Gene detail

Detailed information of g28498.t1 in Acropora digitifera

Genomic Location: chr13Alt:20988751...21006442
NR annotation: XP_044184195.1, LOW QUALITY PROTEIN: AP-2 complex subunit alpha-2-like [Acropora millepora]
Species Acropora digitifera · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

g28498.t1

ATGCCTGCCGTCAAGGGAGAAGGAATGCGCGGATTAGCCGTGTTTATTTCAGATATTCGTAACTGCAAGTCGAAAGAGTCAGAAATTAAGAGAATCAATAAAGAACTTGCGAACATTAGGAATAAATTCAAAGGTGATAAACAATTAGACGGATATCAGAAGAAAAAGTATGTCTGCAAGTTACTCTTTATTTTTCTGCTTGGCCATGACATCGATTTCGGTCACATGGAAGCCGTAAATCTGCTCTCTTCCAACAAGTATACAGAGAAACAAATTGGCTACCTTTTCATCTCTGTCCTGGTAAGTGCCAACAGCGAACTTATCAAACTGATCATTCAGAGCATCAAGAACGACTTGTCAAGTCGCAATCCCATCAATGTTTGTCTTGCACTGCAGTGCATAGCAAATATTGGTAATGAGGAAATGGTTGAAGCAGTGGGCAAAGAGGTTCCAAAGCTTTTAGTCTCTCCAGATACAAATGATAGCGTCAAACAGTGTGCTGCCCTTTGCATTCTGAAGCTGTTTAGACTTAAAACAGATATCTTGCCTCCTGGAGAGTGGACTTCAAGAATAGTACAGCTCTTAAATGATAAGCACTTGGGCGTGGTCACCTCTGCTGCTAGTCTAATCCAGGGTGTTGTCCATGATTATGCCGATGATTACAAGGGATGCGTCCAACTAGCAGTCTCAAGGCTTAGTAGGATTGTAACATCATCGTACACAGACCTTCAAGACTACACTTACTACTTTGTTCCAGCCCCATGGCTGTGTGTGAAACTACTGAAACTTCTGCAGCTTTACCCTCCACCAGATGACCCAGCAATTCATGCAAGGTTAAATGAATGCCTGGAGACCATTTTAAACAAAGCACAGGAGCCCCCTAAATCCAAGAAAGTGCAGCACTCCAATGCAAGAAATGCTGTCCTCTTTGAAGCCATAAACCAGATTATCCACATGGATAGTGAGCAAAGCTTATTGATCAGAGGGTGTAACCAGCTGGGTCAGTTTTTGACACACAGGGAAACTAATCTTAGATATCTAGCTTTAGAGGGCCTCTGTCTTATGTCAAACTCTGAGTTCTCTGCTGATGCAGTCAGGAAACATCAAGAAACTGTTGTGTCAGCACTGAAGACTGAACGCGATGTCAGTGTACGCCAGAGAGCAGTTGATCTTCTCTATGCGATGTGTGATAAGAATAATGCAGAGGAGATTGTGTCGGAAATGTTGACTTATCTTGAAACTGCAGATTATTCCATCAAGGAGGAAATGGTGTTGAAAGTTGCCATTCTTGCCGAGAAGTTTGCCACAGACTATTCCTGGTACATGGACACCATCCTTACACTGATCAGAAATGCTGGGGATTATGTCAGTGAAGAGGTATGGTACCGCGTCATCCAAATTGTCATTAACAGGGATGACATTCAGGGTTATGCAGCTAAGACAGTGTTTGAGGCCCTGCAGTCACCTTCCTGCCATGAGAATATGGTGAAAGTTGGTGGTTACATCTTGGGAGAATTTGGAAATCTTATTGCTGGTGATCCACGCTCAAGCCCAATGGTGCAGTTCCAACTACTTCACAGCAAATTTGCATTGTGCTCTTCTGCAACAAGAGGCTTGCTCATGTCAACTTACGTCAAATTTATTAACCTGTTCCCAGAAATCAAGGGCCACATTCAAGAGATTATGCGAAGTGACTCTAACCTCAAAAACTCAGATGCGGAAATTCAGCAGAGAGCTTTGGAATACTTGAAGCTTAGTACTGTTGCATCTCCTGATGTCTTGGCTACTGTGCTGGAAGAAATGCCACCGTTTCCTGAACGTGAATCTTCTATCCTGGCCAAACTAAAGAAAAAGAAACAAGAGAAAAGTGGAATTGTGGAGAAGGAAGATAAACCAGAACCTGTGGAGAAGCCAACAACCAATGGACAAGTTACAGTTGTTAACGAGCATCCACCTTCCAATCCAGCATTACATGCAGATCTCATTAGTGCAGGAAATGCTCCTGTTGTGAACAATTTTGCCGCAGCTTCTGAGCCTGCAGTTGGTGGAGGAGGAGGAGGAGGAGGAAGCCTTCTTGTGGATGTGTTTGACATGCCGGCAGCAACAACAGTGTTGGGAGGTGTTCCCTCCATCACACCTGGTGCTGAGGAGAATCTTAAAAAATTTGTCTTCAAAAACACTGGAGTGTTGTTTGAAAATGATATTCTACAAGTTGGAATAAAGTCAGAGTTCAGTGAGACCAAGGGAAGTGTTGGTATATTCTATGGCAACAAGACGTCTTCACAATTTGTTAATTTCTCCTCAAGCGTTCATGTTCCCGGTGATCTAAATACTCGTCTGCAAATCGACTCCAGTCCTCCGCCGCCAATCGTAGAGGGTGGGGCCCAGATGAAGCAAATGGTTAATGTGGAGATTATAATGGAATTTAATGATTATCCAATCGTAGATATTCAATTCAGTGTGAACGGCATGAGTCAAAGAATTGCCCTTCCGTTGCCATTGTTTGCGTCCAAGTTCTTCACACCCACAGAAATGAATTCGCAGGATTTCTTTTCAAGATGGAAACAGTTAGGGAGTCCTGGTCAAGAATGCCAGCAGATTTTTAAAGCTAAGTTCCCCATTGACACGGAAACAATTAAAGCAAAGTTATTGCTTGTGCCCAGTAGACCAGTTGAGTGCTTAGTTGTCTGGCCTTTGAATGAAAGCGAGGCTGGAGTTGACCTTGCCTTTCCTATGTCAATGCTTAGCGGCTTTGGCGTGTCCTTGCTTGAGAATGTCGACCCTAATCCAGATAATTTTGTTTGTGCTGGGATTATCAAAGCACGAACGGTGCAAATTGGAACACTGCTGCGACTGGAGCCGAACAGACAAGCACAGATGTTCAGATTGACGATACGAAGCTCAAGGCCAGATGTCGCCAAATACCTTGTAGATATCTTGCTTGACCAGTTTTAA

