAGACGGTCGCTGTCAGTGTTCGTGCTAGTATAGCCTTCCCATCAGCCAGTGGGGTCAGCTCTAGTACGTTTGGTCATGGCCCTAAACGACTGAATGAGATCCTAGGACTGTTAGATTCACCCCCTCCCCTCCCAGTTCGTTGCTCGTCCGTAAGCCGTCACAAACTACCATCACGTGCACCCCCACCACCCCTCCCTAAACCTCTGTTCGACGATAGCCCACTCAAGCCGCTGACAGTACCTGACATGCGAACCGTACCAGAATCCCTGAGACGCGCACCCCCCGTACCACCAGGGGGCGTACCTCCAGGGGGCGTACCACCAGGGGGCGTGTCACCAGAGGGCGTGTCACCAGGGGGTACTACAAACAACATTCCAGCGGATTCAAAATTCAAAGCACCACCCATACCCACCCATAGAAGGTCCCGCTCAGAAGGTAAAACCCCCTTTGGTGAAGAACCGCTCAGCAACCTCGCCAAACAGTGCTTGGTAAAAAAGAAATCGTTACCTCTAGAGGATGGCACACCTAAAGACGATGTGAAACGCAACCGTCCAACTCCCCCTCCAAGACCCGCTAGCCTGAAAAAGCCATCTAACACCAAAACCACTTCTTTGAAGCCTAAATCTGCCACGTTGCCAAGACCACCAGGAATGGCTCCTTCACTGCTTATAACCGACTCGAGCTCGCCGTCTTCTAAAGAACAAAGCGAAGATGATACCTCTGAAATTCCCTCAATACCAGCTCCCGAATTACCTCCAAGACTATACTACACCGCGGCCGCCGCATCTCACCCTCGTAGAGTCCAAGCTCTATACGACTGTGAAGCGGACAATGAAGACGAGCTATCGTTTAAAGAAGGCCAAATCATCATCGTTAACGGTGACGCAGAAGATGCTGAGTGGTGGGTTGGGGAGGTAGAAGGTCATCCAGAAAGACCACACTCGGCGGGTGGATGTTTCCAGACCGGTCACGTGAAAAACGGTGCCGTCATCCTTGTTGGAGCTGTGTCTTCCACGTGTCCCAATGGCGCACCACCAAACAAATCGTGGTTCACTGCAAAGGTGGAGGTCCACGGCAAATCTGTCAGCATCTACAAGGATGGTCAACTGGTGAGAGTGGTGAACAGCCATTTTGCAGCAACTGGAAAAGGAGGCGTGTTGTTGGCAAATGGATACGACAACACCATACGCTATAAGAACTACCAAATTAGTCAATTGCTTTCTCATCCCCACCCAGTTTCCGCTTGCCAAAGTGTTATCCAGTTCCCGTCTTACGTGCAGATGGTAGGAGGACCTGGTGGCTGGCCCGCAGCTGGTTTCTGCAGAACTGTCATCGCAAAGTCAGTTTCTGGCTCCGATTACAGTGTATCTGCGAGTCTGTACAACGAAAAGGGCAGATCCAATTATGGCCACTTGGGGATTTTGTACAACGCTCAAGATATGAACAATTTCGATTTCGTTTACTTCAGACCACACTCGGCAGGTGGATGTTTCCAGACCGGTCACGTGAAAAACGGTGCCGTCATCTTTGCTGGAGCTGTGTCTTCCACGTGTCCCAATGGCGCACCACCAAACAAATCGTGGTTCACTGCAAAGGTGGAGGTCCACGGCAAATCTGTCAGCATCTACAAGGATGGTCAACTGGTGAGAGTGGTGAACAGCCATTTTGCAGCAACTGGAAAAGGAGGCGTGTTGTTGGCAAATGGATACGACAACACCATACGCTATAAGAACTACCAAATTAGTCAATTGCTTTCTCATCCCCACCCAGTTTCCGCTTGCCAAAGTGTTATCCAGTTCCCGTCTTACGTGCAGATGGTAGGAGGACCTGGTGGCTGGCCCGCAGCTGGTTTCTGCAGAACTGTCATCGCAAAGTCAGTTTCTGGCTCCGATTACAGTGTATCTGCGAGTCTGTACAACGAAAAGGGTAGATCCGATTATGGCCACTTGGGGATTTTGTACAACGCTCAAGATATGAACAATTTCGATTTCGTTTACTTTAGACCACACTCGGCGGGTGGATGTTTCCAGACCGGTCACGTGAAAAACGGTGCCGTCATCCTTGTTGGAGCTGTGTCTTCCACGTGTCCCAATGGCGCACCACCAAACAAATCGTGGTTCACTGCAAAGGTGGAGGTCCACGGCAAATCTGTCAGCATCTACAAGGATGGTCAACTGGTGAGAGTGGTGAACAGCCATTTTGCAGCAACTGGAAAAGGAGGCGTGTTGTTGGCAAATGGATACGACAACACCATACGCTATAAGAACTACCAAATTAGTCAATTGCTTTCTCATCCCCACCCAGTTTCCGCTTGCCAAAGTGTTATCCAGTTCCCGTCTTACGTGCAGATGGTAGGAGGACCTGGTGGCTGGCCCGCAGCTGGTTTCTGCAGAACTGTGTTCGCAAAGTCAGTTTCTGGCTCCGATTACAGTGTATCTGCGAGTCTGTACAACGAAAAGGGTAGATCCAATTATGGCCACTTGGGGATTTTGTACAACGCTCAAGATATGAACAATTTCGATTTCGTTTACTTCAGACCACACTCGGCGGGTGGATGTTTCCAGACCGGTCACGTGAAAAACGGTGCCGTCATCCTTGTTGGAGCGGTGTCTTCCACGTGTTCCAATGGCGCACCACCAAACAAATCGTGGTTCACTGCAAAGGTGGAGGTCCGCGGCAAATCTGTCAGCATCTACAAAGATGGTCAACTGGTGAGAGTGGTGAACAGCCATTTTGCAGCGACTGGAAAAGGAGGCGTGTTGTTGGCAAATGGATACGACAACACCATACGCTATAAGAACTACCAAATTAGTCAACTGCTTTCTCATCCCCACTCAGTTTCCGCTTGCCAAAGTGTTATCCAGTTCCCGTCTTACGTGCAGATGGTAGGAGGACCTGGTGGCTGGCCCGCAGCTGGTTTCTGCAGAACTGTGATCGCAAAGTCAGTTTGTGGCTCCGATTACAGTGTATCTGCGAGTCTGTACAACGAAAAGGGTAGATCCAATTATGGCCACTTGGGGATTTTGTACAACGCTCAAGATATGAACAATTTCGATTTCGTTTACTTTAGACCACACTCGGCGGGTGGATGTTTCCAGACCGGTCACGTGAAAAACGGTGCCGTCATCTTTGCTGGAGCTGTGTCTTCCACGTGTCCCAATGGCGCACCACCAAACAAATCGTGGTTCACTGCAAAGGTGGAGGTCCACGGCAAATCTGTCAGAATCTACAAGGATGGTCAACTGGTGAAAGTGGTGAACAGCCATTTTGCAGCGACTGGCAAAGGGGGCGTGTTGCTGGCAAATGGATACGACAACACCATACGCTATAAGAACTACCAAATTAGTATATTGCCTCATTGA

