Gene detail

Detailed information of g2530.t1 in Montipora capitata

Genomic Location: Sc0000039:122437...149650
NR annotation: XP_029195049.1, protein PALS1-like isoform X2 [Acropora millepora]
Species Montipora capitata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

g2530.t1

atggtccgccaaaaagcttacgaagcgacaagcagggaaaatttagtggactatgaactagaccctttcgataattcgttgaaatcggatacggctcaacagatcattcaacaatggattgaggaggcgactggacgactctttcgttcgtcacgattcatcgaatctctccaagacggtgttctcttgtgcaatctcgtgaagcgaatacaaccagactcaaagataattcaggatgttatcgaagacccaaatcctcaagaatgccagataaacttgaagacatttttacacgtttgtgaagatcttggtctaagtgcctggcaactttttgatccacaagatctacaagaacaagataatgtaataaaatataaatcggaagatgaagtgattcagaaggttgtcagcactctttactggcttggttgtactgttcaagggatgtcttattacaaaggtccaagactggatgtcagcaacttccagcgtgaaagtgatggcaccataacagtcaagcctaatgccagaccttctggccatgattattcctacattaggatggatgcacctcatattaatggagcacttccacagaacagaaggccaacccatctcacaaatggctattctgaaaatatgatggccaatggttcagatgatgccgtggaattttctgtcaatgtcaggatacttggagatgaaaagcgctttggcttctcagtgatgggtggtgtggatgaaggattccctccaagaattgatgaaatctcaccagattctcctgctgccaaaactggcctacttgtagatgatgagattctggaagttaatggagtgcctgtaatgaatctctctcacactgaagttattttaagtattcacaaatgtctaagaaacagagttattgctctgaaggtcagaagaggacgacagttcttctcaggggttaatggaacagaaaatcacaaggacctcaatggaaaagtggacgtaaagacaagaagtaaacttcataaaattatcaatgaccatgagaatgacccccaatttgagtactataattcggacgcagaatcagagggctcccattacagccaagaatttcatggaaacagtgacgttggtgtaatatcacctggttcggggtggagcaaggacattgaaaataagaactttgggatatcaagcaaaaacataggacagtcaaacttgcaaaagcacaaatctctgtctacgcctctttttgatttgacaaaacttgataccattgaggcagatgtggatattgaagatggtggcacttacgcccttcaaaatgaagcttacgatagtgataatgaggaggaagactcaggtggagctgacaaagaactgctgttcccctgtatgagtgaagtaaaaggaaagtttgattctggttcagatgctgaggaagttgcatttgttgacagtttgtttgagcagaaacattttcaggatgctaccaaagtatacacaaaaatggtcgagcttgaaaggtcagggcgaggactaagtgcagtcacaccagtggttacaaactcacagcatctttctactcagttaaagcattcgttgcaagctacaagagactcgagggatgcgcaagaattaattgaaattttacaatcaccaaacttccagggtctgttactagcgcacgatagactggcctttagagaggctcttccaagtgaagaagacgttcaagaattggagttcgaacaagatcagccgcaagaaccacagccagttgcaaacgaatattcactggtggaagaggacaacatgaaggtagtgagaattgacaaagcaactgaacctttaggagcaactgtcaagaatgcttatggctctgtattgattggaagaattgtcaaaggcggcgcagcagataagtgtggtcttctccaagaaggcgacgagatcctcgaaatcaatggagtaaatatgagagggaaaactgtcgctgaggtctgcgagttactggctgatatgaacggtacgctgacgtttgttctgaacccagcaaatcggccccgtgttccctcggacagagaggtgcacgtgcgtgcaaatttcaactatcaaccgtacgaggatgaattagtaccgtgcagggaactgggtctagcattcagacgaggtgatatactccatgttgtcaatcaggaggatcctcattggtggcaggcgtggagagttggcgaggaaggcaaaactttagctggtctaattccatccaaacatttccaacaacagaaagaaagtatgagaaaaacagctcgagaaacagaggcagcgtccaaagaaaacaaaggatgcctctgcttcaaacgaaaacgaagaaaaaaagttctttacaatgcacagcataacgaagattatgtcgcggacgaggttctgacgtatgaagaagtagcgctcttagaacccgacccgcagaaaaaacgtccggtggtgcttataggtcctgatagagttggtcgtaaagaactaagacaaaggctgattctcttttctcaagaaagatatgctggggtagtacctcataccagtagaccgaaaagaccggaagaggtaaacggaagagattactattttgtgccgcaatccgcatttgacctggatatagtgtccaataagttcgtggaacacggcgaaatccatggttattgttatggaacagctctggactcaatcagaagagtggccaactctggaaaatattgtattttaaatcttaattgcgaggccctaaaaatactcatggcgtcagatgtcaaaccttacgtggtttttatacaaccgcctccttatgatagaattgtccagcttagaagaggaaaagtggatccttttaaccctaaaccagatgcccaaatgaataacgccgaactccacgaaatggtcgaaaaagcgcaagaaatggaggaaaattacgggcattattttgataaaacgatcgtgaacacggatttggagagaacgttcgatgaactaagacaaaccatcgagaaacttgatgtcgaagctcagtgggttccagctttctgggtacaagagagccgagccattttgtag

