Gene detail

Detailed information of g19356.t1 in Acropora digitifera

Genomic Location: chr9Alt:5095337...5103884
NR annotation: XP_015758739.1, PREDICTED: PHD finger protein 12-like isoform X2 [Acropora digitifera]
Species Acropora digitifera · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

g19356.t1

ATGGACTACGATCATTTGGATCCTGAGGGCAGCTTAATGGATAGGATTCAAGCCCTGATTCAGCCACCACAGTCAGAAGAATCGAGCAAAAAGGTTAAAAAAGTAGATAAAGAAGCTCGAAAACAAGGCAGGTCCGTCAACAACGACAACTGCGACAGTTGTGGGGAAGGAGGCGATTTGCTTTGTTGTGATCGATGCCCGTGTGCGTTTCATCTCACTTGTTGTGATCCTCCTCTGGAAGAAGATGACATTCCTGATGGTGAATGGCTCTGTAATGAATGTAAAGCAAGACCAGAAGAGGATCATGAGTTCAAAGGGAAGGAGCAACCAAATATTGCAAATAACACGGAAGATCACTCAGCTACATCAGCTAAAGATTCTGAGAATTCCAAACCAGAGTCTCCATTTTCAACTCTTGTTAAAATGACAACTGGAAAGAATCCAACAACATTCACTCTTCCTCCAGAACTCAAATGCAACACTTTCTTTCCAGGTGACCGGAAAAGAAAAAATAGCACTGAAGAGAAAGTGGTTCCTGTTAAAAATGGGAGAAGACATGGTGAGGAGGAAGAACGAAGCATCCCACCTGGGCGTCTTTGTTTTGCGTGTAGCAGAAGTGAGCTTACCAATCAGCTCGTTCACTGTGATTTTTGCCCATTGGCATTTCACATGGACTGTCTCAACCCACCACTTACAACAGTGCCAAGCGGTATGTGGATGTGTCCAAACCATGCGGAGCATGCTGAGCCTGGACTACGAGATCCTCGCTTTAGTAAGAGATTACAAGCTTACAATGATCTTAGAAGTAATATTTCACAACATACAATCAAGATGAATTTTCTTCAAAGAGTGCACAGAATGAAGAAACACCCTTCCTTTAAAAGAAAAGCCTTATTACCAACAACAAGACGGGCAACTTTGGTTCCACAAGCTGTAAAAGATCACTACAGGTCTCCACCAATACAACTTCTACCAGAACATATAAGAAAAATGCAAGAACCTCTGCCATTACATGCACTGCCCTTGACTACACCATCAGTCGAAGACCAAGAAGAGTGGTTAAAAAGTGTGATCAGCTTGCAATGTGGAATTGCCAAGCATCTATCTCAGCCACCTGTCAGCAAAACCTCGACTCCAGTTGTTAACCATACAGACAGTTCATCTGTCAAAGGGGAATTTTCAAGCTTAAATACATACTCTTCTACCTCTGCTATTTCTGCAAGCTCTACGGCCGTAAAAGAACCAACTGTCAATGGTTTGAGCCATAAATCAGACTTGACCAATCATATTTCATCATTACCGGCCAGCAGTGGAGTTCAAAGTGCTTGTATAAGTAGAGTTGTTACGACAACAATCACCACAACAAGTGGTGGGAAAACCATAACTAAACCACTCACTATATTGTATGCTTCACCATCAAAGCTTCAAACTCACATGAATGGACCTTTAAGTACAAAGTCAGGTGGAAATTCAAGTAGTTTGGTCAACATGTGTAGCGTATCTTCAACACATTTACCTTCTCAGGTTTTGGTAAAACAGGAACCTAAATCTGTTGAAAAGCAGATGGTGTGCAATGACTTAACCCAACTGAGTGGTGAATGCAAGCAACTCTCCAGTGACCCTGCAAAATTAGTCAATGATATTGGACATGTAAACAATGTGAAAGCAAAAATCAGTGTGGATACTGTAAAAACTTTGGCTGTTCCAACATCAAGTACAAGCTCAGTTGTAAATACAACTGCAAGTGTAGTAGCCAGGAATATCTCAACTGCTATTGCTGCTGGCAGCTCAAGTAGTTCTAATGCAACAAAATCTGCTTCATCAACACCCACTAAACTCATTGTGCTAACAAGCACCAATAGTGGGAATATCATTAAAACAATAGCTACTGCTGGATTGTCTGCGGGAGGTACCAGTCAAATACCCGGTGGAAGCATAGTAACGTTAGCAGCACCAGGAAATTCAACAAATCCTGTTAAAATAGGCGCTGTAAGCGCATCAACATCAGCTTCGGTTGGTTCAAGCCCTAACAAAGGCACCCAAGCAGCTGCGGCATCCACGTCTGTGGCAACTGCAAATGCCATAAATAGCATTTGTGCTGCAGCTGGAGTGGATGCTTTTAATGAGCTTGCCAAGCTGGATCCACGGCTTATTCAAGTGTTGGCTTACCAAAGATTACAGCAACTGCTTACACAAAAGCCTGTTCCTCCAAGCCCAGTTGCATCACGAAAAATTTCTTTCAATGGTTTGAAAGAAACCATAGTTCTTCCACAACAAGCTGTTCCAGCTGGAAGATCCATTGCAGTTCTGTGTCCGTTATCTGGAACTGGTCCTGTGTGTCCAATGATTCACAAGTGTCTGTCATTAGGGCAAGGTCCTGATATGGATTTGTGTCTCCAGGAATATGGGCATTGCAACTTTATATCTCAAAAACACTGCTCTATATTTTATGATGAGACGTCAAAACAGTATGAGCTAATAAACTACAGTGAACATGGAACATATGTAGACAATGTTTTGTATTCGTGTGACTTTTCGGACAAAATGAACAGACATGTCCTTTCTTCAAAGGATCTTGACCCTTCCAAGGTTGCCAAAAACAAACTGCTTGCTGCCGCTTCCTCTCAAGGTCGACAAAACTCCAAAACAAAGGGATCACGTAGAACTGTGGGTTTGGGTGTGCAAAGGATTATGAAAACATGCAACTGTACAACAAGCAGTTCCAACTTGATTGGTGGCAGTGGTGCTGGTTGGGAGGGAACTGCCCTCTTACATCATGGAAGTTACATAAAGCTTGGTTGCGCTCAATTTGTGTTCAGTATAACAAGTCACGCCACAAAGCTTCCTTCATCAGGTGGAAAGGCAAGCAAAGTGGATGATAAAAAAGCAACAACATTGTGA

