Gene detail

Detailed information of g18376.t1 in Montipora capitata

Genomic Location: Sc0000885:79900...97234
NR annotation: CAH3028704.1, unnamed protein product [Porites evermanni]
Species Montipora capitata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

g18376.t1

atggactatgaccatttggatccagagggcagcctaatggacagaattcaagcgctaattcagcctccccagtctgaagaatccagcaaaaaagtcaaaaaagttgataaagaagctcgaaaacaaggcagatccgtcaacaacgataattgcgacagttgtggggaaggaggcgatttgctttgttgtgatcgatgtccgtgcgcttttcatctcacttgttgtgatcctccactggaagaagatgatatccctgatggtgaatggctttgtaatgaatgtaaagcaacaccaaaagaggatcaggactgcaaagggaaagaccaatccaaaatggaagatgataacactgaagatctctcctctacatccactaaagatttagagaattccaagcctgagtcgccattttcaacacttgtaaaaatgacaacagggagaaatccaacaacattcactctcccaccggagctcaaatgcaacactttctttccaggtgataggaaaagaaaaaacagcactgaagagagagcatttccagtaaaaaatgggaaaagaaatggcgacgaagaggagcacactattccacctgggcgtctttgctttgcttgtagcaggagtgaactcattggtcaacttgttcactgtgatttttgtccactggcatttcacatggactgcctcaacccacctctaactacagtaccaagtggcatgtggatgtgtccgaaccatgctgagcatgcggagcccggacttcgcgaacctcgtttcagtaagagattacaggcttacaatgacctaaggagtaacatttctcagcacacaatcaagatgaactttcttcaaagagtgcatagattaaagaaacatccctctttcaaaagaaaagctttgttaccaacaagaaggagggcaactgtggttccacaagcaattaaggatcattacgcatctccaccaatccaactcctaccagaacacataaggaaaatgcaagagcctctgccgttacatgtacttcctttgaatacaccatcatctgaagaacaggaagagtggttaaagtgtgtgatcaacttgcaatgtggtattgcaaagcatctttctcaaccagctgttagcaaaacttcaatttcaaatcatgcagataattcatctggcaaattggaatccttgagccctaatacaagcactttatctacatcatctgcacattctaccagcactggaagtgtgaaagagccaatcataaatggcttgacccccaaatcagactcgaccaatcacatttcatctttacctgcaagtagtggagttcaaaatgcttgtataagtagagttgtaacaacgacaattaccacaacaagtggtggaaaaacaataacaaaaccactgaccattttgtatgcttccccatcaaagcttcaaactcacatgaatggacctttaagtgcaaagtcagttggaaattcaagtagcccagtcaatgtgtgtagtgtgtcttcaacacatttaccgtctcaagttttggtaaagcaggaacccaaatctgttgaaaaacaggtattgagcaatgacttgaatcaacttagtgctgaatgtaaacagctgtcaagtgatactgcaaaattaatcaatgatgttgggcatgtgaacaatgtgaaggcgaaaatcagtgtcgatgttgtaaagactgtagctgttccaacatcaagcacaagctcaattgtaaatacaaccgctagtgtggtaaacagaaccatatcaacggctattgctgcaggaagctcaagtagctccagtgcgacaaaagccgcttcatcaacacctacgaaactaattgtattgacaagcacaaacagtgggaacatcattaaaacaattgcaacagcaggattgtctgctggtggcactgcgggtggcagcatagtaacattgggggctccaggaaattctgcaaacatcaatcctgtaaaaattggaaatgtgaatgcctcaacagcgacatcagttggttcaagcccaaataaagcgactcaggctgcagctgctacgtctgcagccactgccaatgcgattaacagcatttgtgctgcagctggagtagacgcttttaatgaaacagagcttgccaagttggatccaaggcttattcaagttttggcttatcagagactacagcagcttcttactcaaaccaagcctgttcctcaaagtccagctgcagcaaggaaaatttctttcaatgggctaaaggaaactatagttcttcctcaacaagctgttccagctggaagatccatagcagtgctgtgtccgttatctggaacaggtcctgtgtgtccaatgatccataaatgtctatcattgggtcaaggtccagatatggatgtttgtctccaggaatatgggcattgcaacttcatatctcagaaacactgttctatattttacgatgagacctcaaaacagtacgagctcataaactacagtgaacatggaacatatgtagacaatgtgttatactcgtgcgacttttcggacaaaatcaacagacatgttctttcatctaaggatctagacccttccaaggtcaccaaaaacaaactgttggccgcttcccaagttcgacaaaaccccaaaacaaagggatcacgtagaactgttggtcttggtgtgcaaaacattgcaaaggcttgtaactgcacaacaagcagttcaaacttaattggtggcagtggtgctggctgggaaggaacagcccttttacaccatggaagttacataaagcttggttgtgctcaatttgtgttcagtataacaagtcatgccacaaagcttccttcaagtggaaagacaagtaatacaaatgataaaaaaccaactgtttcatga