Transcript

g2530.t1

ATGGTCCGCCAAAAAGCTTACGAAGCGACAAGCAGGGAAAATTTAGTGGACTATGAACTAGACCCTTTCGATAATTCGTTGAAATCGGATACGGCTCAACAGATCATTCAACAATGGATTGAGGAGGCGACTGGACGACTCTTTCGTTCGTCACGATTCATCGAATCTCTCCAAGACGGTGTTCTCTTGTGCAATCTCGTGAAGCGAATACAACCAGACTCAAAGATAATTCAGGATGTTATCGAAGACCCAAATCCTCAAGAATGCCAGATAAACTTGAAGACATTTTTACACGTTTGTGAAGATCTTGGTCTAAGTGCCTGGCAACTTTTTGATCCACAAGATCTACAAGAACAAGATAATGTAATAAAATATAAATCGGAAGATGAAGTGATTCAGAAGGTTGTCAGCACTCTTTACTGGCTTGGTTGTACTGTTCAAGGGATGTCTTATTACAAAGGTCCAAGACTGGATGTCAGCAACTTCCAGCGTGAAAGTGATGGCACCATAACAGTCAAGCCTAATGCCAGACCTTCTGGCCATGATTATTCCTACATTAGGATGGATGCACCTCATATTAATGGAGCACTTCCACAGAACAGAAGGCCAACCCATCTCACAAATGGCTATTCTGAAAATATGATGGCCAATGGTTCAGATGATGCCGTGGAATTTTCTGTCAATGTCAGGATACTTGGAGATGAAAAGCGCTTTGGCTTCTCAGTGATGGGTGGTGTGGATGAAGGATTCCCTCCAAGAATTGATGAAATCTCACCAGATTCTCCTGCTGCCAAAACTGGCCTACTTGTAGATGATGAGATTCTGGAAGTTAATGGAGTGCCTGTAATGAATCTCTCTCACACTGAAGTTATTTTAAGTATTCACAAAtGTCTAAGAAACAGAGTTATTGCTCTGAAGGTCAGAAGAGGACGACAGTTCTTCTCAGGGGTTAATGGAACAGAAAATCACAAGGACCTCAATGGAAAAGTGGACGTAAAGACAAGAAGTAAACTTCATAAAATTATCAATGACCATGAGAATGACCCCCAATTTGAGTACTATAATTCGGACGCAGAATCAGAGGGCTCCCATTACAGCCAAGAATTTCATGGAAACAGTGACGTTGGTGTAATATCACCTGGTTCGGGGTGGAGCAAGGACATTGAAAATAAGAACTTTGGGATATCAAGCAAAAACATAGGACAGTCAAACTTGCAAAAGCACAAATCTCTGTCTACGCCTCTTTTTGATTTGACAAAACTTGATACCATTGAGGCAGATGTGGATATTGAAGATGGTGGCACTTACGCCCTTCAAAATGAAGCTTACGATAGTGATAATGAGGAGGAAGACTCAGGTGGAGCTGACAAAGAACTGCTGTTCCCCTGTATGAGTGAAGTAAAAGGAAAGTTTGATTCTGGTTCAGATGCTGAGGAAGTTGCATTTGTTGACAGTTTGTTTGAGCAGAAACATTTTCAGGATGCTACCAAAGTATACACAAAAATGGTCGAGCTTGAAAGGTCAGGGCGAGGACTAAGTGCAGTCACACCAGTGGTTACAAACTCACAGCATCTTTCTACTCAGttaaAGCATTCGTTGCAAGCTACAAGAGACTCGAGGGATGCGCAAGAATTAATTGAAATTTTACAATCACCAAACTTCCAGGGTCTGTTACTAGCGCACGATAGACTGGCCTTTAGAGAGGCTCTTCCAAGTGAAGAAGACGTTCAAGAATTGGAGTTCGAACAAGATCAGCCGCAAGAACCACAGCCAGTTGCAAACGAATATTCACTGGTGGAAGAGGACAACATGAAGGTAGTGAGAATTGACAAAGCAACTGAACCTTTAGGAGCAACTGTCAAGAATGCTTATGGCTCTGTATTGATTGGAAGAATTGTCAAAGGCGGCGCAGCAGATAAGTGTGGTCTTCTCCAAGAAGGCGACGAGATCCTCGAAATCAATGGAGTAAATATGAGAGGGAAAACTGTCGCTGAGGTCTGCGAGTTACTGGCTGATATGAACGGTACGCTGACGTTTGTTCTGAACCCAGCAAATCGGCCCCGTGTTCCCTCGGACAGAGAGGTGCACGTGCGTGCAAATTTCAACTATCAACCGTACGAGGATGAATTAGTACCGTGCAGGGAACTGGGTCTAGCATTCAGACGAGGTGATATACTCCATGTTGTCAATCAGGAGGATCCTCATTGGTGGCAGgcGTGGAGAGTTGGCGAGGAAGGCAAAACTTTAGCTGGTCTAATTCCATCCAAACATTTCCAACAACAGAAAGAAAGTATGAGAAAAACAGCTCGAGAAACAGAGGCAGCGTCCAAAGAAAACAAAGGATGCCTCTGCTTCAAacgaaaacgaagaaaaaaagttcTTTACAATGCACAGCATAACGAAGATTATGTCGCGGACGAGGTTCTGACGTATGAAGAAGTAGCGCTCTTAGAACCCGACCCGCAGAAAAAACGTCCGGTGGTGCTTATAGGTCCTGATAGAGTTGGTCGTAAAGAACTAAGACAAAGGCTGATTCTCTTTTCTCAAGAAAGATATGCTGGGGTAGTACCTCATACCAGTAGACCGAAAAGACCGGAAGAGGTAAACGGAAGAGATTACTATTTTGTGCCGCAATCCGCATTTGACCTGGATATAGTGTCCAATAAGTTCGTGGAACACGGCGAAATCCATGGTTATTGTTATGGAACAGCTCTGGACTCAATCAGAAGAGTGGCCAACTCTGGaaaatattgtattttaaaTCTTAATTGCGAGGCCCTAAAAATACTCATGGCGTCAGATGTCAAACCTTACGTGGTTTTTATACAACCGCCTCCTTATGATAGAATTGTCCAGCTTAGAAGAGGAAAAGTGGATCCTTTTAACCCTAAACCAGATGCCCAAATGAATAACGCCGAACTCCACGAAATGGTCGAAAAAGCGCAAGAAATGGAGGAAAATTACGGGCATTATTTTGATAAAACGATCGTGAACACGGATTTGGAGAGAACGTTCGATGAACTAAGACAAACCATCGAGAAACTTGATGTCGAAGCTCAGTGGGTTCCAGCTTTCTGGGTACAAGAGAGCCGAGCCATTTTGTAG