Transcript

chr9Alt.g19356.t1

ACGAGAAACTTGGTTCTTCTGTTTTTCGAGGTGTAAGAGGTTTTCTCGAACTTCAAAACATCTTTTAACAGTAATCCATTATTTTATGCATACAAATTCGTTATAGTCTTTCAAAACATTAAGAATACTATCTCTGAGCTGAGTTTAAAGCTATTGCAATGGCGAGGGGCTGAGATAATGCCCCTTGTTTGAGAACAACTGGAGAGAGGCGATTCGTTCGAACTGTTCCCCTGAGCTGGAATTTCGCGCAGCACTAAAAGCCAGCTTTCATCTGTTGGTCGAATAGATTACGGGTAACTATTTGGAGACCTTTTAAGAAGCGGAAAAATGGACTACGATCATTTGGATCCTGAGGGCAGCTTAATGGATAGGATTCAAGCCCTGATTCAGCCACCACAGTCAGAAGAATCGAGCAAAAAGGTTAAAAAAGTAGATAAAGAAGCTCGAAAACAAGGCAGGTCCGTCAACAACGACAACTGCGACAGTTGTGGGGAAGGAGGCGATTTGCTTTGTTGTGATCGATGCCCGTGTGCGTTTCATCTCACTTGTTGTGATCCTCCTCTGGAAGAAGATGACATTCCTGATGGTGAATGGCTCTGTAATGAATGTAAAGCAAGACCAGAAGAGGATCATGAGTTCAAAGGGAAGGAGCAACCAAATATTGCAAATAACACGGAAGATCACTCAGCTACATCAGCTAAAGATTCTGAGAATTCCAAACCAGAGTCTCCATTTTCAACTCTTGTTAAAATGACAACTGGAAAGAATCCAACAACATTCACTCTTCCTCCAGAACTCAAATGCAACACTTTCTTTCCAGGTGACCGGAAAAGAAAAAATAGCACTGAAGAGAAAGTGGTTCCTGTTAAAAATGGGAGAAGACATGGTGAGGAGGAAGAACGAAGCATCCCACCTGGGCGTCTTTGTTTTGCGTGTAGCAGAAGTGAGCTTACCAATCAGCTCGTTCACTGTGATTTTTGCCCATTGGCATTTCACATGGACTGTCTCAACCCACCACTTACAACAGTGCCAAGCGGTATGTGGATGTGTCCAAACCATGCGGAGCATGCTGAGCCTGGACTACGAGATCCTCGCTTTAGTAAGAGATTACAAGCTTACAATGATCTTAGAAGTAATATTTCACAACATACAATCAAGATGAATTTTCTTCAAAGAGTGCACAGAATGAAGAAACACCCTTCCTTTAAAAGAAAAGCCTTATTACCAACAACAAGACGGGCAACTTTGGTTCCACAAGCTGTAAAAGATCACTACAGGTCTCCACCAATACAACTTCTACCAGAACATATAAGAAAAATGCAAGAACCTCTGCCATTACATGCACTGCCCTTGACTACACCATCAGTCGAAGACCAAGAAGAGTGGTTAAAAAGTGTGATCAGCTTGCAATGTGGAATTGCCAAGCATCTATCTCAGCCACCTGTCAGCAAAACCTCGACTCCAGTTGTTAACCATACAGACAGTTCATCTGTCAAAGGGGAATTTTCAAGCTTAAATACATACTCTTCTACCTCTGCTATTTCTGCAAGCTCTACGGCCGTAAAAGAACCAACTGTCAATGGTTTGAGCCATAAATCAGACTTGACCAATCATATTTCATCATTACCGGCCAGCAGTGGAGTTCAAAGTGCTTGTATAAGTAGAGTTGTTACGACAACAATCACCACAACAAGTGGTGGGAAAACCATAACTAAACCACTCACTATATTGTATGCTTCACCATCAAAGCTTCAAACTCACATGAATGGACCTTTAAGTACAAAGTCAGGTGGAAATTCAAGTAGTTTGGTCAACATGTGTAGCGTATCTTCAACACATTTACCTTCTCAGGTTTTGGTAAAACAGGAACCTAAATCTGTTGAAAAGCAGATGGTGTGCAATGACTTAACCCAACTGAGTGGTGAATGCAAGCAACTCTCCAGTGACCCTGCAAAATTAGTCAATGATATTGGACATGTAAACAATGTGAAAGCAAAAATCAGTGTGGATACTGTAAAAACTTTGGCTGTTCCAACATCAAGTACAAGCTCAGTTGTAAATACAACTGCAAGTGTAGTAGCCAGGAATATCTCAACTGCTATTGCTGCTGGCAGCTCAAGTAGTTCTAATGCAACAAAATCTGCTTCATCAACACCCACTAAACTCATTGTGCTAACAAGCACCAATAGTGGGAATATCATTAAAACAATAGCTACTGCTGGATTGTCTGCGGGAGGTACCAGTCAAATACCCGGTGGAAGCATAGTAACGTTAGCAGCACCAGGAAATTCAACAAATCCTGTTAAAATAGGCGCTGTAAGCGCATCAACATCAGCTTCGGTTGGTTCAAGCCCTAACAAAGGCACCCAAGCAGCTGCGGCATCCACGTCTGTGGCAACTGCAAATGCCATAAATAGCATTTGTGCTGCAGCTGGAGTGGATGCTTTTAATGAGCTTGCCAAGCTGGATCCACGGCTTATTCAAGTGTTGGCTTACCAAAGATTACAGCAACTGCTTACACAAAAGCCTGTTCCTCCAAGCCCAGTTGCATCACGAAAAATTTCTTTCAATGGTTTGAAAGAAACCATAGTTCTTCCACAACAAGCTGTTCCAGCTGGAAGATCCATTGCAGTTCTGTGTCCGTTATCTGGAACTGGTCCTGTGTGTCCAATGATTCACAAGTGTCTGTCATTAGGGCAAGGTCCTGATATGGATTTGTGTCTCCAGGAATATGGGCATTGCAACTTTATATCTCAAAAACACTGCTCTATATTTTATGATGAGACGTCAAAACAGTATGAGCTAATAAACTACAGTGAACATGGAACATATGTAGACAATGTTTTGTATTCGTGTGACTTTTCGGACAAAATGAACAGACATGTCCTTTCTTCAAAGGATCTTGACCCTTCCAAGGTTGCCAAAAACAAACTGCTTGCTGCCGCTTCCTCTCAAGGTCGACAAAACTCCAAAACAAAGGGATCACGTAGAACTGTGGGTTTGGGTGTGCAAAGGATTATGAAAACATGCAACTGTACAACAAGCAGTTCCAACTTGATTGGTGGCAGTGGTGCTGGTTGGGAGGGAACTGCCCTCTTACATCATGGAAGTTACATAAAGCTTGGTTGCGCTCAATTTGTGTTCAGTATAACAAGTCACGCCACAAAGCTTCCTTCATCAGGTGGAAAGGCAAGCAAAGTGGATGATAAAAAAGCAACAACATTGTGATTAGTGTGGTCTGTTTGGTTTTAAATGCAAAGTGATAGGTCAGTCATAAGATTTTGGTCAATTTGCTGTTGAAAGGAAAGTGACAGTCATTCAAAAGAAATGTTTTTGAACTCAGAGTAAATTAAATGCTCTTAAAAAAA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q96QT6	PHD finger protein 12 OS=Homo sapiens OX=9606 GN=PHF12 PE=1 SV=2
Q5SPL2	PHD finger protein 12 OS=Mus musculus OX=10090 GN=Phf12 PE=1 SV=1
Q09698	Uncharacterized protein C2F7.07c OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=SPAC2F7.07c PE=1 SV=1

