Gene detail

Detailed information of amic_s0113.g31.t1 in Acropora microphthalma

Genomic Location: sc0000113_pilon:476382...486716
NR annotation: XP_044168375.1, NHL repeat-containing protein 2-like [Acropora millepora]
Species Acropora microphthalma · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

amic_s0113.g31.t1

ATGGTCCTTGCAGAAAGTTGGTTTGTAAAACGTGGAGAAGAGCTTATAGTTGCATTAAAATCCGCCTCATCGAACGAAGAACAAAACAAAGCCATTTGCAGCCATATTGAATGGATAGACTCCAAAGATTCCGCCAAGATTCCAGAGTTCGATTCTAAACTAGAGTGGCTTAACTGTACCCATCCTTTATCATTTGAAAATGAGCTTCGTGGAAAGTTATGCGTTTTAGACTTTTTCACGTATTGTTGTATAAACTGCATGCATATTTTTCCAGATCTAGAAGCTTTGGAACAACTTTACTCCGACAAAGATGGGCTTGTTATTCTGGGGGTGCACTCCGCGAAATTCGAGAATGAAAAGTTATCCACGAACATTTTAAGTGCGATTTTACGGTACGATATCAGGCATCCCGTCGTGAATGATTCTGAAGCGAACCTGTGGAACATCTTAGGAGTTCAGTGTTGGCCGACTCTTGTCGTATTGAGTCCTGAAGGAAAAATCTTACTCAGCCTTGTAGGAGAAGGGCACAAGGACACCTTAATACAGTTTATTGGTGCAGCACTTAAATTTTACAAAGATAAAGGAAAAATCAGAGATCATTCCATTGGAATTTCATTATCCAAGGATACCCTTCCCAAGACTAGCCTCTCATTTCCTGGAAAAATCTGCGTTGATAATGACGGGAAGAGGCTTGTTGTGGCTGACTCTGGGCATCATAGAATTCTCATAGTAAACAGTGAAGGGATCGTCTTGAGCACCATTGGTGGAGGAGAAAACTGTGAAACAGGATTTGTTGATGGGTCTTATCAAGAAGCCAGATTCCACTCTCCACAAGGGGTTACTTTTGAAAATGATGTCATATTTGTAGCAGATACAGAAAATCATGCAATTAGAAAGATAAATCTCAAGACGGAGAAAGTCACTACAATTGCTGGGAATGGCATTCAGGGAAGTGATAAGGAAGGAGGTAAAATTGGGCCATTGCAGAGCATCAGCTCCCCTTGGGATGTTACTGTGGGACCACCCCCAGGACCCATAAAAGATGAACTTGATGGAGATATACTGTATATTGCTATGGCTGGAACTCATCAAATCTGGGCTTTATTTTTAAAAGACAGTTCCTGGCTTAAAGGAGGGTCACACCCAGAAGGCACTTGCCTACGGTTTTCCGGCAGTGGTGCAGAAGAGAATCGTAACAACAGTTATCCTCACAAAGCAGGCTTTGCCCAGCCATCAGGAGTCAGCCTAGCACTGGACAAGCCATTCAGGTGTTTATTTGTCGCAGACAGTGAGAGCAGCAGCGTCCGGTCTGTTGATGTCGCTACTGGTGCTACCAAAGCGCTGGTTGGAGCGGACAGAGATCCTACGAATTTATTTGCATTTGGTGATCAAGATGGCAAAGGCGTGGAGGCAAAGCTACAACATCCTCTCGCAGTTGCGTGGAACCCACACTCTCAGAAGCTTTTTGTAGCGGACTCCTACAACCACAAGATTAAGGAGATTGATCCGGCGAAGAAGACATGCGCCACTTTCCTGGGAACTGGTAAGCCAGGAATGTGTTCCGAGGAAGACTCTGTCCAGTTTGATGAACCGAGTGGACTCTGTGTCAGCCCAGACGGCCATTACTTGTATGTGGCGGACACTAACAATCACGCTATTCGAGTCGTTGACTTACGAACCAAATCTGTGTCACAGCTAAATATCGTGAAACATCCGCGAAGTTCAAAGGACCAACCGGACGCTGAAGAACGAAAAGAGAACGCCACCGTGAAACGTTTAACCTCGAAACGAACTCCGATCATGCGCAAAGAAGCAATTAACGTAAGCGGTAACACGTGCCTTGAAGTCACGTTGAATGTTGGTCTTCCTGTGGGATGTTACTTGACAGAGGGCGTGAACAGTAAATGGCAGATAAGTGTCTTCAGCCAGCTCGAGGATAAGGAAGTGAACCTTGACAGCTTTGAACTGGAAGCTCCGTCGGGAGTGATAACCCAAGAACTTATGCAAGCTGATTGCAAAATACGCATGCCCGCAGATTGGGAATCTCGGGCTACTGCAAGGATCGAGGCCTTGGTTTACTTCTGTGAGCCAAGTGGCACGTGCAGAATGGAAGGGATTGCTTACGATGTACCTCTTTTGAAGACAGACGGAGAGAGTAAGCTGTCATTGCAGATACAACACGAGGTCAAGTTGTAA

