Gene detail

Detailed information of g10871.t1 in Acropora digitifera

Genomic Location: chr5Alt:9116694...9148150
NR annotation: XP_029179721.2, ATP-dependent DNA helicase DDX11-like [Acropora millepora]
Species Acropora digitifera · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

g10871.t1

ATGGAAAAGGCACAAAAGCACATAAATGTTGAAGAAAAGAAGACAAAGAGCTGTGATTTGAAGCAATTATCTTTACATCAATCGCCGTCAATCAAACCCGCAGCTGATAAGAAGCCGGTATTTTTTCCATTTCCTTTCTCGCCATACGACATCCAGGAAGACTTTATGCACACTTTGTTTGATGTGCTCAACAATGGAGAAGTTGGAATCTTCGAGAGCCCCACTGGAACGGGCAAGTCATTAAGTTTGATTTGTGGTGCACTGACTTGGTTGAAGAATTATGAGGAGAGAAGACAAGAAGAGTTAGAGAATGCACTGTCAAGTTCGGATAAAGATGATAATCAAAGGAACATTACAACAAAAGATGTACAAAATGACTCTGCATCAACACCAGACTGGGTCATAGAATTTGCTGAAAAACAAGCTAAGCAAGAAAAGGAAGACAGATTGAAGGAAGAAAGAGAAAGGATTGAAAAACAAAGGGCTCAAATTTACAAGCTCAAGAATGAAATAAGACCTGCTTTTGCCATTAAAGGGAAGAGAAAACATAGTGATGACAAGCTAAGTGACTTTCACATGGGAGAAGAATTATCAGAAGACAAAATTTCTGAAGAGATCAATGAGGTGTTAGGCAAAACCATTAAAAAAGATCCCGATGCGGATATTGTATTGACTGAGTATTTCAGTGAAGGAGAAGATGCAGGCTCAGACCAAGAGGAAGATAACGATAAACACGAAGAGCCTCACTGCCTAAAGATTTACTATTGCAGTCGAACACACTCACAATTAGCTCAATTTGTGCGAGAGGTGCAAAAGAGTCCCTTTAATGAAAGCACTAGAGTGGTTTCCTTGGGATCAAGACAGAACCTCTGCATTAATGATGATGTTAAGCAACTAAAACATATAAACAAAATTAATGACAGATGTTTAGAACTTCAGAAAAAAGACAAAGAGAAGAAAACATCTGATGGAGAGAAGGCTCCAAAGAGGAAAAAACTTCTGACAGGGTGTCCTTATTATTCTTACCAACAGTTGCAGAGATTTCGAGACAATGTTTTGATTGACATTAAAGATATCGAACAGCTCGTTTCTATTGGAGAAGAACTTCAAGCGTGTCCTTACTATGGCACAAGATTAGCCATACCTGCTGCACAACTTGTTGTTTTACCCTACAACTTACTTCTTCACAAGTCTACAAGAGAAGCTTGTGGAATAAAGCTTAATGGCAATGTAGTTATCATAGACGAGGCACACAACTTAATTGACACAATCAGCAGTGTCTACAGCGTGGAGATTATGGGTTCTCAGATTTCACGTGCCCATTCTCAGCTAACACAATATCAAGATCGTTACAGGACAAGGTTAAAAGCAAAGAATTTACTCTACATCCAGCAACTCCTGTACATTCTTATCTGCTTCTTAAACTGTTTAGGGGAGAAGGAGATGCTTTCAAATTCCAAAATGCTCTTAACAGCTCCTGCTGAAAATGGTGTTCTCACTGGCCTAAGGGAACAAAGGGTACCAGCGGAAGTGAAATTAAAAACAATCAATGACTTCTTGTTTTCTGCAAAAATGGACAACGTTAACCTTTTTAAGATAAAAAAATACTGTGAGAAGAGCATGATTTCGAAGAAGCTTAATGGATTTGTCGACAAATACCAGTCTGGGCAGGTAGACACAGGGCTTAATGTGGAACAGGCATACCACAGTAGCAGCTCACCACTACAAATCATTGAGAGCTTTTTAGAAGCACTAACAAATGCTGACAAAGATGGAAGGGTGGTAGTAAATAGACAAGGTCGACTAAGCTGTTCCAGTCTCAAATTTCTTCTGTTGAATCCAGCTGTTCACTTTACCAACATTGTGAGAGAAGCAAGGGCAGTTGTTGTTGCTGGAGGAACAATGCAACCTATGTCAGATTTCAAAGATCAGTTATTCGCTTGTGCTGGGCTTCCTAATGAAAATATAGTAGAGTTCTCCTGTGGTCATGTTATTCCAGCAGAGCATTTATTGGCAGTAGCGCTCGATAGAGGACCATCAGGCAAAGAACTTGACTTCACATATCAATCCCGAGGCTCCACTGAATTGAAAGACGAGTTAGGCCGTCTCCTCGTCAACATTTTTGCTGTAGTTACTGGCGGAGTTGTCTGCTTTTTCTCCTCGTATGACTACGAGGACAAAGTTTATTCACACTGGCAAAAAACAGGCATTCTTGAAAGGATGAACGCGAGGAAAAAGGTCTTTAGAGAACCAAGAAAAACGAACCAACTCGACCAAGTCCTCTCCTCTTATTCATCTTACATTAAGAATTCTGCGGACAACAACCCATCTCCAAATGGTGCAGTTTTGTTCTGCGTTGTCGGAGGCAAAATGAGTGAGGGTATTAACTTTTCAGATGACCTTGGAAGATGTATTGTGATGGTGGGTCTTCCGTATCCTAACATGTATTCACCAGAGTTGAAGGAAAAAATGACGTATCTTGACTCCACCTTAGGGCCCAAAGCTGGACAAAGTCATTACGAAAATCTTTGCATGAAAGCTGTTAACCAATCAATAGGTCGAGCTATTCGTCACAGAGGGGACTATGCGACGATTCTTCTGTTAGATCAACGCTACGGCTCTGCCAGAATAACGAAAAGTTTGCCTGATTGGATATCAAACAGGCTCCAACATCACACTCGCTTTGGCTCTGCATTTGCCGCCATTCGTAAGTTCTTCGTGGATAAGAGGCAATTCATCGGTATCAAAGATTAG

