Gene detail

Detailed information of g12698.t1 in Montipora capitata

Genomic Location: Sc0000416:10036...26732
NR annotation: XP_044172155.1, protein PAT1 homolog 1-like isoform X1 [Acropora millepora]
Species Montipora capitata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

g12698.t1

atgggcgaaaacttgcgtgaagactggacaaaagtccttgacatgcgccaatcagttcatcatgtcaacatggcgggttctctcttcggactcaattcagagattccggcctttgaagatgaagaactttctgaattggatccaactctgacgaatctcgacgatggagatagttatgaccaacttaacgacgacacgtttggctcaggagccttagaagctgagaagctacatgtaaatgcaactcttgtgattgtagaagatgactgggagcttgctcataggaaactatcaggcttacacgaggaagggacacaggaggtgcagtatgccaactggctcaagcagaaaggctttgagtgtaagcagggtgaagagaaatctacaacagcaaaatatttgcatagttcaactcatgaagattttgaggatgaattgaatcgtgaagaggaaatcctggaacagaatttaactaaacttgtggaagatgatgaagctgactcaattcttgttcctagggtatcatctaagcacaaggagattaagcacccatctggcataaacccaacatgggatggaacttcacctttgtccagcccaacatcatcaacatcaataaatgatctgatctcaccatcctccaaaatatggggatccccttctaaacttgataaagagaacaaaaacaaaggaccagtcaatacccaacagtcagtgtcaccattggataaattgataaaagcagaggctgaaaggaaacagaaacttaggagaccattttctccagcctttgaggatgattccattgttacagcaattcctccaccaggcctggtgcctccaagtcgattcatgaagaaacccccacctgtaaatgctattaagctagaggacctggaaaaggagctcacaggggataccagtgctcctcagcaagtaccagagggtccaaagcaaacaccgcgcaagacaatgataggtcaaccacctcccggtattccgaggcccatgatgacccctcctggttttcagtctcctttgacaagaatgcatactcccccattgccacgtcagatgtttcaaccaccaagacccagtccctctaaacatccaatttctgcaatgtctggaatgcatggtatgcctggaatgctaggtccaggtccagggccagggccagggccagggccacatttgttaagaacccccaggacacctctgtttccaagggatccattttccatgttgcattctgaccctggtagacagcagcaggacaggggggaacatcagcatcagtttaccgacttagaaaggaagattcacaacatactgactttggctgaaagtggtccaagaaaagatgacccttatgcagggctgatgaccagaagagaaaaagaatggttgatcaagattcaattacttcaactcactagcaatgaaccagaactagatgattattactttcagacttacacacggagaacagcggccaaggagcatgttaaacacagtgagggtgtacagttaagacctaatgtacaagacaatagagaagttagagagacaacaaacatggccttaccgcagtttgaacgagagaagaagaagacttacactccagtggactttcatgggtccttaggaaaggtttcttctgcgtcagttcaacaccccaggcaaatggtggatttgaatgtagtgcatatcacaaaaggtcttgaacaggataaacaaggcagttcagctcccttgaaggacaacaagaggcgcagccaactgttgcttacaatagaaaagggttatgactatcttttgacagttgaaagttttgataaaaagttgattcatattgaggaacaagaaaggattgaagttcttgaaactaggcaacttactgttacaaagctgtttaccatattaaagctatccacagagggttgtgaaaagtgtgatgatgaattctttattcaatttctctccatccaaaaaggaaagcatcttctgagtagagcattagtaatgttcagcaaggttcaaatagaagcagtattaatggccataacaagaaatattttactccttattaaaagggacagcgctgaagagttcttgaatcatgtgatggttcctcttaatcgtgtgtcagagcttatgtctccaccggcagtgatccgctgtcttcaaaacatggtgtttgcacaaggcaattccactactcaagcatcaccgctttctgtggtcctggtaaatcagtttggcttagggattttcagcacattattgggaagagcagccgtcatttcaaacagtttatccgaagcggaagatgagatgagaaattcttggttaaacatcgtctctcaggtatcaaccgagtttcaagatatccctctcaagcaactggcaaggaatctagaagcagctaagacattagttgctttgttgtccacatgtaccgacgtccagaccagagctttactacaggagcacttgaggtttgaaataggccacgtttttgacatatag

