Gene detail

Detailed information of FUN_003896-T1 in Acropora pulchra

Genomic Location: ntLink_8:16600602...16624569
NR annotation: XP_015780253.1, PREDICTED: probable ATP-dependent RNA helicase DDX4 isoform X3 [Acropora digitifera]
Species Acropora pulchra · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

FUN_003896-T1

ATGGACGGGCCTTCACGTTCTTGGCAACCTACCTCGAGGCCAAATGACTCGAGTTTCGGTGAGCGAATGACATCCCACAACAGTCAAAGAAACCCTAAATTCGCAAGCACTAGAACTCCACAGTATGAGGAATGCAAGGTGTACGTTAAAAATGTTCCAGCAGACATGACAAGGGAAAGTTTTGAAGCACTGTTCAGAAACTGTGGAAATGTTTTGTCCGTGCACATTTTGGAGCCAAAGGAAGGAAGAAACAGTACTATCGGATTTGTAAAGTACGCATCAGATGAGGAAGTGATGAAGGCGATAGAGAGATTCAATGGCACTCAGTTGGGTCAAAGTGTCCTCGTGGTTGAAAGAGCTGTTCAGAAAGACCGAGATCGAAACACGACAAGAAACCAAGAGCAAGGATATTATCCAAAGGGAGATTTGCAAGGAAATCAATACGATTCACCTTCATTTCAAGGATACAGAGCACAAAACGATCATTCTCAGAGAGATTATCCTCGGCAAACCCTAAATGCACCTGAAACGAACAACAACCATTTTGGTATGGGCAACCGACAGGAAGAAGCTATATTTAACCCCAGAGGACCTGGCAGGGGAGAGCCTCCAAGGGTTGGAAATATGGGACAACAAAGTAATTATTACAGTGGACAAGTTGTGAATGGTGGTGAAGTGGCGGTCAACAATTCCCAAGGGACTGGTGTTGGATATGAACAGGCAGTGTTTAATCCGAGAGGACCTGGTCGTGGAGGAATCCAGAACAGTCACTTGCAGCCTTACCAAAATTCCATGGTTGGCCAGGCCACATACAGGCAGCCATATGAACTGAATAATCAACCAGCAGCCATGGGTGTGAGAGTTGAAGAGGCAGTTTTCAATCCTCGAGGACCTGGCAGGGGAGGTGGAATGGTCCCCCAATCAGTCCCTAGTTATTCCCCAGGAAGAAACAGCGGTTTCATGAATGGGAGTAATAATGACTCCTCTTACAGCCAAGGCAATCATACTTCATGGATGAGTGACGGCCATCAGCAGCATACTACACACATTGCTGATGATCTCCATCAAGAAATCAATGTCACAGGACGACTATCTCAAGTATCATCTCCTCAAGACACTCAACACATGACGAATGGTCCACAAACTGGTGAGAGAGGATATTTTGCTCGAGAAAGCCCAAACCAATCACCCCAACGCAGAGAAAGAGGTGGGCATAATGGCTATAAACGTGGTGAAGCTGGACACTTTGCAAGGGAATATCAAAACCAAGAAGAAGAAGGAGGAGAGCCTGTGAAAAGGATGCCTCCAGTGACATACATTCCACCAGAACTGCCTCGGGACATTGATGAGCTCTTTCGAGATGCACCACATAGTGGTTTGAATTTTGAAAAATATGACAGCATTCCTGTCATTGTTACTGGCAAAGACAAACCACCTCCAATTGAAACCTTTGAACAGGCTGGTATCTTAGACCAATGTGCTACGAACATCAGAAGAGCACAGTTTACCAAGCCAACACCAATTCAGAAGTATGCTATCCCAATAACTCTGGCTGGCAGAGACTTGATGGCCTGTGCCCAAACTGGTTCAGGAAAAACTGTGGCATACTTACTTCCTGTTCTGACTGGGATGATTAAACGTGGCCTGCTTGACAGTGGCAGTTACTTGTCTGGTGGTACTCAGTCTCCTGCAGCCCTCTGTCTTGCACCAACACGTGAGCTGGCAGTGCAGATCCATAAAGAAGTTTGCAAGTTTGCTTATGACACTGTAGTGCAAGCCAAAGTTTGTTATGGAGGAGTTAGCGTGCAGCATCAGTTGGATAAAATACAGCGGGGATGTCACTTTCTGATTGCCACCCCTGGAAGGCTTATTGACTTTGTTGAAAGGAGTCGGATAAGTTTGGCCAACGTGCAGTATCTTGTCTTAGATGAAGCTGATCGTATGCTGGATATGGGGTTTGAAGGTGATGTTCGTAAGATTGTGGAAAAACTTGGAATGCCTGACAAAATGAGCAGACAGACGTTGATGTTTAGCGCCACTTTCCCTGATGAGATTCAGCGATTGGCAGCTGACTTCTTGAAAGAAAGCTATCTGTTTGTTGCCGTTGGCACCGTCGGAGGCTCGAATCTCGACATAAGTCAAACTGTCATTTCTGTTGCTGGAGATGACAAACAGGAGAAGCTTTTTGACATTTTGCTTCATTCTGGCACAGACCGCACTCTTATATTTGTGGAACTGAAGCGAGTTGCAGACTTCTTGGCGTGTCTCTTATCACAAAACAAGTTCCCCACTACAAGCATTAGTGGGGACAGAACACAACAGGAGCGTGAGGCTGCTCTGCTTGACTTCAGAACTGGCCGAGCACCAGTCCTTGTTGCGACATCAGTGGCTGCACGTGGTCTTGATATTGCAGATGTCAAGCACGTGATCAACTATGATCTGCCCCAGGATATTGATGAGTATGTGCACAGGATAGGGCGCACAGGACGAATTGGCAATAAAGGAAAAGCCACATCATTCTTTCAACCTGACAGAGATGAGAAACTTGCTCGCAGTTTGGTGAAGGTCTTATCACAGGCATACCAGGAGGTCCCTGAGTGGCTTGAGCAAGTGGCAGAAGAGGCAGTTGGCTCATCATATGGGCCTGCTGGAGGAAGATTCGCTTCCAAAGATAGAAGAGAGAGAGACCGTCCTAGAGGGTCAGCCCATGTCCAGCCGCAAATGAGTGCCTTTACGAACGGAATGAATGCTGTGACCAAGAGATTGGAACAAACTAGCATCCAGCCTGTCAGCGTTCCAACAGAATGCACAGAGGATGGGGAGGACTGGGACTGA