Transcript

chr5Alt.g10871.t1

CCCCCAAGAAAATCTTCTGCCACAGTTTCCGCACATCAGAGCGAGGCTATTTGATTTGTGCGCGAAATTTGGGAACCAAAATACAATTCTTGTACAAGGTTTCAATCTTTTGGGATGGAAAAGGCACAAAAGCACATAAATGTTGAAGAAAAGAAGACAAAGAGCTGTGATTTGAAGCAATTATCTTTACATCAATCGCCGTCAATCAAACCCGCAGCTGATAAGAAGCCGGTATTTTTTCCATTTCCTTTCTCGCCATACGACATCCAGGAAGACTTTATGCACACTTTGTTTGATGTGCTCAACAATGGAGAAGTTGGAATCTTCGAGAGCCCCACTGGAACGGGCAAGTCATTAAGTTTGATTTGTGGTGCACTGACTTGGTTGAAGAATTATGAGGAGAGAAGACAAGAAGAGTTAGAGAATGCACTGTCAAGTTCGGATAAAGATGATAATCAAAGGAACATTACAACAAAAGATGTACAAAATGACTCTGCATCAACACCAGACTGGGTCATAGAATTTGCTGAAAAACAAGCTAAGCAAGAAAAGGAAGACAGATTGAAGGAAGAAAGAGAAAGGATTGAAAAACAAAGGGCTCAAATTTACAAGCTCAAGAATGAAATAAGACCTGCTTTTGCCATTAAAGGGAAGAGAAAACATAGTGATGACAAGCTAAGTGACTTTCACATGGGAGAAGAATTATCAGAAGACAAAATTTCTGAAGAGATCAATGAGGTGTTAGGCAAAACCATTAAAAAAGATCCCGATGCGGATATTGTATTGACTGAGTATTTCAGTGAAGGAGAAGATGCAGGCTCAGACCAAGAGGAAGATAACGATAAACACGAAGAGCCTCACTGCCTAAAGATTTACTATTGCAGTCGAACACACTCACAATTAGCTCAATTTGTGCGAGAGGTGCAAAAGAGTCCCTTTAATGAAAGCACTAGAGTGGTTTCCTTGGGATCAAGACAGAACCTCTGCATTAATGATGATGTTAAGCAACTAAAACATATAAACAAAATTAATGACAGATGTTTAGAACTTCAGAAAAAAGACAAAGAGAAGAAAACATCTGATGGAGAGAAGGCTCCAAAGAGGAAAAAACTTCTGACAGGGTGTCCTTATTATTCTTACCAACAGTTGCAGAGATTTCGAGACAATGTTTTGATTGACATTAAAGATATCGAACAGCTCGTTTCTATTGGAGAAGAACTTCAAGCGTGTCCTTACTATGGCACAAGATTAGCCATACCTGCTGCACAACTTGTTGTTTTACCCTACAACTTACTTCTTCACAAGTCTACAAGAGAAGCTTGTGGAATAAAGCTTAATGGCAATGTAGTTATCATAGACGAGGCACACAACTTAATTGACACAATCAGCAGTGTCTACAGCGTGGAGATTATGGGTTCTCAGATTTCACGTGCCCATTCTCAGCTAACACAATATCAAGATCGTTACAGGACAAGGTTAAAAGCAAAGAATTTACTCTACATCCAGCAACTCCTGTACATTCTTATCTGCTTCTTAAACTGTTTAGGGGAGAAGGAGATGCTTTCAAATTCCAAAATGCTCTTAACAGCTCCTGCTGAAAATGGTGTTCTCACTGGCCTAAGGGAACAAAGGGTACCAGCGGAAGTGAAATTAAAAACAATCAATGACTTCTTGTTTTCTGCAAAAATGGACAACGTTAACCTTTTTAAGATAAAAAAATACTGTGAGAAGAGCATGATTTCGAAGAAGCTTAATGGATTTGTCGACAAATACCAGTCTGGGCAGGTAGACACAGGGCTTAATGTGGAACAGGCATACCACAGTAGCAGCTCACCACTACAAATCATTGAGAGCTTTTTAGAAGCACTAACAAATGCTGACAAAGATGGAAGGGTGGTAGTAAATAGACAAGGTCGACTAAGCTGTTCCAGTCTCAAATTTCTTCTGTTGAATCCAGCTGTTCACTTTACCAACATTGTGAGAGAAGCAAGGGCAGTTGTTGTTGCTGGAGGAACAATGCAACCTATGTCAGATTTCAAAGATCAGTTATTCGCTTGTGCTGGGCTTCCTAATGAAAATATAGTAGAGTTCTCCTGTGGTCATGTTATTCCAGCAGAGCATTTATTGGCAGTAGCGCTCGATAGAGGACCATCAGGCAAAGAACTTGACTTCACATATCAATCCCGAGGCTCCACTGAATTGAAAGACGAGTTAGGCCGTCTCCTCGTCAACATTTTTGCTGTAGTTACTGGCGGAGTTGTCTGCTTTTTCTCCTCGTATGACTACGAGGACAAAGTTTATTCACACTGGCAAAAAACAGGCATTCTTGAAAGGATGAACGCGAGGAAAAAGGTCTTTAGAGAACCAAGAAAAACGAACCAACTCGACCAAGTCCTCTCCTCTTATTCATCTTACATTAAGAATTCTGCGGACAACAACCCATCTCCAAATGGTGCAGTTTTGTTCTGCGTTGTCGGAGGCAAAATGAGTGAGGGTATTAACTTTTCAGATGACCTTGGAAGATGTATTGTGATGGTGGGTCTTCCGTATCCTAACATGTATTCACCAGAGTTGAAGGAAAAAATGACGTATCTTGACTCCACCTTAGGGCCCAAAGCTGGACAAAGTCATTACGAAAATCTTTGCATGAAAGCTGTTAACCAATCAATAGGTCGAGCTATTCGTCACAGAGGGGACTATGCGACGATTCTTCTGTTAGATCAACGCTACGGCTCTGCCAGAATAACGAAAAGTTTGCCTGATTGGATATCAAACAGGCTCCAACATCACACTCGCTTTGGCTCTGCATTTGCCGCCATTCGTAAGTTCTTCGTGGATAAGAGGCAATTCATCGGTATCAAAGATTAGGGCAATAGTTGTAATCACAAGAGTTCCGAGGGGGTAGTTTTTCAAAATAGACCCTGTTCTTAAGTCCAACTCTCAAGGTATTTGTGAAAAGAATGTATTTATGTTCTTGAGTTGACTCAATGAAGTGTTTTTTGGGAAATAAAGTGTACCATCTATT