Gene family

Family type	Membership / link
Ubiquitin family	E3\|E3 activity RING\|PHD · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00628 all species →	PHD	PHD-finger	Domain	Interproscan
PF00498 all species →	FHA	FHA domain	Family	Interproscan
PF16737 all species →	PHF12_MRG_bd	PHD finger protein 12 MRG binding domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001965 all species →	Domain	Zinc finger, PHD-type	Interproscan
IPR019786 all species →	Conserved_site	Zinc finger, PHD-type, conserved site	Interproscan
IPR019787 all species →	Domain	Zinc finger, PHD-finger	Interproscan
IPR008984 all species →	Homologous_superfamily	SMAD/FHA domain superfamily	Interproscan
IPR000253 all species →	Domain	Forkhead-associated (FHA) domain	Interproscan
IPR031966 all species →	Domain	PHD finger protein 12, MRG binding domain	Interproscan
IPR038098 all species →	Homologous_superfamily	PHD finger protein 12, MRG binding domain superfamily	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR011011 all species →	Homologous_superfamily	Zinc finger, FYVE/PHD-type	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46309 all species →	PHD FINGER PROTEIN 12	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0000122 all species →	Biological Process	negative regulation of transcription by RNA polymerase II	Interproscan
GO:0003714 all species →	Molecular Function	transcription corepressor activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:0070822 all species →	Cellular Component	Sin3-type complex	Interproscan
GO:0140110 all species →	Molecular Function	transcription regulator 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
K26244	PHF12, RCO1; transcriptional regulatory protein PHF12/RCO1	-	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 g19356.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