Transcript

FUN_003896-T1

GCAAAGAACGCGAGTAAGGTCATTGGCGGTAATTCCGAAATACAGGGAAAAAATGGACGGGCCTTCACGTTCTTGGCAACCTACCTCGAGGCCAAATGACTCGAGTTTCGGTGAGCGAATGACATCCCACAACAGTCAAAGAAACCCTAAATTCGCAAGCACTAGAACTCCACAGTATGAGGAATGCAAGGTGTACGTTAAAAATGTTCCAGCAGACATGACAAGGGAAAGTTTTGAAGCACTGTTCAGAAACTGTGGAAATGTTTTGTCCGTGCACATTTTGGAGCCAAAGGAAGGAAGAAACAGTACTATCGGATTTGTAAAGTACGCATCAGATGAGGAAGTGATGAAGGCGATAGAGAGATTCAATGGCACTCAGTTGGGTCAAAGTGTCCTCGTGGTTGAAAGAGCTGTTCAGAAAGACCGAGATCGAAACACGACAAGAAACCAAGAGCAAGGATATTATCCAAAGGGAGATTTGCAAGGAAATCAATACGATTCACCTTCATTTCAAGGATACAGAGCACAAAACGATCATTCTCAGAGAGATTATCCTCGGCAAACCCTAAATGCACCTGAAACGAACAACAACCATTTTGGTATGGGCAACCGACAGGAAGAAGCTATATTTAACCCCAGAGGACCTGGCAGGGGAGAGCCTCCAAGGGTTGGAAATATGGGACAACAAAGTAATTATTACAGTGGACAAGTTGTGAATGGTGGTGAAGTGGCGGTCAACAATTCCCAAGGGACTGGTGTTGGATATGAACAGGCAGTGTTTAATCCGAGAGGACCTGGTCGTGGAGGAATCCAGAACAGTCACTTGCAGCCTTACCAAAATTCCATGGTTGGCCAGGCCACATACAGGCAGCCATATGAACTGAATAATCAACCAGCAGCCATGGGTGTGAGAGTTGAAGAGGCAGTTTTCAATCCTCGAGGACCTGGCAGGGGAGGTGGAATGGTCCCCCAATCAGTCCCTAGTTATTCCCCAGGAAGAAACAGCGGTTTCATGAATGGGAGTAATAATGACTCCTCTTACAGCCAAGGCAATCATACTTCATGGATGAGTGACGGCCATCAGCAGCATACTACACACATTGCTGATGATCTCCATCAAGAAATCAATGTCACAGGACGACTATCTCAAGTATCATCTCCTCAAGACACTCAACACATGACGAATGGTCCACAAACTGGTGAGAGAGGATATTTTGCTCGAGAAAGCCCAAACCAATCACCCCAACGCAGAGAAAGAGGTGGGCATAATGGCTATAAACGTGGTGAAGCTGGACACTTTGCAAGGGAATATCAAAACCAAGAAGAAGAAGGAGGAGAGCCTGTGAAAAGGATGCCTCCAGTGACATACATTCCACCAGAACTGCCTCGGGACATTGATGAGCTCTTTCGAGATGCACCACATAGTGGTTTGAATTTTGAAAAATATGACAGCATTCCTGTCATTGTTACTGGCAAAGACAAACCACCTCCAATTGAAACCTTTGAACAGGCTGGTATCTTAGACCAATGTGCTACGAACATCAGAAGAGCACAGTTTACCAAGCCAACACCAATTCAGAAGTATGCTATCCCAATAACTCTGGCTGGCAGAGACTTGATGGCCTGTGCCCAAACTGGTTCAGGAAAAACTGTGGCATACTTACTTCCTGTTCTGACTGGGATGATTAAACGTGGCCTGCTTGACAGTGGCAGTTACTTGTCTGGTGGTACTCAGTCTCCTGCAGCCCTCTGTCTTGCACCAACACGTGAGCTGGCAGTGCAGATCCATAAAGAAGTTTGCAAGTTTGCTTATGACACTGTAGTGCAAGCCAAAGTTTGTTATGGAGGAGTTAGCGTGCAGCATCAGTTGGATAAAATACAGCGGGGATGTCACTTTCTGATTGCCACCCCTGGAAGGCTTATTGACTTTGTTGAAAGGAGTCGGATAAGTTTGGCCAACGTGCAGTATCTTGTCTTAGATGAAGCTGATCGTATGCTGGATATGGGGTTTGAAGGTGATGTTCGTAAGATTGTGGAAAAACTTGGAATGCCTGACAAAATGAGCAGACAGACGTTGATGTTTAGCGCCACTTTCCCTGATGAGATTCAGCGATTGGCAGCTGACTTCTTGAAAGAAAGCTATCTGTTTGTTGCCGTTGGCACCGTCGGAGGCTCGAATCTCGACATAAGTCAAACTGTCATTTCTGTTGCTGGAGATGACAAACAGGAGAAGCTTTTTGACATTTTGCTTCATTCTGGCACAGACCGCACTCTTATATTTGTGGAACTGAAGCGAGTTGCAGACTTCTTGGCGTGTCTCTTATCACAAAACAAGTTCCCCACTACAAGCATTAGTGGGGACAGAACACAACAGGAGCGTGAGGCTGCTCTGCTTGACTTCAGAACTGGCCGAGCACCAGTCCTTGTTGCGACATCAGTGGCTGCACGTGGTCTTGATATTGCAGATGTCAAGCACGTGATCAACTATGATCTGCCCCAGGATATTGATGAGTATGTGCACAGGATAGGGCGCACAGGACGAATTGGCAATAAAGGAAAAGCCACATCATTCTTTCAACCTGACAGAGATGAGAAACTTGCTCGCAGTTTGGTGAAGGTCTTATCACAGGCATACCAGGAGGTCCCTGAGTGGCTTGAGCAAGTGGCAGAAGAGGCAGTTGGCTCATCATATGGGCCTGCTGGAGGAAGATTCGCTTCCAAAGATAGAAGAGAGAGAGACCGTCCTAGAGGGTCAGCCCATGTCCAGCCGCAAATGAGTGCCTTTACGAACGGAATGAATGCTGTGACCAAGAGATTGGAACAAACTAGCATCCAGCCTGTCAGCGTTCCAACAGAATGCACAGAGGATGGGGAGGACTGGGACTGAATACAATCCAGTTGAAACCGTTTATTGTAAACAAGATAGTTGATTGGACATTGTAAAAACTGTTTCATTTCCAGAGAAGATGCTCTTTGTTCCATTTCTATTTACATATTTCAGTGAACTGTTTGCTGTTATTGACTGTGTTAGCTGTAAATTCTATAGCTTTATTTAACGGCTTCTGCAGATAAAAATTTTAATAAGAGGGGTGAATAGGGGTATGCAAATCTGTGAAAAAAAAAAAAAAAAACAAGTACTCCTTTCGATATGTCAGATCCACGATCTGGACTTTCGGACGAGAGCAAAGTCAATAATCCGGGCGAAAAACAAGAATGAAACCACAATCCACTGGAATTGCAGGATCCGAAAATCTGTGAAAATCTCGCTCAGAATTCGAAATCCATACTAAAATATCATATAGCCTAGTCACCCCATCTTAGAATGACTTCTATGTGTTGTGGTTCCGTCACACTGCCTTCCAAAACCTTCTTCTCTTCCTGGAAGCATTTTGTGACAAGTTATACCACAATACTATTAAATTGATGAGTGTCAGCCAAAATCTGTTCATCTTTGTTGATTAATTTTGTGCTGTTGTTTTTCAAAACGTTAAAGATAGCATTTTCTATTATATGAAATTATTATATCGTATTATACTTGATGTGTTGTGGATAAATGAAGGCTGCATAGTGTTGAGGACTGGTTAGATCGGATGTCTTATCTACCTTCTTCCTAATCGCTGTCAGTCAACGTTTGGGCTGTGTCGTTTCTGTTAGGGTTAGAGCCAAAGCTGACGGGATAAGCTCTGGCATTAGATATTAGCTTCATTAAAATTATCGGTTATATTGCACTGGTAGTTGTTGTTCTGGAATTGTTCACTTAAGGCCTCAAAAATTTTTTGCCCTTCAATTTTCTTTTTGCCTTTTCCTCGCGGCATGTTTTACTGATTATGTTTTGCTTTCAGATTTTAGTCGTTTACATTTACTTCCCTTGTGAAGTTTTGGAAAATAGCCCTTATTACATTTATCAGCGGTGCAGGACTTAAACGAGGATAATTAACAATAAGACCCGTAGCCCGAAAGGGCTACGGGTCAATAGCCCATGAGGCTATTGATCCGTGGCCCTTGAGGAGGAAGGGTCTAATTGTTTTAGTATCACCCAACTAGTCGGAGAGGAAAAAGCAATAATAAATTCAGCAAAAAACATTTGTTTGGGAATAAAACGAAATAAATAGGTTTACAAAACCGGCGAACCTCGCTACTCTATGACTATTACTAATAGACCCATAGTAGCGTAGCCAATCAAAATGCAGGATTTGCATTTAGTCCACTAGTAGGGTGATACTAATGTGTGATGGTATCGAGTCTGTATGCAGTGTTAAACAAAAGAGGTTTTGACTGCAAGCTCATTTGCAATAACATCCATTGCTTTCTACTGTTGCTC