Transcript

amic_s0113.g31.t1

CTCATATTACGCAGCAATTTTTTTTCGGACGTTTCTAAAACTTCTTAATTCAGAAACCAGTACCTACTTTCCCTAAATATGGTCCTTGCAGAAAGTTGGTTTGTAAAACGTGGAGAAGAGCTTATAGTTGCATTAAAATCCGCCTCATCGAACGAAGAACAAAACAAAGCCATTTGCAGCCATATTGAATGGATAGACTCCAAAGATTCCGCCAAGATTCCAGAGTTCGATTCTAAACTAGAGTGGCTTAACTGTACCCATCCTTTATCATTTGAAAATGAGCTTCGTGGAAAGTTATGCGTTTTAGACTTTTTCACGTATTGTTGTATAAACTGCATGCATATTTTTCCAGATCTAGAAGCTTTGGAACAACTTTACTCCGACAAAGATGGGCTTGTTATTCTGGGGGTGCACTCCGCGAAATTCGAGAATGAAAAGTTATCCACGAACATTTTAAGTGCGATTTTACGGTACGATATCAGGCATCCCGTCGTGAATGATTCTGAAGCGAACCTGTGGAACATCTTAGGAGTTCAGTGTTGGCCGACTCTTGTCGTATTGAGTCCTGAAGGAAAAATCTTACTCAGCCTTGTAGGAGAAGGGCACAAGGACACCTTAATACAGTTTATTGGTGCAGCACTTAAATTTTACAAAGATAAAGGAAAAATCAGAGATCATTCCATTGGAATTTCATTATCCAAGGATACCCTTCCCAAGACTAGCCTCTCATTTCCTGGAAAAATCTGCGTTGATAATGACGGGAAGAGGCTTGTTGTGGCTGACTCTGGGCATCATAGAATTCTCATAGTAAACAGTGAAGGGATCGTCTTGAGCACCATTGGTGGAGGAGAAAACTGTGAAACAGGATTTGTTGATGGGTCTTATCAAGAAGCCAGATTCCACTCTCCACAAGGGGTTACTTTTGAAAATGATGTCATATTTGTAGCAGATACAGAAAATCATGCAATTAGAAAGATAAATCTCAAGACGGAGAAAGTCACTACAATTGCTGGGAATGGCATTCAGGGAAGTGATAAGGAAGGAGGTAAAATTGGGCCATTGCAGAGCATCAGCTCCCCTTGGGATGTTACTGTGGGACCACCCCCAGGACCCATAAAAGATGAACTTGATGGAGATATACTGTATATTGCTATGGCTGGAACTCATCAAATCTGGGCTTTATTTTTAAAAGACAGTTCCTGGCTTAAAGGAGGGTCACACCCAGAAGGCACTTGCCTACGGTTTTCCGGCAGTGGTGCAGAAGAGAATCGTAACAACAGTTATCCTCACAAAGCAGGCTTTGCCCAGCCATCAGGAGTCAGCCTAGCACTGGACAAGCCATTCAGGTGTTTATTTGTCGCAGACAGTGAGAGCAGCAGCGTCCGGTCTGTTGATGTCGCTACTGGTGCTACCAAAGCGCTGGTTGGAGCGGACAGAGATCCTACGAATTTATTTGCATTTGGTGATCAAGATGGCAAAGGCGTGGAGGCAAAGCTACAACATCCTCTCGCAGTTGCGTGGAACCCACACTCTCAGAAGCTTTTTGTAGCGGACTCCTACAACCACAAGATTAAGGAGATTGATCCGGCGAAGAAGACATGCGCCACTTTCCTGGGAACTGGTAAGCCAGGAATGTGTTCCGAGGAAGACTCTGTCCAGTTTGATGAACCGAGTGGACTCTGTGTCAGCCCAGACGGCCATTACTTGTATGTGGCGGACACTAACAATCACGCTATTCGAGTCGTTGACTTACGAACCAAATCTGTGTCACAGCTAAATATCGTGAAACATCCGCGAAGTTCAAAGGACCAACCGGACGCTGAAGAACGAAAAGAGAACGCCACCGTGAAACGTTTAACCTCGAAACGAACTCCGATCATGCGCAAAGAAGCAATTAACGTAAGCGGTAACACGTGCCTTGAAGTCACGTTGAATGTTGGTCTTCCTGTGGGATGTTACTTGACAGAGGGCGTGAACAGTAAATGGCAGATAAGTGTCTTCAGCCAGCTCGAGGATAAGGAAGTGAACCTTGACAGCTTTGAACTGGAAGCTCCGTCGGGAGTGATAACCCAAGAACTTATGCAAGCTGATTGCAAAATACGCATGCCCGCAGATTGGGAATCTCGGGCTACTGCAAGGATCGAGGCCTTGGTTTACTTCTGTGAGCCAAGTGGCACGTGCAGAATGGAAGGGATTGCTTACGATGTACCTCTTTTGAAGACAGACGGAGAGAGTAAGCTGTCATTGCAGATACAACACGAGGTCAAGTTGTAAAGCAAGTAATTCCTCTCATAGCTATCTACAGTGCCATCAGCTTATGAAGTTTTCAAGGCAGGTGGATTGTAGGAGAAGTACTTGCCCAGTATCCGCCATTATTGTAATGGCAGAAATCTTGATGATCCAAGAACCTCTTCATAGTTAGTCGACTTACTTTGCCCAGTTTTATGAAGAATTCGCGTCATTACCTTGAAATTAAAGTCAAAATATAGAATAAGTCAACGTGAAGTAGGTGTATGCCATTATAGCCTATATCACTGGTATAAACTCCAATGTGTATCACCAATGTCGTCATGCAATACCGACAAAGAAGACAAGCGTATCATCAA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q8NBF2	NHL repeat-containing protein 2 OS=Homo sapiens OX=9606 GN=NHLRC2 PE=1 SV=1
Q8BZW8	NHL repeat-containing protein 2 OS=Mus musculus OX=10090 GN=Nhlrc2 PE=1 SV=1
A4IF69	NHL repeat-containing protein 2 OS=Bos taurus OX=9913 GN=NHLRC2 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006177 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13905 all species →	Thioredoxin_8	Thioredoxin-like	Domain	Interproscan
PF01436 all species →	NHL	NHL repeat	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR011042 all species →	Homologous_superfamily	Six-bladed beta-propeller, TolB-like	Interproscan
IPR012336 all species →	Domain	Thioredoxin-like fold	Interproscan
IPR045302 all species →	Domain	NHL2, NHL repeat domain	Interproscan
IPR001258 all species →	Repeat	NHL repeat	Interproscan
IPR013766 all species →	Domain	Thioredoxin domain	Interproscan
IPR036249 all species →	Homologous_superfamily	Thioredoxin-like superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46388 all species →	NHL REPEAT-CONTAINING PROTEIN 2	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 amic_s0113.g31.t1.

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 microphthalma 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 microphthalma, 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 →