Transcript

chr13Alt.g28498.t1

CTCGCTCTGGAAAGCGTTTGATGGCGGCTGCCATCTTCCGTGTCGAATTGAGATCAAGAGCGGAAAACGCCTTTTCGCCATCTGACTGATCGCTCAATCCGCCTTTTTTGCCATTACTACAGTCTCTTTGTGGGATTTATAGCTCTGTGAACTGTCATCTTTGGAGATTTCATGTGCATCGTAGCTGGTAGTAAGCATACTCGTTGAAGTGGGCTGTGTCAAATTTTGAAGACTTTGATATTGCGGTGGGACCGAAACATCCAACATGCCTGCCGTCAAGGGAGAAGGAATGCGCGGATTAGCCGTGTTTATTTCAGATATTCGTAACTGCAAGTCGAAAGAGTCAGAAATTAAGAGAATCAATAAAGAACTTGCGAACATTAGGAATAAATTCAAAGGTGATAAACAATTAGACGGATATCAGAAGAAAAAGTATGTCTGCAAGTTACTCTTTATTTTTCTGCTTGGCCATGACATCGATTTCGGTCACATGGAAGCCGTAAATCTGCTCTCTTCCAACAAGTATACAGAGAAACAAATTGGCTACCTTTTCATCTCTGTCCTGGTAAGTGCCAACAGCGAACTTATCAAACTGATCATTCAGAGCATCAAGAACGACTTGTCAAGTCGCAATCCCATCAATGTTTGTCTTGCACTGCAGTGCATAGCAAATATTGGTAATGAGGAAATGGTTGAAGCAGTGGGCAAAGAGGTTCCAAAGCTTTTAGTCTCTCCAGATACAAATGATAGCGTCAAACAGTGTGCTGCCCTTTGCATTCTGAAGCTGTTTAGACTTAAAACAGATATCTTGCCTCCTGGAGAGTGGACTTCAAGAATAGTACAGCTCTTAAATGATAAGCACTTGGGCGTGGTCACCTCTGCTGCTAGTCTAATCCAGGGTGTTGTCCATGATTATGCCGATGATTACAAGGGATGCGTCCAACTAGCAGTCTCAAGGCTTAGTAGGATTGTAACATCATCGTACACAGACCTTCAAGACTACACTTACTACTTTGTTCCAGCCCCATGGCTGTGTGTGAAACTACTGAAACTTCTGCAGCTTTACCCTCCACCAGATGACCCAGCAATTCATGCAAGGTTAAATGAATGCCTGGAGACCATTTTAAACAAAGCACAGGAGCCCCCTAAATCCAAGAAAGTGCAGCACTCCAATGCAAGAAATGCTGTCCTCTTTGAAGCCATAAACCAGATTATCCACATGGATAGTGAGCAAAGCTTATTGATCAGAGGGTGTAACCAGCTGGGTCAGTTTTTGACACACAGGGAAACTAATCTTAGATATCTAGCTTTAGAGGGCCTCTGTCTTATGTCAAACTCTGAGTTCTCTGCTGATGCAGTCAGGAAACATCAAGAAACTGTTGTGTCAGCACTGAAGACTGAACGCGATGTCAGTGTACGCCAGAGAGCAGTTGATCTTCTCTATGCGATGTGTGATAAGAATAATGCAGAGGAGATTGTGTCGGAAATGTTGACTTATCTTGAAACTGCAGATTATTCCATCAAGGAGGAAATGGTGTTGAAAGTTGCCATTCTTGCCGAGAAGTTTGCCACAGACTATTCCTGGTACATGGACACCATCCTTACACTGATCAGAAATGCTGGGGATTATGTCAGTGAAGAGGTATGGTACCGCGTCATCCAAATTGTCATTAACAGGGATGACATTCAGGGTTATGCAGCTAAGACAGTGTTTGAGGCCCTGCAGTCACCTTCCTGCCATGAGAATATGGTGAAAGTTGGTGGTTACATCTTGGGAGAATTTGGAAATCTTATTGCTGGTGATCCACGCTCAAGCCCAATGGTGCAGTTCCAACTACTTCACAGCAAATTTGCATTGTGCTCTTCTGCAACAAGAGGCTTGCTCATGTCAACTTACGTCAAATTTATTAACCTGTTCCCAGAAATCAAGGGCCACATTCAAGAGATTATGCGAAGTGACTCTAACCTCAAAAACTCAGATGCGGAAATTCAGCAGAGAGCTTTGGAATACTTGAAGCTTAGTACTGTTGCATCTCCTGATGTCTTGGCTACTGTGCTGGAAGAAATGCCACCGTTTCCTGAACGTGAATCTTCTATCCTGGCCAAACTAAAGAAAAAGAAACAAGAGAAAAGTGGAATTGTGGAGAAGGAAGATAAACCAGAACCTGTGGAGAAGCCAACAACCAATGGACAAGTTACAGTTGTTAACGAGCATCCACCTTCCAATCCAGCATTACATGCAGATCTCATTAGTGCAGGAAATGCTCCTGTTGTGAACAATTTTGCCGCAGCTTCTGAGCCTGCAGTTGGTGGAGGAGGAGGAGGAGGAGGAAGCCTTCTTGTGGATGTGTTTGACATGCCGGCAGCAACAACAGTGTTGGGAGGTGTTCCCTCCATCACACCTGGTGCTGAGGAGAATCTTAAAAAATTTGTCTTCAAAAACACTGGAGTGTTGTTTGAAAATGATATTCTACAAGTTGGAATAAAGTCAGAGTTCAGTGAGACCAAGGGAAGTGTTGGTATATTCTATGGCAACAAGACGTCTTCACAATTTGTTAATTTCTCCTCAAGCGTTCATGTTCCCGGTGATCTAAATACTCGTCTGCAAATCGACTCCAGTCCTCCGCCGCCAATCGTAGAGGGTGGGGCCCAGATGAAGCAAATGGTTAATGTGGAGATTATAATGGAATTTAATGATTATCCAATCGTAGATATTCAATTCAGTGTGAACGGCATGAGTCAAAGAATTGCCCTTCCGTTGCCATTGTTTGCGTCCAAGTTCTTCACACCCACAGAAATGAATTCGCAGGATTTCTTTTCAAGATGGAAACAGTTAGGGAGTCCTGGTCAAGAATGCCAGCAGATTTTTAAAGCTAAGTTCCCCATTGACACGGAAACAATTAAAGCAAAGTTATTGCTTGTGCCCAGTAGACCAGTTGAGTGCTTAGTTGTCTGGCCTTTGAATGAAAGCGAGGCTGGAGTTGACCTTGCCTTTCCTATGTCAATGCTTAGCGGCTTTGGCGTGTCCTTGCTTGAGAATGTCGACCCTAATCCAGATAATTTTGTTTGTGCTGGGATTATCAAAGCACGAACGGTGCAAATTGGAACACTGCTGCGACTGGAGCCGAACAGACAAGCACAGATGTTCAGATTGACGATACGAAGCTCAAGGCCAGATGTCGCCAAATACCTTGTAGATATCTTGCTTGACCAGTTTTAAAACCAGTTTAGCTTAATGTGTCAACAGGAGAAAGATACGCATTCCAGAATAACCAGTAAAGTTATTTTACATCCCCTCCAGTGGAAAACGTCTAATGAAGTTTTTTTTTCATA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q0VCK5	AP-2 complex subunit alpha-2 OS=Bos taurus OX=9913 GN=AP2A2 PE=1 SV=1
P18484	AP-2 complex subunit alpha-2 OS=Rattus norvegicus OX=10116 GN=Ap2a2 PE=1 SV=3
P17427	AP-2 complex subunit alpha-2 OS=Mus musculus OX=10090 GN=Ap2a2 PE=1 SV=2

