Gene detail

Detailed information of gene27520.t1 in Actinoscyphia liui

Genomic Location: chr8:24346323...24362533
NR annotation: XP_020897174.1, translation initiation factor IF-2, mitochondrial [Exaiptasia diaphana]
Species Actinoscyphia liui · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

gene27520.t1

ATGCACTGGCTTCTGAGAGCAAGATCTCTACAAGTTATTACATGCCGTACATGTAGTGTTTGTAGGTCATTTGTATCTCATGCAACACAGAACGTTAGTAAACCCAGACAGAGCTCTTACTTTAGACTGATTTCTTCCAAGGATGTTTCCTATAGTCAGTTTAGAAGGTTTGCATCGTCTAGTAGCAGTACAACAGTAGGAGGGCCTACTATTACAAGGAAACAGCACACTGTATCTCCTAAACTAAAGACACGTTATGCAAGGAGAGAGTATTTACAGGGTGGTAATGATATTGTAACTGTCAGTCAACTAGCACATCATATTGACATTGACGAAGGAAAGCTTATTGATATTCTTGACGACATGGGAGAAAACATACGTAGTCCAAACTGTGCTGTTGCTCCTGAAGTAGCTGAGTTTATGTGTATGGAGTTCAATAAACCAACATTAGCTGAGACAAGACAGTCTGAAAGTCTAGTTACTAGACCACCAGTAGTTACAATAATGGGCCATGTTGACCATGGTAAAACTACACTACTTGATGCACTACGTAATAGTTCTATTGCTGCCGGTGAAGCTGGAGGAATAACTCAACATATTGGTGCCTTCTTAGTTACCTTACCATCTGGTGAAGAAATCACGTTCATCGACACACCTGGTCATGCAGCGTTTGAATCAATGAGAGCAAGAGGTGCTAATGTTACCGATATAGTGGTCCTTGTCGTTGCTGCCGATGACGGTGTTAAAACACAGACAGTTGAGTCCATCAGACACGCTGTCCATGCCAATGTTCCAATAATAGTAGCTATTAACAAGATTGATAAGGGAAGAAAGAATGTGGATCTTCTCAAGCGACAGCTTCTTTCCCATGGGATTCAGCTGGAAGAGTATGGTGGAGATGTCCAAGTGGTGGAGATCTCAGCACTGAAAAGAACCAACTTAGATAGTTTAACAGAGGCCATTATAACTTTAGCAGAGATGAATGATTTGCAGGCTGATACTGACACCAACATTGAGGGTGTGGTCATCGAGGCGAAGAAAGACAAAGGATTGGGACCTGTTGTAACAGCACTGGTCCAGAATGGAACATTAAAGATAGGGGACATTATTGTCGCTGGAAGTACATTTGCCAAGGTCCGTCAAATGTACACAGACAGGGGAACCATTGTCAGCACAGCACCACCCTCCACCCCAGTACAGGTCACTGGTTGGAAGGACTTGCCAGCTGCTGGTGAAAAACTCCATCAAGTGGACACAGAGAAAAAAGCTAATGAGCTTGCATTGTCAAGAAGATCATATGATGACCAGAAAAGAAAAGAGACTTTATCACAAAGCTTTGACTTGAGTGAAATAATTAAAGATGATGGACGAAGGATAAAGATATCTAAAGGGGAATATGATGCTGCTAATAAAATAGACGTAGTGGTTAAAGGTGATGTTGATGGTTCAGTAGAAGCAGTAGTTGATGCTCTAAACACGTGCAAATCGGACAAAATCAAACTAAGTGTTCTCCATGCTGGAGTTGGTTCAGTGTCTGAGTATGACATCAAGACAGCACATTCATTCAAAGGTGTGGTACTAGGTTTTAATATCAAGATATCTAAAGAAATCCAGCAGCTAGCAAGACAAATGGATGTTGAGATCAAGAACCATACAGTCATCTACAAGCTGTTAGCCGACCTCAAGAATGAAATGAGCAGCCGTCTTCCCCCTGTCCGGGAAGAAACGTCAGTGGGTGAAGCAGAGATCTTGAAGGTGTTTAGATTTACTGGTTCCAAGAAGGCTTGTGTCGCTGGCTGTAGAGTAAAGCAAGGTGTTCTGAACAAGGACTGTAGATACAGAATAGTACGACGAGACAATACCATCCATGAAGGTAAACTCTCAACTCTCAAACGAGGATCAGACAATGTTGACGTTGTCAAGAAAGAGCAAGAATGTGGGTTAAGCTTTGAAAAGTTTTCTGGGTTCAAAGAAGCAGACAGAGTAGAATGTTATCAAATAAATATGAAGCAGGACGAGGTGGACTGGGAATGGGGGTTCTGA