Transcript

g18376.t1

ATGGACTATGACCATTTGGATCCAGAGGGCAGCCTAATGGACAGAATTCAAGCGCTAATTCAGCCTCCCCAGTCTGAAGAATCCAGCAAAAAAGTCAAAAAAGTTGATAAAGAAGCTCGAAAACAAGGCAGATCCGTCAACAACGATAATTGCGACAGTTGTGGGGAAGGAGGCGATTTGCTTTGTTGTGATCGATGTCCGTGCGCTTTTCATCTCACTTGTTGTGATCCTCCACTGGAAGAAGATGATATCCCTGATGGTGAATGGCTTTGTAATGAATGTAAAGCAACaccaaaagagGATCAGGACTGCAAAGGGAAAGACCAATCCAAAATGGAAGATGATAACACTGAAGATCTCTCCTCTACATCCACTAAAGATTTAGAGAATTCCAAGCCTGagtcgccattttcaacacttgtAAAAATGACAACAGGGAGAAATCCAACAACATTCACTCTCCCACCGGAGCTCAAATGCAACACTTTCTTTCCAGGtgataggaaaagaaaaaacagcacTGAAGAGAGAGCATTTCCAGTAAAAAATGGGAAAAGAAATGGCGACGAAGAGGAGCACACTATTCCACCTGGGCGTCTTTGCTTTGCTTGTAGCAGGAGTGAACTCATTGGTCAACTTGTTCACTGTGATTTTTGTCCACTGGCATTTCACATGGACTGCCTCAACCCACCTCTAACTACAGTACCAAGTGGCATGTGGATGTGTCCGAACCATGCTGAGCATGCGGAGCCCGGACTTCGCGAACCTCGTTTCAGTAAGAGATTACAGGCTTACAATGACCTAAGGAGTAACATTTCTCAGCACACAATCAAGATGAACTTTCTTCAAAGAGTGCATAGATTAAAGAAACATCCctctttcaaaagaaaagcttTGTTACCAACAAGAAGGAGGGCAACTGTGGTTCCACAAGCAATTAAGGATCATTACGCATCTCCACCAATCCAACTCCTACCAGAACACATAAGGAAAATGCAAGAGCCTCTGCCGTTACATGTACTTCCTTTGAATACACCATCATCTGAAGAACAGGAAGAGTGGTTAAAGTGTGTGATCAACTTGCAATGTGGTATTGCAAAGCATCTTTCTCAACCAGCTGTTAGCAAAACTTCAATTTCAAATCATGCAGATAATTCATCTGGCAAATTGGAATCCTTGAGCCCTAATACAAGCACTTTATCTACATCATCTGCACATTCTACCAGCACTGGAAGTGTGAAAGAGCCAATCATAAATGGCTTGACCCCCAAATCAGACTCGACCAATCACATTTCATCTTTACCTGCAAGTAGTGGAGTTCAAAATGCTTGTATAAGTAGAGTTGTAACAACGACAATTACCACAACAAGTGGtggaaaaacaataacaaaaccactgaccatTTTGTATGCTTCCCCATCAAAGCTTCAAACTCACATGAATGGACCTTTAAGTGCAAAGTCAGTTGGAAATTCAAGTAGCCCAGTCAATGTGTGTAGTGTGTCTTCAACACATTTACCGTCTCAAGTTTTGGTAAAGCAGGAACCCAAATCTGTTGAAAAACAGGTATTGAGCAATGACTTGAATCAACTTAGTGCTGAATGTAAACAGCTGTCAAGTGATACTGCAAAATTAATCAATGATGTTGGGCATGTGAACAATGTGAAGGCGAAAATCAGTGTCGATGTTGTAAAGACTGTAGCTGTTCCAACATCAAGCACAAGCTCAATTGTAAATACAACCGCTAGTGTGGTAAACAGAACCATATCAACGGCTATTGCTGCAGGAAGCTCAAGTAGCTCCAGTGCGACAAAAGCCGCTTCATCAACACCTACGAAACTAATTGTATTGACAAGCACAAACAGTGGGAACATCATTAAAACAATTGCAACAGCAGGATTGTCTGCTGGTGGCACTGCGGGTGGCAGCATAGTAACATTGGGGGCTCCAGGAAATTCTGCAAACATCAATCCtgtaaaaattggaaatgtgaatGCCTCAACAGCGACATCAGTTGGTTCAAGCCCAAATAAAGCGACTCAGGCTGCAGCTGCTACGTCTGCAGCCACTGCCAATGCGATTAACAGCATTTGTGCTGCAGCTGGAGTAGACGCTTTTAATGAAACAGAGCTTGCCAAGTTGGATCCAAGGCTTATTCAAGTTTTGGCTTATCAGAGACTACAGCAGCTTCTTACTCAAACCAAGCCTGTTCCTCAAAGTCCAGCTGCAGCAAGGAAAATTTCTTTCAATGGGCTAAAGGAAACTATAGTTCTTCCTCAACAAGCTGTTCCAGCTGGAAGATCCATAGCAGTGCTGTGTCCGTTATCTGGAACAGGTCCTGTGTGTCCAATGATCCATAAATGTCTATCATTGGGTCAAGGTCCAGATATGGATGTTTGTCTCCAGGAATATGGGCATTGCAACTTCATATCTCAGAAACACTGTTCTATATTTTACGATGAGACCTCAAAACAGTACGAGCTCATAAACTACAGTGAACATGGAACATATGTAGACAATGTGTTATACTCGTGCGACTTTTCGGACAAAATCAACAGACATGTTCTTTCATCTAAGGATCTAGACCCTTCCAAGGTCACCAAAAACAAACTGTTGGCCGCTTCCCAAGTTCGACAAAACCCCAAAACAAAGGGATCACGTAGAACTGTTGGTCTTGGTGTGCAAAACATTGCAAAGGCTTGTAACTGCACAACAAGCAGTTCAAACTTAATTGGTGGCAGTGGTGCTGGCTGGGAAGGAACAGCCCTTTTACACCATGGAAGTTACATAAAGCTTGGTTGTGCTCAATTTGTGTTCAGTATAACAAGTCATGCCACAAAGCTTCCTTCAAGTGGAAAGACAAGTAATACAAATGATAAAAAACCAACTGTTTCATGA

