Detailed information of g24978.t1 in Acropora digitifera

Genomic Location: chr12Alt:57866...76392
NR annotation: XP_029213960.2, phosphatidylinositol-binding clathrin assembly protein LAP-like [Acropora millepora]
Species Acropora digitifera · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q9VI75Phosphatidylinositol-binding clathrin assembly protein LAP OS=Drosophila melanogaster OX=7227 GN=lap PE=1 SV=3
O55012Phosphatidylinositol-binding clathrin assembly protein OS=Rattus norvegicus OX=10116 GN=Picalm PE=1 SV=1
Q13492Phosphatidylinositol-binding clathrin assembly protein OS=Homo sapiens OX=9606 GN=PICALM PE=1 SV=2
 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF07651
all species →		ANTHANTH domainRepeatInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR008942
all species →		Homologous_superfamilyENTH/VHSInterproscan
IPR014712
all species →		Homologous_superfamilyANTH domain superfamilyInterproscan
IPR013809
all species →		DomainENTH domainInterproscan
IPR011417
all species →		DomainAP180 N-terminal homology (ANTH) domainInterproscan
IPR045192
all species →		FamilyClathrin coat assembly protein AP180-likeInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR22951
all species →		CLATHRIN ASSEMBLY PROTEINInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005545
all species →		Molecular Function1-phosphatidylinositol bindingInterproscan
GO:0030136
all species →		Cellular Componentclathrin-coated vesicleInterproscan
GO:0030276
all species →		Molecular Functionclathrin bindingInterproscan
GO:0048268
all species →		Biological Processclathrin coat assemblyInterproscan
GO:0005543
all species →		Molecular Functionphospholipid bindingInterproscan
GO:0000149
all species →		Molecular FunctionSNARE bindingInterproscan
GO:0005546
all species →		Molecular Functionphosphatidylinositol-4,5-bisphosphate bindingInterproscan
GO:0005905
all species →		Cellular Componentclathrin-coated pitInterproscan
GO:0006900
all species →		Biological Processvesicle budding from membraneInterproscan
GO:0008021
all species →		Cellular Componentsynaptic vesicleInterproscan
GO:0016185
all species →		Biological Processsynaptic vesicle budding from presynaptic endocytic zone membraneInterproscan
GO:0032050
all species →		Molecular Functionclathrin heavy chain bindingInterproscan
GO:0072583
all species →		Biological Processclathrin-dependent endocytosisInterproscan
GO:0098894
all species →		Cellular Componentextrinsic component of presynaptic endocytic zone membraneInterproscan

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
KOEnzymeEnzyme IDPathwayMap IDSource
K20044PICALM; phosphatidylinositol-binding clathrin assembly protein-Membrane traffickingko04131deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of g24978.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
179.3Max TPM
129.6Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Coral branch 39 39 129.63 179.33

Per sample · hover a bar for the full sample record

Show the sample table (39 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR23047210 Coral branch Coral branch adult not recorded SRP416931 179.33
SRR23047208 Coral branch Coral branch adult not recorded SRP416931 172.77
SRR23047221 Coral branch Coral branch adult not recorded SRP416931 157.34
SRR23047222 Coral branch Coral branch adult not recorded SRP416931 149.87
SRR23047243 Coral branch Coral branch adult not recorded SRP416931 146.81
SRR23047234 Coral branch Coral branch adult not recorded SRP416931 146.28
SRR23047220 Coral branch Coral branch adult not recorded SRP416931 143.52
SRR23047240 Coral branch Coral branch adult not recorded SRP416931 141.87
SRR23047237 Coral branch Coral branch adult not recorded SRP416931 138.46
SRR23047232 Coral branch Coral branch adult not recorded SRP416931 134.82
SRR23047207 Coral branch Coral branch adult not recorded SRP416931 133.58
SRR23047214 Coral branch Coral branch adult not recorded SRP416931 133.34
SRR23047209 Coral branch Coral branch adult not recorded SRP416931 132.91
SRR23047227 Coral branch Coral branch adult not recorded SRP416931 132.05
SRR23047224 Coral branch Coral branch adult not recorded SRP416931 131.56
SRR23047235 Coral branch Coral branch adult not recorded SRP416931 131.03
SRR23047206 Coral branch Coral branch adult not recorded SRP416931 130.13
SRR23047233 Coral branch Coral branch adult not recorded SRP416931 129.54
SRR23047231 Coral branch Coral branch adult not recorded SRP416931 129.15
SRR23047241 Coral branch Coral branch adult not recorded SRP416931 129.11
SRR23047215 Coral branch Coral branch adult not recorded SRP416931 128.56
SRR23047216 Coral branch Coral branch adult not recorded SRP416931 128.03
SRR23047217 Coral branch Coral branch adult not recorded SRP416931 127.49
SRR23047219 Coral branch Coral branch adult not recorded SRP416931 126.86
SRR23047242 Coral branch Coral branch adult not recorded SRP416931 124.53
SRR23047218 Coral branch Coral branch adult not recorded SRP416931 123.64
SRR23047225 Coral branch Coral branch adult not recorded SRP416931 123.49
SRR23047239 Coral branch Coral branch adult not recorded SRP416931 122.21
SRR23047213 Coral branch Coral branch adult not recorded SRP416931 120.55
SRR23047223 Coral branch Coral branch adult not recorded SRP416931 120.52
SRR23047211 Coral branch Coral branch adult not recorded SRP416931 117.66
SRR23047238 Coral branch Coral branch adult not recorded SRP416931 114.99
SRR23047226 Coral branch Coral branch adult not recorded SRP416931 114.30
SRR23047230 Coral branch Coral branch adult not recorded SRP416931 113.02
SRR23047236 Coral branch Coral branch adult not recorded SRP416931 112.67
SRR23047212 Coral branch Coral branch adult not recorded SRP416931 112.43
SRR23047228 Coral branch Coral branch adult not recorded SRP416931 106.84
SRR23047229 Coral branch Coral branch adult not recorded SRP416931 100.81
SRR23047244 Coral branch Coral branch adult not recorded SRP416931 93.34

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.

DirectionPartnersMost correlated partnerPCC
Positively correlated30g20983.t10.874404847952724
Negatively correlated12g2579.t1-0.767220658554951

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

AssaySamplePeaksRegion
DNase-seq (DHS)WholeAnimal1Intron 1

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.

AnalysisWhat it doesStatus
Primer designDesign PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.template foundopen →
BLASTSearch 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 foundopen →
Expression heatmapDraw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it.readyopen →
Gene family / orthogroupLook 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 analysisStart a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.open →
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