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q6AXC6	ATP-dependent DNA helicase DDX11 OS=Mus musculus OX=10090 GN=Ddx11 PE=1 SV=2
F1R345	ATP-dependent DNA helicase DDX11 OS=Danio rerio OX=7955 GN=ddx11 PE=2 SV=1
A8MPP1	Putative ATP-dependent DNA helicase DDX11-like protein 8 OS=Homo sapiens OX=9606 GN=DDX11L8 PE=1 SV=1

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF06733 all species →	DEAD_2	DEAD_2	Family	Interproscan
PF13307 all species →	Helicase_C_2	Helicase C-terminal domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR006554 all species →	Domain	Helicase-like, DEXD box c2 type	Interproscan
IPR014013 all species →	Domain	Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type	Interproscan
IPR010614 all species →	Domain	RAD3-like helicase, DEAD	Interproscan
IPR006555 all species →	Domain	ATP-dependent helicase, C-terminal	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR013020 all species →	Family	ATP-dependent helicase Rad3/Chl1-like	Interproscan
IPR045028 all species →	Family	Helicase superfamily 1/2, DinG/Rad3-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11472 all species →	DNA REPAIR DEAD HELICASE RAD3/XP-D SUBFAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003678 all species →	Molecular Function	DNA helicase activity	Interproscan
GO:0016818 all species →	Molecular Function	hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0004386 all species →	Molecular Function	helicase activity	Interproscan
GO:0006139 all species →	Biological Process	nucleobase-containing compound metabolic process	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0032508 all species →	Biological Process	DNA duplex unwinding	Interproscan
GO:0034085 all species →	Biological Process	establishment of sister chromatid cohesion	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
K11273	DDX11, CHL1, CTF1; chromosome transmission fidelity protein 1	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.

Expression pattern (RNA-seq)

Transcript abundance of g10871.t1 across 39 RNA-seq samples of Acropora digitifera. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.

39Samples

39TPM > 0

1Conditions

14.0Max TPM

9.2Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
Coral branch	39	39	9.24	14.00