Transcript

gene27520.t1

AACCGGTCTAAAGTGAACACCTACCGGCTGCAAAATATTGAACTTTTCTTGGTTTTACAAGATGCACTGGCTTCTGAGAGCAAGATCTCTACAAGTTATTACATGCCGTACATGTAGTGTTTGTAGGTCATTTGTATCTCATGCAACACAGAACGTTAGTAAACCCAGACAGAGCTCTTACTTTAGACTGATTTCTTCCAAGGATGTTTCCTATAGTCAGTTTAGAAGGTTTGCATCGTCTAGTAGCAGTACAACAGTAGGAGGGCCTACTATTACAAGGAAACAGCACACTGTATCTCCTAAACTAAAGACACGTTATGCAAGGAGAGAGTATTTACAGGGTGGTAATGATATTGTAACTGTCAGTCAACTAGCACATCATATTGACATTGACGAAGGAAAGCTTATTGATATTCTTGACGACATGGGAGAAAACATACGTAGTCCAAACTGTGCTGTTGCTCCTGAAGTAGCTGAGTTTATGTGTATGGAGTTCAATAAACCAACATTAGCTGAGACAAGACAGTCTGAAAGTCTAGTTACTAGACCACCAGTAGTTACAATAATGGGCCATGTTGACCATGGTAAAACTACACTACTTGATGCACTACGTAATAGTTCTATTGCTGCCGGTGAAGCTGGAGGAATAACTCAACATATTGGTGCCTTCTTAGTTACCTTACCATCTGGTGAAGAAATCACGTTCATCGACACACCTGGTCATGCAGCGTTTGAATCAATGAGAGCAAGAGGTGCTAATGTTACCGATATAGTGGTCCTTGTCGTTGCTGCCGATGACGGTGTTAAAACACAGACAGTTGAGTCCATCAGACACGCTGTCCATGCCAATGTTCCAATAATAGTAGCTATTAACAAGATTGATAAGGGAAGAAAGAATGTGGATCTTCTCAAGCGACAGCTTCTTTCCCATGGGATTCAGCTGGAAGAGTATGGTGGAGATGTCCAAGTGGTGGAGATCTCAGCACTGAAAAGAACCAACTTAGATAGTTTAACAGAGGCCATTATAACTTTAGCAGAGATGAATGATTTGCAGGCTGATACTGACACCAACATTGAGGGTGTGGTCATCGAGGCGAAGAAAGACAAAGGATTGGGACCTGTTGTAACAGCACTGGTCCAGAATGGAACATTAAAGATAGGGGACATTATTGTCGCTGGAAGTACATTTGCCAAGGTCCGTCAAATGTACACAGACAGGGGAACCATTGTCAGCACAGCACCACCCTCCACCCCAGTACAGGTCACTGGTTGGAAGGACTTGCCAGCTGCTGGTGAAAAACTCCATCAAGTGGACACAGAGAAAAAAGCTAATGAGCTTGCATTGTCAAGAAGATCATATGATGACCAGAAAAGAAAAGAGACTTTATCACAAAGCTTTGACTTGAGTGAAATAATTAAAGATGATGGACGAAGGATAAAGATATCTAAAGGGGAATATGATGCTGCTAATAAAATAGACGTAGTGGTTAAAGGTGATGTTGATGGTTCAGTAGAAGCAGTAGTTGATGCTCTAAACACGTGCAAATCGGACAAAATCAAACTAAGTGTTCTCCATGCTGGAGTTGGTTCAGTGTCTGAGTATGACATCAAGACAGCACATTCATTCAAAGGTGTGGTACTAGGTTTTAATATCAAGATATCTAAAGAAATCCAGCAGCTAGCAAGACAAATGGATGTTGAGATCAAGAACCATACAGTCATCTACAAGCTGTTAGCCGACCTCAAGAATGAAATGAGCAGCCGTCTTCCCCCTGTCCGGGAAGAAACGTCAGTGGGTGAAGCAGAGATCTTGAAGGTGTTTAGATTTACTGGTTCCAAGAAGGCTTGTGTCGCTGGCTGTAGAGTAAAGCAAGGTGTTCTGAACAAGGACTGTAGATACAGAATAGTACGACGAGACAATACCATCCATGAAGGTAAACTCTCAACTCTCAAACGAGGATCAGACAATGTTGACGTTGTCAAGAAAGAGCAAGAATGTGGGTTAAGCTTTGAAAAGTTTTCTGGGTTCAAAGAAGCAGACAGAGTAGAATGTTATCAAATAAATATGAAGCAGGACGAGGTGGACTGGGAATGGGGGTTCTGATTACTATTGTCCCCAGGTTTCACTCTCATCTTGTTGGCTGTGAGGGGACTGGAATGAGTGAAGATACTATTATAGTACATCAAGACAGTATAACTAAGAGAGTGCATCGCTATCCTATGATCAGTCGCTCTGTTACTATTTTTAGATTTTGTTACCAGGTTCCACGCACTATTCGCTTTCATATCTTGAATTTGGGACTGCGAATGAATGATGTTATTGAAAAGCTGGAATCTGATTGGTTCCAAAAACTAGAAATATGGGATATTACGTGGCTTTCACTCTCTTAGTTATACTCTCTTGAGTGTATAGATCCTGAAGATATATTATGACTGTGACATGCATTGACAATTCTGTGATGTGACCGTGCCATGGTTTATCCCAGTCGCATGAAAACTGCTCTAGTTTTAATTGTGTTGTACAATAGCAAACATAGAGTATATTTCATACTACACCCTAAAACCATGGTCACTGAACCTCAGGATAATTGAGTTTTTCACAGTCTACTCTATTATTCTGCATTATAATTCAAATTTGGAACAAATTGGATGATATAAAATATCACAGAGAAACTAAATTGGCATAAGATAATATTGATCACTGATTCTTGTAAAGG