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
Orthogroup (gene family)	OG0005117 (this species only) · gene tree & orthology
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
IPR000253 all species →	Domain	Forkhead-associated (FHA) domain	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR011011 all species →	Homologous_superfamily	Zinc finger, FYVE/PHD-type	Interproscan
IPR019787 all species →	Domain	Zinc finger, PHD-finger	Interproscan
IPR019786 all species →	Conserved_site	Zinc finger, PHD-type, conserved site	Interproscan
IPR038098 all species →	Homologous_superfamily	PHD finger protein 12, MRG binding domain superfamily	Interproscan
IPR001965 all species →	Domain	Zinc finger, PHD-type	Interproscan
IPR008984 all species →	Homologous_superfamily	SMAD/FHA domain superfamily	Interproscan
IPR031966 all species →	Domain	PHD finger protein 12, MRG binding domain	Interproscan

PANTHER

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

Gene Ontology

GO term	Category	Description	Source
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
GO:0005515 all species →	Molecular Function	protein 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
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 g18376.t1 across 48 RNA-seq samples of Montipora capitata. 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.

48Samples

41TPM > 0

3Conditions

27.5Max TPM

7.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole organisms · ambient pH treatment	21	17	8.06	27.52
whole organisms · low pH treatment	15	13	6.84	24.57
whole organisms · extra low pH treatment pH treatment	12	11	7.55	22.60

Per sample · hover a bar for the full sample record · show / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11452242	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	27.52
SRR11452234	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	18.00
SRR11452243	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	15.61
SRR11452237	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	15.14
SRR11452228	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	14.46
SRR11452232	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	14.28
SRR11452230	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	13.24
SRR11452222	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	12.93
SRR11452233	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	12.12
SRR11452231	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	8.72
SRR11452250	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	5.28
SRR11452252	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	3.43
SRR11452246	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	3.13
SRR11452240	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	2.02
SRR11452259	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	1.74
SRR11452263	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	0.88
SRR11452254	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	0.85
SRR11452217	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	0.00
SRR11452251	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	0.00
SRR11452260	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	0.00
SRR11452262	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	0.00
SRR11452241	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	24.57
SRR11452236	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	14.30
SRR11452238	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	12.34
SRR11452224	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	12.18
SRR11452223	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	12.12
SRR11452221	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	11.26
SRR11452247	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	4.05
SRR11452249	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	3.72
SRR11452245	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	3.71
SRR11452258	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	1.77
SRR11452255	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	1.28
SRR11452229	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	0.82
SRR11452253	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	0.51
SRR11452216	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	0.00
SRR11452218	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	0.00
SRR11452239	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	22.60
SRR11452235	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	17.61
SRR11452225	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	13.76
SRR11452227	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	13.47
SRR11452226	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	11.54
SRR11452244	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	4.18
SRR11452248	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	3.18
SRR11452220	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	2.08
SRR11452261	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	1.00
SRR11452257	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	0.62
SRR11452256	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	0.59
SRR11452219	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	0.00

Source: CnidoSite RNA-seq expression matrices (MCAPI_TPM, StringTie quantification over 48 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.