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01602 all species →	Adaptin_N	Adaptin N terminal region	Repeat	Interproscan
PF02883 all species →	Alpha_adaptinC2	Adaptin C-terminal domain	Domain	Interproscan
PF02296 all species →	Alpha_adaptin_C	Alpha adaptin AP2, C-terminal domain	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR017104 all species →	Family	Adaptor protein complex AP-2, alpha subunit	Interproscan
IPR011989 all species →	Homologous_superfamily	Armadillo-like helical	Interproscan
IPR013041 all species →	Homologous_superfamily	Clathrin adaptor, appendage, Ig-like subdomain superfamily	Interproscan
IPR009028 all species →	Homologous_superfamily	Coatomer/calthrin adaptor appendage, C-terminal subdomain	Interproscan
IPR002553 all species →	Domain	Clathrin/coatomer adaptor, adaptin-like, N-terminal	Interproscan
IPR008152 all species →	Domain	Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain	Interproscan
IPR016024 all species →	Homologous_superfamily	Armadillo-type fold	Interproscan
IPR012295 all species →	Homologous_superfamily	TBP domain superfamily	Interproscan
IPR003164 all species →	Domain	Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain	Interproscan
IPR050840 all species →	Family	Adaptor Complexes Large Subunit	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR22780 all species →	ADAPTIN, ALPHA/GAMMA/EPSILON	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0015031 all species →	Biological Process	protein transport	Interproscan
GO:0030122 all species →	Cellular Component	AP-2 adaptor complex	Interproscan
GO:0035615 all species →	Molecular Function	clathrin adaptor activity	Interproscan
GO:0072583 all species →	Biological Process	clathrin-dependent endocytosis	Interproscan
GO:0006886 all species →	Biological Process	intracellular protein transport	Interproscan
GO:0016192 all species →	Biological Process	vesicle-mediated transport	Interproscan
GO:0030117 all species →	Cellular Component	membrane coat	Interproscan
GO:0030131 all species →	Cellular Component	clathrin adaptor complex	Interproscan
GO:0140312 all species →	Molecular Function	cargo adaptor activity	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
K11824	AP2A; AP-2 complex subunit alpha	-	Exosome	ko04147	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g28498.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