Transcript

gene23827.t2

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
B8WI85	Uncharacterized skeletal organic matrix protein 7 OS=Acropora millepora OX=45264 PE=1 SV=1
O97902	Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1 OS=Bos taurus OX=9913 GN=ASAP1 PE=1 SV=1
Q1AAU6	Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1 OS=Rattus norvegicus OX=10116 GN=Asap1 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003082 (this species only) · gene tree & orthology
Ubiquitin family	UBD\|Other\|SH3 · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF12796 all species →	Ank_2	Ankyrin repeats (3 copies)	Repeat	Interproscan
PF01412 all species →	ArfGap	Putative GTPase activating protein for Arf	Domain	Interproscan
PF00018 all species →	SH3_1	SH3 domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR036770 all species →	Homologous_superfamily	Ankyrin repeat-containing domain superfamily	Interproscan
IPR002110 all species →	Repeat	Ankyrin repeat	Interproscan
IPR001164 all species →	Domain	Arf GTPase activating protein	Interproscan
IPR001452 all species →	Domain	SH3 domain	Interproscan
IPR038508 all species →	Homologous_superfamily	ArfGAP domain superfamily	Interproscan
IPR037278 all species →	Homologous_superfamily	ARFGAP/RecO-like zinc finger	Interproscan
IPR043593 all species →	Family	Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein	Interproscan
IPR036028 all species →	Homologous_superfamily	SH3-like domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45854 all species →	ASAP FAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005096 all species →	Molecular Function	GTPase activator activity	Interproscan
GO:0043547 all species →	Biological Process	positive regulation of GTPase 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

No KEGG orthology assignment for gene23827.t2.

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 Actinoscyphia liui 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 Actinoscyphia liui, 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 →