Gene detail

Detailed information of g915.t1 in Montipora capitata

Genomic Location: Sc0000009:1150346...1176446
NR annotation: XP_029189471.2, protein patched homolog 1-like isoform X2 [Acropora millepora]
Species Montipora capitata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

g915.t1

atgaaacatgctgtactttatcacgagtgcctagctggccagttatcgccatttaccatgttaattttattgtcttggttaaagattttttcacagcttttgccatgcttgatagttactccattggactgcttttgggagggtgctataccgcttggtccaagatacaaggtccttgggaacttcaagtggaaagatctcaatccagagaaattaatcaattctttcaaaccaaacatgagtccagtagtgtttggtaaactcgaggcacttttcagagaggctggagtcagcagtggttatatggaaaaaccctgtttggatccatatgaccctgaatgtccctcaactgcgtcaaacttccaaacaaaggagaggcatcattttccacagaaaccagatattggtgttgagctgaccaatggttgtcagggcattgcaaaaaactttatggactggccagaggagcttcttgtgggaggtattaaaaaaaaccaagaaaagatcataagaagcgccaaggcctaccaaagcatcattgttctgcgaggtactcaacaactgcaccatcactggtatggaaaagcaaaagtgaatcatttggagtggactgaagaagaagcatcgcaagtcctagaagcatggaagcgccagttcacagagacaatcaactctagatccgtggaacaagaaaaagaagattcaacagtgcttgccttctcctcaacttcatttaatgatctgcttcaagacttctctaagacaagttacagtaaagtggcaattggatatgcccttatgctggtttatgcttgcttgactctcaaacactggagtgatcccgttgagtccaatggtgcattgggatttgctggagttcttcttgtcactgtagctgtttcttctggtcttgggttttgttcattcattgggataaagttcaatgcagcatcaacccaagagcctgtggcatattgccttgctagcactggagtcagtgtttttctaacgtccttcaacaacatgtttgcatttttcatggcagcactgatacctattccagctttaaggtctttttcatttcaggctggtattgtggtggcattcaacttttatgctgtcatcatcattttcccggcaatgatagctattgataagtgcagaaggaagtctggcagatatgacttgttctgttgtaaggaaagaacggtgcctcggacaatttccaccccaccaagcacctcaggagatagcagtttcatgcatcattgctatcacaactctcgcaattctacgttggataactctgccattttgcagggtcttagtgggactgttattcttcctggcagcgtgcaagcaactgcttcccagacgatacatttaccaagtgttgtgactgtccaagcctcggccttagcagaagtggacagtcaaccaacaatacagtgtcagcataagagaggacaggggagaaaaccctatcaggtatcagaaccagaagagtttgagctgactgccttagggaatattcataaaggcacttgccactctagagctaaagctgaggctatggcaaatgttgtgcaagttcagctggctacagaccagaaaggcagcagagaaacagctgtcagaccctcatgccaaggctttaacaggatgatgaagattcatccagaatcaaacaatagttatgactgtgctttctcagaaggggcatttgagcaaagagtcaagaggtatgctggtaacagtcattcacaagactgtgttgtcaatgagaacaggatgatgaagattcatccagaatcaaacaatagtaatgactgtgcttgctcagaaggggcatttgagcaaagagtcaagaggtatgctggtaacagtcattcacaagactgtgttgtcaatgagaatgcaaaatatcctagcaagagttactccagggacggtgtaatcaatgaaaacgcggtcctctttaccagcagaaaagacagcaagtcacagggtgtgcccagaaatgttcagtttcagttgtctgcaaatgctgcatcaagtggagaaactgccgtggcaatggcagagtgttcctctacacacgaatctttgagaacactgagttcgcagtcgaggttgtcaccagggttagaatccagatcttcaacctcgcaaagtatccaggggcctttggcagaaaatgccagaagtgggtggagaaaggtgacagagaagatgagcaagtgttccttgtactgcattgctagagattactatgggccatggctacaacaaatgcctgtgaagattactgttttgtttatgtttgcctgtctttttgctgctgggttgtatggttgtatgaaagtggaagaaggcttggatctaacagatgtggtcccaaggaaaagcccagagcacaagtttgttgaagcccagttcaagtatttctcattttatgagattgctggtgtgaccatggaaggatatgattatgcaaatggccaagacttactttacaagtttcacaatgcttttaagaagattccaaacatcatcaaaaccccagaggaggagctgccaaaattctggttgatgtattttagagattggctaaaaggtctgcaagaagcttttgacaaagactgggaagcaggaagaataacttacaccggatggttgcagaatgcatctgacgatggtgtgattgggtataaacttttagcacaaactggagaaaaagagaccatcaacagatccattgcgaacataagacctgaaccagaggtatcctgggtcaacaaaagaagctctcaagactacaatgccatgagagaagaagaagaagaagaagacgaagaagatgaagagaagaagaagaagaagaagacgaagaagaagaagaagacgaagacgaggaagaggaagaagaagaagaagaagaattggagcgcaccagttgagccaccatccccacctataaacttctcttacattccgttcaatgtgatcaacttacggaagacgaaggatttcattgatgcaataaagagtgtccgtgccatatcagaggaattttccaaactgggtttgcccaactacccgactggaattccttttactttctgggagcagtacatttggctgggagagcaccttttggttgctcttgcaattgtcctggctgcaagttttgtggtcatggcacttatattatgcaatgtctgggcatcagtgttcatagtgatagtgctgattatgatcactgtggagttgtatggcttcatggggttgacccacattaaactcagtgctgtacctgccgtcacgctgattctttctgttggagtcggtgttgagttcactgttcacatgtgtatgcaatttttgacaagcgtaggagacagaaatcaacggatgcaaaaagcggtagagcacgtcttctcgcctgttgttgatggcgctgtttccactttacttggtgttatcatgctggcgggatcagaatttgatttcattgtcagatatttctttcatttgttggccgcgctgattgtaattggaacattaaacggtttggtgtttttaccggtattattgtctctagtgggaccaggacctgagatcgaagagatcgctccacccggaacagcctcatcagctggttccaatagggagtttcttccaagttcaacgtgcaggcagagaactcctcctaccgactccgagttgtgtattgttgctaagcaagaagagctgtcttctggttcaaggggtaggcctcaccgccacaagagaaatcctcataaaagtaaaagccgtggcactaggcgtccacgccaaaactgcagtcctccttcggtggattccgactcgtccagttcgacagtgactcgagtgactgcgcgcgccacggtcacggtcgaactccacacttcggaaagatcatcgtacccgaattaccgaagcggagcgcagatcgctagtccacttcacaacgagggcgaaagagagaaggaggacatgcgcattacgaatatggaggagtatggtggtgatccaagaagatga