163.8Max TPM

134.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
Coral branch	39	39	134.58	163.80

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
SRR23047235	Coral branch	Coral branch	adult	not recorded	SRP416931	163.80
SRR23047219	Coral branch	Coral branch	adult	not recorded	SRP416931	157.90
SRR23047211	Coral branch	Coral branch	adult	not recorded	SRP416931	153.93
SRR23047241	Coral branch	Coral branch	adult	not recorded	SRP416931	152.93
SRR23047222	Coral branch	Coral branch	adult	not recorded	SRP416931	152.31
SRR23047231	Coral branch	Coral branch	adult	not recorded	SRP416931	150.41
SRR23047237	Coral branch	Coral branch	adult	not recorded	SRP416931	149.50
SRR23047232	Coral branch	Coral branch	adult	not recorded	SRP416931	148.77
SRR23047209	Coral branch	Coral branch	adult	not recorded	SRP416931	147.62
SRR23047217	Coral branch	Coral branch	adult	not recorded	SRP416931	147.42
SRR23047207	Coral branch	Coral branch	adult	not recorded	SRP416931	145.68
SRR23047216	Coral branch	Coral branch	adult	not recorded	SRP416931	143.76
SRR23047224	Coral branch	Coral branch	adult	not recorded	SRP416931	143.37
SRR23047220	Coral branch	Coral branch	adult	not recorded	SRP416931	142.05
SRR23047223	Coral branch	Coral branch	adult	not recorded	SRP416931	141.07
SRR23047214	Coral branch	Coral branch	adult	not recorded	SRP416931	140.97
SRR23047206	Coral branch	Coral branch	adult	not recorded	SRP416931	139.98
SRR23047225	Coral branch	Coral branch	adult	not recorded	SRP416931	139.74
SRR23047213	Coral branch	Coral branch	adult	not recorded	SRP416931	139.11
SRR23047215	Coral branch	Coral branch	adult	not recorded	SRP416931	137.41
SRR23047208	Coral branch	Coral branch	adult	not recorded	SRP416931	133.96
SRR23047227	Coral branch	Coral branch	adult	not recorded	SRP416931	133.72
SRR23047234	Coral branch	Coral branch	adult	not recorded	SRP416931	132.35
SRR23047243	Coral branch	Coral branch	adult	not recorded	SRP416931	132.22
SRR23047221	Coral branch	Coral branch	adult	not recorded	SRP416931	129.85
SRR23047210	Coral branch	Coral branch	adult	not recorded	SRP416931	129.22
SRR23047238	Coral branch	Coral branch	adult	not recorded	SRP416931	128.89
SRR23047239	Coral branch	Coral branch	adult	not recorded	SRP416931	124.32
SRR23047236	Coral branch	Coral branch	adult	not recorded	SRP416931	123.16
SRR23047212	Coral branch	Coral branch	adult	not recorded	SRP416931	120.88
SRR23047230	Coral branch	Coral branch	adult	not recorded	SRP416931	118.68
SRR23047233	Coral branch	Coral branch	adult	not recorded	SRP416931	117.29
SRR23047226	Coral branch	Coral branch	adult	not recorded	SRP416931	117.27
SRR23047218	Coral branch	Coral branch	adult	not recorded	SRP416931	115.19
SRR23047228	Coral branch	Coral branch	adult	not recorded	SRP416931	114.99
SRR23047240	Coral branch	Coral branch	adult	not recorded	SRP416931	114.80
SRR23047242	Coral branch	Coral branch	adult	not recorded	SRP416931	114.67
SRR23047229	Coral branch	Coral branch	adult	not recorded	SRP416931	104.79
SRR23047244	Coral branch	Coral branch	adult	not recorded	SRP416931	104.65

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	17	g8119.t1	0.796189607706684
Negatively correlated	6	g16693.t1	-0.679217489963794

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 →