Transcript

g12698.t1

ATGGGCGAAAACTTGCGTGAAGACTGGACAAAAGTCCTTGACATGCGCCAATCAGTTCATCATGTCAACATGGCGGGTTCTCTCTTCGGACTCAATTCAGAGATTCCGgCCTTTGAAGATGAAGAACTTTCTGAATTGGATCCAACTCTGACGAATCTCGACGATGGAGATAGTTATGACCAACTTAACGACGACACGTTTGGCTCAGGAGCCTTAGAAGCTGAGaagctacatgtaaatgcaACTCTTGTGATTGTAGAAGATGACTGGGAGCTTGCTCATAGGAAACTATCAGGCTTACACGAGGAAGGGACACAGGAGGTGCAGTATGCCAACTGGCTCAAGCAGAAAGGCTTTGAGTGTAAGCAGGGTGAAGAGAAATCTACAACAGCAAAATATTTGCATAGTTCAACTCATGAAGATTTTGAGGATGAATTGAATCGTGAAGAGGAAATCCTGGAACAGAATTTAACTAAACTTGTGGAAGATGATGAAGCTGACTCAATTCTTGTTCCTAGGGTATCATCTAAGCACAAGGAGATTAAGCACCCATCTGGCATAAACCCAACATGGGATGGAACTTCACCTTTGTCCAGCCCAACATCATCAACATCAATAAATGATCTGATCTCACCATCCTCCAAAATATGGGGATCCCCTTCTAAACTTgataaagagaacaaaaacaaaggaccaGTCAATACCCAACAGTCAGTGTCACCATTGGATAAATTGATAAAAGCAGAGGCTGAAAGGAAACAGAAACTTAGGAGACCATTTTCTCCAGCCTTTGAGGATGATTCCATTGTTACAGCAATTCCTCCACCAGGCCTGGTGCCTCCAAGTCGATTCATGAAGAAACCCCCACCTGTAAATGCTATTAAGCTAGAGGACCTGGAAAAGGAGCTCACAGGGGATACCAGTGCTCCTCAGCAAGTACCAGAGGGTCCAAAGCAAACACCGCGCAAGACAATGATAGGTCAACCACCTCCCGGTATTCCGAGGCCCATGATGACCCCTCCTGGTTTTCAGTCTCCTTTGACAAGAATGCATACTCCCCCATTGCCACGTCAGATGTTTCAACCACCAAGACCCAGTCCCTCTAAACATCCAATTTCTGCAATGTCTGGAATGCATGGTATGCCTGGAATGCTAGGTCCAGGTCCAGGGCCAGGGCCAGGGCCAGGGCCACATTTGTTAAGAACCCCCAGGACACCTCTGTTTCCAAGGGATCCATTTTCCATGTTGCATTCTGACCCTGGTAGACAGCAGCAGGACAGGGGGGAACATCAGCATCAGTTTACCGACTTAGAAAGGAAGATTCACAACATACTGACTTTGGCTGAAAGTGGTCCAAGAAAAGATGACCCTTATGCAGGGCTGATGACCAGAAGAGAAAAAGAATGGTTGATCAAGATTCAATTACTTCAACTCACTAGCAATGAACCAGAACTAGATGATTATTACTTTCAGACTTACACACGGAGAACAGCGGCCAAGGAGCATGTTAAACACAGTGAGGGTGTACAGTTAAGACCTAATGTACAAGACAATAGAGAAGTTAGAGAGACAACAAACATGGCCTTACCGCAGTTTGAACGAGAGAAGAAGAAGACTTACACTCCAGTGGACTTTCATGGGTCCTTAGGAAAGGTTTCTTCTGCGTCAGTTCAACACCCCAGGCAAATGGTGGATTTGAATGTAGTGCATATCACAAAAGGTCTTGAACAGgATAAACAAGGCAGTTCAGCTCCCTTGAAGGACAACAAGAGGCGCAGCCAACTGTTGCTTACAATAGAAAAGGGTTATGACTATCTTTTGACAGTTGAAAGTTTTGATAAAAAGTTGATTCATATTGAGGAACAAGAAAGgaTTGAAGTTCTTGAAACTAGGCAACTTACTGTTACAAAGCTGTTTACCATATTAAAGCTATCCACAGAGGGTTGTGAAAAGTGTGATGATGAATTCTTTATTCAATTTCTCTCCATCCAAAAAGGAAAGCATCTTCTGAGTAGAGCATTAGTAATGTTCAGCAAGGTTCAAATAGAAGCAGTATTAATGGCCATAACAAGAAATATTTTACTCCTTATTAAAAGGGACAGCGCTGAAGAGTTCTTGAATCATGTGATGGTTCCTCTTAATCGTGTGTCAGAGCTTATGTCTCCACCGGCAGTGATCCGCTGTCTTCAAAACATGGTGTTTGCACAAGGCAATTCCACTACTCAAGCATCACCGCTTTCTGTGGTCCTGGTAAATCAGtTTGGCTTAGGGATTTTCAGCACATTATTGGGAAGAGCAGCCGTCATTTCAAACAGTTTATCCGAAGCGGAAGATGAGATGAGAAATTCTTGGTTAAACATCGTCTCTCAGGTATCAACCGAGTTTCAAGATATCCCTCTCAAGCAACTGGCAAGGAATCTAGAAGCAGCTAAGACATTAGTTGCTTTGTTGTCCACATGTACCGACGTCCAGACCAGAGCTTTACTACAGGAGCACTTGAGGTTTGAAATAGGCCACGTTTTTGACATATAG