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q5RDQ2	Protein PALS1 OS=Pongo abelii OX=9601 GN=PALS1 PE=2 SV=1
Q8N3R9	Protein PALS1 OS=Homo sapiens OX=9606 GN=PALS1 PE=1 SV=3
E2QY99	Protein PALS1 OS=Canis lupus familiaris OX=9615 GN=PALS1 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000787 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00595 all species →	PDZ	PDZ domain	Domain	Interproscan
PF07653 all species →	SH3_2	Variant SH3 domain	Domain	Interproscan
PF00625 all species →	Guanylate_kin	Guanylate kinase	Domain	Interproscan
PF02828 all species →	L27	L27 domain	Domain	Interproscan
PF00307 all species →	CH	Calponin homology (CH) domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001452 all species →	Domain	SH3 domain	Interproscan
IPR036028 all species →	Homologous_superfamily	SH3-like domain superfamily	Interproscan
IPR001478 all species →	Domain	PDZ domain	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR001715 all species →	Domain	Calponin homology domain	Interproscan
IPR050716 all species →	Family	Membrane-associated guanylate kinase	Interproscan
IPR004172 all species →	Domain	L27 domain	Interproscan
IPR036872 all species →	Homologous_superfamily	CH domain superfamily	Interproscan
IPR008144 all species →	Domain	Guanylate kinase-like domain	Interproscan
IPR020590 all species →	Conserved_site	Guanylate kinase, conserved site	Interproscan
IPR036892 all species →	Homologous_superfamily	L27 domain superfamily	Interproscan
IPR036034 all species →	Homologous_superfamily	PDZ superfamily	Interproscan
IPR008145 all species →	Domain	Guanylate kinase/L-type calcium channel beta subunit	Interproscan
IPR014775 all species →	Domain	L27 domain, C-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23122 all species →	MEMBRANE-ASSOCIATED GUANYLATE KINASE MAGUK	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0005911 all species →	Cellular Component	cell-cell junction	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

No KEGG orthology assignment for g2530.t1.

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

Expression pattern (RNA-seq)

Transcript abundance of g2530.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

175.1Max TPM

88.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole organisms · ambient pH treatment	21	21	82.70	175.07
whole organisms · low pH treatment	15	15	95.45	160.20
whole organisms · extra low pH treatment pH treatment	12	12	88.34	172.05

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11452263	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	175.07
SRR11452259	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	154.92
SRR11452250	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	153.29
SRR11452254	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	132.35
SRR11452260	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	129.22
SRR11452251	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	120.41
SRR11452262	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	114.70
SRR11452246	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	103.41
SRR11452252	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	101.37
SRR11452240	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	74.95
SRR11452217	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	73.78
SRR11452242	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	65.00
SRR11452234	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	52.65
SRR11452243	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	45.63
SRR11452230	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	44.36
SRR11452222	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	41.64
SRR11452233	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	39.83
SRR11452228	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	36.56
SRR11452232	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	34.33
SRR11452237	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	32.80
SRR11452231	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	10.51
SRR11452247	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	160.20
SRR11452253	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	157.61
SRR11452249	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	149.05
SRR11452258	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	132.27
SRR11452229	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	129.21
SRR11452255	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	126.34
SRR11452218	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	115.23
SRR11452245	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	111.23
SRR11452216	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	103.92
SRR11452241	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	84.28
SRR11452238	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	50.27
SRR11452236	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	39.62
SRR11452223	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	25.77
SRR11452221	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	25.72
SRR11452224	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	21.01
SRR11452257	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	172.05
SRR11452248	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	143.20
SRR11452219	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	139.11
SRR11452256	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	118.86
SRR11452244	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	111.31
SRR11452261	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	89.24
SRR11452239	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	80.94
SRR11452220	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	57.81
SRR11452235	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	41.96
SRR11452227	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	38.99
SRR11452225	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	38.51
SRR11452226	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	28.14

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.