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q3MSQ8	Probable ATP-dependent RNA helicase DDX4 OS=Pelophylax lessonae OX=45623 GN=ddx4 PE=2 SV=1
Q61496	ATP-dependent RNA helicase DDX4 OS=Mus musculus OX=10090 GN=Ddx4 PE=1 SV=2
Q9NQI0	Probable ATP-dependent RNA helicase DDX4 OS=Homo sapiens OX=9606 GN=DDX4 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000960 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00271 all species →	Helicase_C	Helicase conserved C-terminal domain	Domain	Interproscan
PF00076 all species →	RRM_1	RNA recognition motif	Domain	Interproscan
PF00270 all species →	DEAD	DEAD/DEAH box helicase	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan
IPR001650 all species →	Domain	Helicase, C-terminal domain-like	Interproscan
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan
IPR014014 all species →	Domain	RNA helicase, DEAD-box type, Q motif	Interproscan
IPR014001 all species →	Domain	Helicase superfamily 1/2, ATP-binding domain	Interproscan
IPR000504 all species →	Domain	RNA recognition motif domain	Interproscan
IPR000629 all species →	Conserved_site	ATP-dependent RNA helicase DEAD-box, conserved site	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR011545 all species →	Domain	DEAD/DEAH box helicase domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR47958 all species →	ATP-DEPENDENT RNA HELICASE DBP3	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0003724 all species →	Molecular Function	RNA helicase activity	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0007276 all species →	Biological Process	gamete generation	Interproscan
GO:0030154 all species →	Biological Process	cell differentiation	Interproscan
GO:0043186 all species →	Cellular Component	P granule	Interproscan
GO:0005524 all species →	Molecular Function	ATP 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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K13982	DDX4, VASA; probable ATP-dependent RNA helicase DDX4	EC:5.6.2.7	Chromosome and associated proteins	ko03036	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 Acropora pulchra 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 pulchra, 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 →