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q5R8Q4	Protein PAT1 homolog 1 OS=Pongo abelii OX=9601 GN=PATL1 PE=2 SV=1
Q86TB9	Protein PAT1 homolog 1 OS=Homo sapiens OX=9606 GN=PATL1 PE=1 SV=2
B5DF93	Protein PAT1 homolog 1 OS=Rattus norvegicus OX=10116 GN=Patl1 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004039 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF09770 all species →	PAT1	Topoisomerase II-associated protein PAT1	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR039900 all species →	Family	Pat1-like	Interproscan
IPR019167 all species →	Domain	mRNA decay factor PAT1 domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR21551 all species →	TOPOISOMERASE II-ASSOCIATED PROTEIN PAT1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000290 all species →	Biological Process	deadenylation-dependent decapping of nuclear-transcribed mRNA	Interproscan
GO:0000932 all species →	Cellular Component	P-body	Interproscan
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0033962 all species →	Biological Process	P-body assembly	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
K12617	PATL1, PAT1; DNA topoisomerase 2-associated protein PAT1	-	Messenger RNA biogenesis	ko03019	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g12698.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

48TPM > 0

3Conditions

262.4Max TPM

85.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole organisms · ambient pH treatment	21	21	75.76	262.40
whole organisms · low pH treatment	15	15	97.78	258.40
whole organisms · extra low pH treatment pH treatment	12	12	86.83	245.13

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11452250	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	262.40
SRR11452246	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	211.72
SRR11452252	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	196.47
SRR11452259	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	122.86
SRR11452243	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	113.80
SRR11452242	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	104.12
SRR11452260	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	98.92
SRR11452254	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	96.00
SRR11452237	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	91.12
SRR11452263	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	41.86
SRR11452262	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	36.92
SRR11452222	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	31.15
SRR11452230	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	28.97
SRR11452251	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	27.61
SRR11452240	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	25.29
SRR11452232	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	23.48
SRR11452228	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	21.17
SRR11452217	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	17.79
SRR11452234	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	17.46
SRR11452233	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	15.64
SRR11452231	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	6.30
SRR11452249	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	258.40
SRR11452247	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	247.92
SRR11452245	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	228.69
SRR11452241	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	130.51
SRR11452238	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	111.88
SRR11452236	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	102.97
SRR11452258	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	98.20
SRR11452253	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	89.32
SRR11452255	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	66.45
SRR11452229	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	28.99
SRR11452216	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	26.70
SRR11452218	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	24.50
SRR11452221	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	19.09
SRR11452223	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	17.11
SRR11452224	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	15.95
SRR11452248	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	245.13
SRR11452244	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	208.74
SRR11452239	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	140.29
SRR11452235	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	110.44
SRR11452257	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	105.92
SRR11452256	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	86.09
SRR11452219	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	36.68
SRR11452227	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	28.70
SRR11452225	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	26.66
SRR11452261	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	20.65
SRR11452226	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	19.67
SRR11452220	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	12.96

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.