Transcript

g915.t1

atgAAACATGCTGTACTTTATCACGAGTGCCTAGCTGGCCAGTTATCGCCATTTACCATGTTAATTTTATTGTCTTGGTTAAAGATTTTTTCACAGCTTTTGCCATGCTTGATAGTTACTCCATTGGACTGCTTTTGGGAGGGTGCTATACCGCTTGGTCCAAGATACAAGGTCCTTGGGAACTTCAAGTGGAAAGATCTCAATCCAGAGAAATTAATCAATTCTTTCAAACCAAACATGAGTCCAGTAGTGTTTGGTAAACTCGAGGCACTTTTCAGAGAGGCTGGAGTCAGCAGTGGTTATATGGAAAAACCCTGTTTGGATCCATATGACCCTGAATGTCCCTCAACTGCGTCAAACTTCCAAACAAAGGAGAGGCATCATTTTCCACAGAAACCAGATATTGGTGTTGAGCTGACCAATGGTTGTCAGGGCATTGCAAAAAACTTTATGGACTGGCCAGAGGAGCTTCTTGTGGGAGGtattaaaaaaaaccaagaaaagaTCATAAGAAGCGCCAAGGCCTACCAAAGCATCATTGTTCTGCGAGGTACTCAACAACTGCACCATCACTGGTATGGAAAAGCAAAAGTGAATCATTTGGAGTGGACTGAAGAAGAAGCATCGCAAGTCCTAGAAGCATGGAAGCGCCAGTTCACAGAGACAATCAACTCTAGATCCGTggaacaagaaaaagaagattCAACAGTGCTTGCCTTCTCCTCAACTTCATTTAATGATCTGCTTCAAGACTTCTCTAAGACAAGTTACAGTAAAGTGGCAATTGGATATGCCCTTATGCTGGTTTATGCTTGCTTGACTCTCAAACACTGGAGTGATCCCGTTGAGTCCAATGGTGCATTGGGATTTGCTGGAGTTCTTCTTGTCACTGTAGCTGTTTCTTCTGGTCTTGGGTTTTGTTCATTCATTGGGATAAAGTTCAATGCAGCATCAACCCAAgagCCTGTGGCATATTGCCTTGCTAGCACTGGAGTCAGTGTTTTTCTAACGTCCTTCAACAACATGTTTGCATTTTTCATGGCAGCACTGATACCTATTCCAGCTTTAAGGTCTTTTTCATTTCAGGCTGGTATTGTGGTGGCATTCAACTTTTATGCTGTCATCATCATTTTCCCGGCAATGATAGCTATTGATAAGTGCAGAAGGAAGTCTGGCAGATATGACTTGTTCTGTTGTAAGGAAAGAACGGTGCCTCGGACAATTTCCACCCCACCAAGCACCTCAGGAGATAGCAGTTTCATGCATCATTGCTATCACAACTCTCGCAATTCTACGTTGGATAACTCTGCCATTTTGCAGGGTCTTAGTGGGACTGTTATTCTTCCTGGCAGCGTGCAAGCAACTGCTTCCCAGACGATACATTTACCAAGTGTTGTGACTGTCCAAGCCTCGGCCTTAGCAGAAGTGGACAGTCAACCAACAATACAGTGTCAGCATAAGAGAGGACAGGGGAGAAAACCCTATCAGGTATCAGAACCAGAAGAGTTTGAGCTGACTGCCTTAGGGAATATTCATAAAGGCACTTGCCACTCTAGAGCTAAAGCTGAGGCTATGGCAAATGTTGTGCAAGTTCAGCTGGCTACAGACCAGAAAGGCAGCAGAGAAACAGCTGTCAGACCCTCATGCCAAGGCTTTAACAGGATGATGAAGATTCATCCAGAATCAAACAATAGTTATGACTGTGCTTTCTCAGAAGGGGCATTTGAGCAAAGAGTCAAGAGGTATGCTGGTAACAGTCATTCACAAGACTGTGTTGTCAATGAGAACAGGATGATGAAGATTCATCCAGAATCAAACAATAGTAATGACTGTGCTTGCTCAGAAGGGGCATTTGAGCAAAGAGTCAAGAGGTATGCTGGTAACAGTCATTCACAAGACTGTGTTGTCAATGAGAATGCAAAATATCCTAGCAAGAGTTACTCCAGGGACGGTGTAATCAATGAAAACGCGGTCCTCTTTACCAGCAGAAAAGACAGCAAGTCACAGGGTGTGCCCAGAAATGTTCAGTTTCAGTTGTCTGCAAATGCTGCATCAAGTGGAGAAACTGCCGTGGCAATGGCAGAGTGTTCCTCTACACACGAATCTTTGAGAACACTGAGTTCGCAGTCGAGGTTGTCACCAGGGTTAGAATCCAGATCTTCAACCTCGCAAAGTATCCAGGGGCCTTTGGCAGAAAATGCCAGAAGTGGGTGGAGAAAGGTGACAGAGAAGATGAGCAAGTGTTCCTTGTACTGCATTGCTAGAGATTACTATGGGCCATGGCTACAACAAATGCCTGTGAAGATTACTGTTTTGTTTATGTTTGCCTGTCTTTTTGCTGCTGGGTTGTATGGTTGTATGAAAGTGGAAGAAGGCTTGGATCTAACAGATGTGGTCCCAAGGAAAAGCCCAGAGCACAAGTTTGTTGAAGCCCAGTTCAAGTATTTCTCATTTTATGAGATTGCTGGTGTGACCATGGAAGGATATGATTATGCAAATGGCCAAGACTTACTTTACAAGTTTCACAATGCTTTTAAGAAGATTCCAAACATCATCAAAACCCCAGAGGAGGAGCTGCCAAAATTCTGGTTGATGTATTTTAGAGATTGGCTAAAAGGTCTGCAAGAAGCTTTTGACAAAGACTGGGAAGCAGGAAGAATAACTTACACCGGATGGTTGCAGAATGCATCTGACGATGGTGTGATTGGGTATAAACTTTTAGCACAAACTGGAGAAAAAGAGACCATCAACAGATCCATTGCGAACATAAGACCTGAACCAGAGGTATCCTGGGTCAACAAAAGAAGCTCTCAAGACTACAATGCCATGAGAGaagaagaagaagaagaagacgaagaagatgaagagaagaagaagaagaagaagacgaagaagaagaagaagacgaagacgaggaagaggaagaagaagaagaagaagaattggAGCGCACCAGTTGAGCCACCATCCCCACCTATAAACTTCTCTTACATTCCGTTCAATGTGATCAACTTACGGAAGACGAAGGATTTCATTGATGCAATAAAGAGTGTCCGTGCCATATCAGAGGAATTTTCCAAACTGGGTTTGCCCAACTACCCGACTGGAATTCCTTTTACTTTCTGGGAGCAGTACATTTGGCTGGGAGAGCACCTTTTGGTTGCTCTTGCAATTGTCCTGGCTGCAAGTTTTGTGGTCATGGCACTTATATTATGCAATGTCTGGGCATCAGTGTTCATAGTGATAGTGCTGATTATGATCACTGTGGAGTTGTATGGCTTCATGGGGTTGACCCACATTAAACTCAGTGCTGTACCTGCCGTCACGCTGATTCTTTCTGTTGGAGTCGGTGTTGAGTTCACTGTTCACATGTGTATGCAATTTTTGACAAGCGTAGGAGACAGAAATCAACGGATGCAAAAAGCGGTAGAGCACGTCTTCTCGCCTGTTGTTGATGGCGCTGTTTCCACTTTACTTGGTGTTATCATGCTGGCGGGATCAGAATTTGATTTCATTGTCAGatatttctttcatttgttgGCCGCGCTGATTGTAATTGGAACATTAAACGGTTTGGTGTTTTTACCGGTATTATTGTCTCTAGTGGGACCAGGACCTGAGATCGAAGAGATCGCTCCACCCGGAACAGCCTCATCAGCTGGTTCCAATAGGGAGTTTCTTCCAAGTTCAACGTGCAGGCAGAGAACTCCTCCTACCGACTCCGAGTTGTGTATTGTTGCTAAGCAAGAAGAGCTGTCTTCTGGTTCAAGGGGTAGGCCTCACCGCCACAAGAGAAATCCTCATAAAAGTAAAAGCCGTGGCACTAGGCGTCCACGCCAAAACTGCAGTCCTCCTTCGGTGGATTCCGACTCGTCCAGTTCGACAGTGACTCGAGTGACTGCGCGCGCCACGGTCACGGTCGAACTCCACACTTCGGAAAGATCATCGTACCCGAATTACCGAAGCGGAGCGCAGATCGCTAGTCCACTTCACAACGAGGGCGAAAGAGAGAAGGAGGACATGCGCATTACGAATATGGAGGAGTATGGTGGTGATCCAAGAAGATGA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q90693	Protein patched homolog 1 OS=Gallus gallus OX=9031 GN=PTCH1 PE=1 SV=1
Q98864	Protein patched homolog 1 OS=Danio rerio OX=7955 GN=ptch1 PE=2 SV=1
Q13635	Protein patched homolog 1 OS=Homo sapiens OX=9606 GN=PTCH1 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002058 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF12349 all species →	Sterol-sensing	Sterol-sensing domain of SREBP cleavage-activation	Family	Interproscan
PF02460 all species →	Patched	Patched family	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000731 all species →	Domain	Sterol-sensing domain	Interproscan
IPR003392 all species →	Family	Protein patched/dispatched	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR46022 all species →	PROTEIN PATCHED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0005119 all species →	Molecular Function	smoothened binding	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0008158 all species →	Molecular Function	hedgehog receptor activity	Interproscan
GO:0045879 all species →	Biological Process	negative regulation of smoothened signaling pathway	Interproscan
GO:0097108 all species →	Molecular Function	hedgehog family 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
K06225	PTCH1; patched 1	-	Basal cell carcinoma	ko05217	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g915.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