Per sample · hover a bar for the full sample record

Show the sample table (39 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR23047208	Coral branch	Coral branch	adult	not recorded	SRP416931	14.00
SRR23047210	Coral branch	Coral branch	adult	not recorded	SRP416931	13.46
SRR23047209	Coral branch	Coral branch	adult	not recorded	SRP416931	13.30
SRR23047240	Coral branch	Coral branch	adult	not recorded	SRP416931	12.68
SRR23047233	Coral branch	Coral branch	adult	not recorded	SRP416931	12.33
SRR23047221	Coral branch	Coral branch	adult	not recorded	SRP416931	12.02
SRR23047206	Coral branch	Coral branch	adult	not recorded	SRP416931	11.64
SRR23047242	Coral branch	Coral branch	adult	not recorded	SRP416931	11.49
SRR23047238	Coral branch	Coral branch	adult	not recorded	SRP416931	10.76
SRR23047239	Coral branch	Coral branch	adult	not recorded	SRP416931	10.63
SRR23047229	Coral branch	Coral branch	adult	not recorded	SRP416931	10.48
SRR23047214	Coral branch	Coral branch	adult	not recorded	SRP416931	10.37
SRR23047231	Coral branch	Coral branch	adult	not recorded	SRP416931	10.15
SRR23047232	Coral branch	Coral branch	adult	not recorded	SRP416931	10.05
SRR23047213	Coral branch	Coral branch	adult	not recorded	SRP416931	9.84
SRR23047216	Coral branch	Coral branch	adult	not recorded	SRP416931	9.39
SRR23047215	Coral branch	Coral branch	adult	not recorded	SRP416931	9.26
SRR23047241	Coral branch	Coral branch	adult	not recorded	SRP416931	8.89
SRR23047243	Coral branch	Coral branch	adult	not recorded	SRP416931	8.81
SRR23047234	Coral branch	Coral branch	adult	not recorded	SRP416931	8.78
SRR23047225	Coral branch	Coral branch	adult	not recorded	SRP416931	8.73
SRR23047227	Coral branch	Coral branch	adult	not recorded	SRP416931	8.70
SRR23047219	Coral branch	Coral branch	adult	not recorded	SRP416931	8.41
SRR23047220	Coral branch	Coral branch	adult	not recorded	SRP416931	8.33
SRR23047228	Coral branch	Coral branch	adult	not recorded	SRP416931	8.25
SRR23047207	Coral branch	Coral branch	adult	not recorded	SRP416931	8.19
SRR23047230	Coral branch	Coral branch	adult	not recorded	SRP416931	8.01
SRR23047223	Coral branch	Coral branch	adult	not recorded	SRP416931	7.92
SRR23047237	Coral branch	Coral branch	adult	not recorded	SRP416931	7.89
SRR23047222	Coral branch	Coral branch	adult	not recorded	SRP416931	7.81
SRR23047226	Coral branch	Coral branch	adult	not recorded	SRP416931	7.62
SRR23047212	Coral branch	Coral branch	adult	not recorded	SRP416931	7.36
SRR23047235	Coral branch	Coral branch	adult	not recorded	SRP416931	6.84
SRR23047224	Coral branch	Coral branch	adult	not recorded	SRP416931	6.72
SRR23047218	Coral branch	Coral branch	adult	not recorded	SRP416931	6.71
SRR23047217	Coral branch	Coral branch	adult	not recorded	SRP416931	6.62
SRR23047211	Coral branch	Coral branch	adult	not recorded	SRP416931	6.59
SRR23047236	Coral branch	Coral branch	adult	not recorded	SRP416931	5.63
SRR23047244	Coral branch	Coral branch	adult	not recorded	SRP416931	5.56

Source: CnidoSite RNA-seq expression matrices (ADIGI_TPM, StringTie quantification over 39 runs), joined to SRA sample metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped by the descriptor carried in the expression matrix itself.

Co-expression network

Genes whose expression across the transcriptome samples of Acropora digitifera 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.

Direction	Partners	Most correlated partner	PCC
Positively correlated	7	g10321.t1	0.730813792104653
Negatively correlated	16	g7807.t1	-0.745221822502701

Open this gene in Network Analysis → The network opens with the gene already entered and both directions selected. There you can add up to 9 more genes, switch between the positive and negative network, and export the edge list.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Acropora digitifera, 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.

Peak calls overlapping this gene

Assay	Sample	Peaks	Region

No called peak overlaps this gene in 1 available assay. Either the gene is not near an accessible or marked region in those samples, or it is not represented in the peak caller’s annotation.

Browse the full epigenomic landscape of this species: DNase-seq (DHS).

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.	ready	open →
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 →