20.1Max TPM

15.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
Coral branch	39	39	15.71	20.09

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
SRR23047210	Coral branch	Coral branch	adult	not recorded	SRP416931	20.09
SRR23047240	Coral branch	Coral branch	adult	not recorded	SRP416931	19.78
SRR23047222	Coral branch	Coral branch	adult	not recorded	SRP416931	18.98
SRR23047225	Coral branch	Coral branch	adult	not recorded	SRP416931	18.66
SRR23047209	Coral branch	Coral branch	adult	not recorded	SRP416931	18.20
SRR23047232	Coral branch	Coral branch	adult	not recorded	SRP416931	17.92
SRR23047208	Coral branch	Coral branch	adult	not recorded	SRP416931	17.87
SRR23047206	Coral branch	Coral branch	adult	not recorded	SRP416931	17.82
SRR23047227	Coral branch	Coral branch	adult	not recorded	SRP416931	17.80
SRR23047234	Coral branch	Coral branch	adult	not recorded	SRP416931	17.65
SRR23047219	Coral branch	Coral branch	adult	not recorded	SRP416931	17.16
SRR23047241	Coral branch	Coral branch	adult	not recorded	SRP416931	16.95
SRR23047221	Coral branch	Coral branch	adult	not recorded	SRP416931	16.94
SRR23047229	Coral branch	Coral branch	adult	not recorded	SRP416931	16.24
SRR23047214	Coral branch	Coral branch	adult	not recorded	SRP416931	16.19
SRR23047243	Coral branch	Coral branch	adult	not recorded	SRP416931	16.08
SRR23047242	Coral branch	Coral branch	adult	not recorded	SRP416931	15.94
SRR23047226	Coral branch	Coral branch	adult	not recorded	SRP416931	15.93
SRR23047211	Coral branch	Coral branch	adult	not recorded	SRP416931	15.79
SRR23047217	Coral branch	Coral branch	adult	not recorded	SRP416931	15.69
SRR23047220	Coral branch	Coral branch	adult	not recorded	SRP416931	15.47
SRR23047231	Coral branch	Coral branch	adult	not recorded	SRP416931	15.46
SRR23047216	Coral branch	Coral branch	adult	not recorded	SRP416931	15.24
SRR23047230	Coral branch	Coral branch	adult	not recorded	SRP416931	15.07
SRR23047213	Coral branch	Coral branch	adult	not recorded	SRP416931	14.99
SRR23047237	Coral branch	Coral branch	adult	not recorded	SRP416931	14.76
SRR23047224	Coral branch	Coral branch	adult	not recorded	SRP416931	14.72
SRR23047235	Coral branch	Coral branch	adult	not recorded	SRP416931	14.68
SRR23047238	Coral branch	Coral branch	adult	not recorded	SRP416931	14.58
SRR23047239	Coral branch	Coral branch	adult	not recorded	SRP416931	14.46
SRR23047223	Coral branch	Coral branch	adult	not recorded	SRP416931	14.40
SRR23047215	Coral branch	Coral branch	adult	not recorded	SRP416931	14.09
SRR23047233	Coral branch	Coral branch	adult	not recorded	SRP416931	14.01
SRR23047207	Coral branch	Coral branch	adult	not recorded	SRP416931	13.96
SRR23047236	Coral branch	Coral branch	adult	not recorded	SRP416931	13.70
SRR23047228	Coral branch	Coral branch	adult	not recorded	SRP416931	12.65
SRR23047218	Coral branch	Coral branch	adult	not recorded	SRP416931	11.90
SRR23047244	Coral branch	Coral branch	adult	not recorded	SRP416931	11.56
SRR23047212	Coral branch	Coral branch	adult	not recorded	SRP416931	9.25

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	13	g6965.t1	0.821257255805291
Negatively correlated	23	g18962.t1	-0.704293830503817

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 →