26TPM > 0

3Conditions

16.2Max TPM

2.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole organisms · ambient pH treatment	21	13	3.07	16.22
whole organisms · low pH treatment	15	7	1.62	8.11
whole organisms · extra low pH treatment pH treatment	12	6	2.80	12.70

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11452222	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	16.22
SRR11452230	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	15.27
SRR11452232	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	7.98
SRR11452228	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	7.91
SRR11452234	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	6.07
SRR11452242	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	3.10
SRR11452233	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	3.08
SRR11452231	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	1.85
SRR11452243	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	1.39
SRR11452237	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	0.97
SRR11452250	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	0.43
SRR11452252	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	0.17
SRR11452246	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	0.13
SRR11452217	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	0.00
SRR11452240	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
SRR11452254	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	0.00
SRR11452259	whole organisms · ambient pH treatment	whole organisms	cleavage	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
SRR11452263	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	0.00
SRR11452223	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	8.11
SRR11452221	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	6.50
SRR11452224	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	5.16
SRR11452241	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	2.55
SRR11452238	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	0.97
SRR11452236	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	0.87
SRR11452249	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	0.20
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
SRR11452229	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	0.00
SRR11452245	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	0.00
SRR11452247	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	0.00
SRR11452253	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	0.00
SRR11452255	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	0.00
SRR11452258	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	0.00
SRR11452225	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	12.70
SRR11452227	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	11.71
SRR11452226	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	6.05
SRR11452239	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	1.74
SRR11452235	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	1.13
SRR11452244	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	0.26
SRR11452219	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	0.00
SRR11452220	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	0.00
SRR11452248	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	0.00
SRR11452256	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	0.00
SRR11452257	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	0.00
SRR11452261	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.