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P46198	Translation initiation factor IF-2, mitochondrial OS=Bos taurus OX=9913 GN=MTIF2 PE=1 SV=1
Q91YJ5	Translation initiation factor IF-2, mitochondrial OS=Mus musculus OX=10090 GN=Mtif2 PE=1 SV=2
P46199	Translation initiation factor IF-2, mitochondrial OS=Homo sapiens OX=9606 GN=MTIF2 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002679 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00009 all species →	GTP_EFTU	Elongation factor Tu GTP binding domain	Domain	Interproscan
PF11987 all species →	IF-2	Translation-initiation factor 2	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR005225 all species →	Domain	Small GTP-binding protein domain	Interproscan
IPR036925 all species →	Homologous_superfamily	Translation initiation factor IF-2, domain 3 superfamily	Interproscan
IPR000795 all species →	Domain	Translational (tr)-type GTP-binding domain	Interproscan
IPR015760 all species →	Family	Translation initiation factor IF- 2	Interproscan
IPR023115 all species →	Domain	Translation initiation factor IF- 2, domain 3	Interproscan
IPR009000 all species →	Homologous_superfamily	Translation protein, beta-barrel domain superfamily	Interproscan
IPR000178 all species →	Family	Translation initiation factor IF-2, bacterial-like	Interproscan
IPR044145 all species →	Domain	Translation initiation factor IF-2, domain II	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR43381 all species →	TRANSLATION INITIATION FACTOR IF-2-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005525 all species →	Molecular Function	GTP binding	Interproscan
GO:0003924 all species →	Molecular Function	GTPase activity	Interproscan
GO:0003743 all species →	Molecular Function	translation initiation factor activity	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0006413 all species →	Biological Process	translational initiation	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
K02519	infB, MTIF2; translation initiation factor IF-2	-	Mitochondrial biogenesis	ko03029	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 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 →