Gene detail

Detailed information of XP_068720302.1 in Montipora capricornis

Genomic Location: chr9:36110155...36123020
NR annotation: XP_029212195.2, paired box protein Pax-6 isoform X2 [Acropora millepora]
Species Montipora capricornis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_068864201.1

ctTTGTGAAGCATCTTGGACAGAAGCAAGCGAATTGATAGCACCCGCTCTAGAAGGCTTTCGCTTACGGCCAAGTCACAGTGTTTAGTAACGCCTGACTGAGCTTAAACGGTCGTAGCGCCTGAGTGATTTTTGGAAAGGCAAAATACACACGGATCAACGGGTGCACTGGAATGGCTCATACTACAAAACAAGGACACGGTGGAGTTAACCAACTTGGAGGTTTGTTCGTGAATGGAAGACCTCTCCCAGATGTTGTTCGATCAAGAATTGTTGAGTTGGCTCAGAGCGGAGTACGGCCATGTGACATTTCGCGGCAACTAAGGGTATCTCACGGCTGTGTAAGCAAGATTCTTTGCCGTTTCTACGAGACAGGCTCCATCAAACCGGGGGTAATTGGCGGGAGCAAGCCGAAGGTAGCAACAGGTCCCGTTGTCAACAAGATCGCGGACTACAAGCGTGCGAACCCAACAATGTTCGCTTGGGAGATTCGAGACCGGCTTCTTAGCGAAGGTGTTTGCACGACAGACAATGTTCCCAGTGTCAGCTCCATAAATAGGATTGTTCGAAATCGAATCAACAGCTCCGACAGCAAAATTGGCCCCGGAAAGACGGAGGAGATTGTTAGCGACGTTCCCGATGGCAGCATGAAAGTTGAGCCGTCAAGTGTTCATATGCCTCGGAATTCCTACTCTATCAACGGGATTCTAGGCATGGCCGCCCACTCAGTTAATTCTGTTCCCCCAAGCAAAAGAAAGCATTCAGTGGAAAGCGCCGAAAGCACAGGGAGTCATTCTGAAGAAGAGGGTCCAGAGGGCCAAATGGATGCTGGGTCACCCTCAGATCTCCGGGGACACAAGATAGTGCGCCGTCAACGCACAACATTTTCTGGAGACCAAATTGAACAGTTAGAAAAGACTTTTGAGAAGACCCATTACCCTGAtgtcttcacacgtgaaaagctGGCACAGGATGTTGATCTTTCTGAGGTTTGGTTCTCTAATCGACGGGCCAAGTGGAGGAAGCAAGAAAAGATCCCCTCCATCGGCAGTCCTACAGCTGCAAGCCCTGCGCAATCAGTGCCAACAACCTTTATTAACACTGCAACTGGGTATCCCACCACAGTCATAAGTCCACCACCCAACCACCCCACCCCTGTACAAGATGAGGGCTTGTCATCTGCTCATTATGCGCATCATGCTAGTGATTCAGATCCACCTGTGAAAACAGAATTGACAGAGCTGAAGCCAGTATCTGACCCAACCCTTTCCATGCATACCACAATGGGAATGCCAAACCTGGCACCAGCTCATCAAATTCAGCAGCAGCCTCCGTATGAAATGATGCGAACAGCAGCTGCCCCACCCAGCCAGACATTTATTGCAGTACCAAGTGCTAACCTTGTACAGGCCTCCCACCCCATGGTTGGTGGACAAGGTTACACCATGCGTATCAGCGACAACACCCAGTCATCTGTCAGCAGTAATGCAACATCAGTAGGGTACTCATCAGTTGGACAAAGTGTCATGACAACTTCCCCATCTTATGCAACGCGGAGTCCAATACAGTATCAGAGAGTTATCACAAGTGGTGGTGACATTGGTCAGGCTACATCCCCACCTGCAGCCAATCCTGCCCCTGGTTATGTCCTCCCACCTGTTAGCACGCTCACTAAAGGTCAGATCCCAGGAGATATGACTGGCCAATTTCCACCATCAAGCTACTCCCAAGTTCAGGCACCCTACCCTGACCAATGGATTCCATATGCAGCTCAAGGGTTCATTGGCAGACCTACAGTGTTCCTGCCTGCCAACTGGACAACCTCTGCTCCACCACCATCAAGAGTTCCTCCTCCCAAACTGACCACATCTGCCTGAGGTGAATTTAAGTGGTCAATCCTGAACATCGCAGTCACTAACCTGCATCATTGCCGCCAAGTGTCCAAATTCGTACTGAAAGTATTTCTTAATATTATTATGACCAAGTACAGTACTTAAAATGGGGTTTTAAATCCAGTAATGTTATTTTTGTTCGGCATTGTCCGATGCTACAGTACATTTAGTTTTACTGGCTTTTGGATCAATACTGATCAATGCAATTGATCTAGTGTTTGGTTTAAGTGAAAGGTTAACATTTGACCTTCCATGCAAGGccatttatgtttttttttaataggatTTCAACTAGTCGTTTTCAGTGGTCGCCCCAAAGAACATCTTTTGTAGATTGTGTTTATACATGCATGTAGAAAGAAGTTCCATGCTGGTTTAGAACCTTGTGGGAACCTGAAAGACAAGCATTCTAGGAAATATTGAATTACCCATTTTGTCAATGCACAATATTATAGTATCTCAGAATCTGAAAaccaatatattttttctaCTGCTGTAGGTACATTATTATTCCGACATCAATACCATGAAATCACACTTAGATAGTTTTaatcaatttcaattttccaaAGGTTGATTGACCATGTACATGTTGTAATAACTAAATTCTCAGCAATGATGTACAATGAAGTAAATGTCGAGTCAGTAATTATTACCGGTAATTGCTACATAATCATTTGTACGGGCTGATTCGTGCGTGTTAATTTTTATAGCTAAGAAATTGCAAATTTTTGTAGATAGTTTGGTAGACTTGGATGTAATTGCATCCAACAAAATTGAAGAATTGTCATCCTTCGATAAAATCACAGATCTGGTCAAGATTTTGTACCTGGTGTATAATCTTCCAGAAAACAAGGTAGATTAGAGGTGAACGAATGCCATTTGAGTACCATTTGGTGGCGGTCTTGATCGATCGTCctatttttgaagttatttcACTGGTTTAATCAGCAGGAATGTCTTGAAAGAGATTTAGATCCCTTGTTTAGGAAGATCAAATCATTTCAGAATCCATCGCCCAATCAACGGAACATGACCTTGGTGTCCATAGAAACCCAAGATATTTGGTGCCTGTTGCAGTGCAACCATAAGAATCGGAAACTGACCTTTGGTTAAAACGCAATGAAACGGTGTTGTGAGTTTAAAGCATCCTTAGTGAGTCATGCATGAGAAGTTTGCCAGTGTAACCCATTTAGAATAGAAGGGAACGAGCCTTAATTTGATTTGTCAAACGTATCGTCATTTCTCGTGTAAATAATATCAAAAATGTTTGGACAATGTGAGACCGAGAAGAGATTTTCTCGACGGCTGTATTTTTTATAACGTTTCCAACCAACTTTAGATAGCGTTTCAATTCTTGTCTTGAAGGCAACGAAATAGTCTGTCAGACATTCAAAGGAGATCAGATTTTCTACTTATTTTTGTAACAAAGCATTTTGGTTTGTCGAAACAAGTAATTTTGATGTCGTAATATTTTCTAATGGTCGCAGTATTTTTTATTCAATACTTTACACAAAACTATTTCTATCTTTCTACTAAGTGAGGTCGTGCTAGCTCCTTCCGTGCTCTGAATGCAATGTCGTTGTTCGTCGTATTTTCCATACTCTTTTAGGAGCAATAATTACGCTCATTATGAGCCTGCTATATGCAATCTCAAATCAGAAACGACATTCTTTTATAACAGGTTAGGCACTGGAATCGGTAGTTTTCGTATACCTACAAGTATTTTTCCATCTAAGCATATTTTTTTACATACAAACTGAAGTATATTTTTTGTCTAGCAATGCGATTTCTCAGTATTTAAAGCACTGCAATATGTATTTAAAGGGTACATTTAGTCGATTTGTCAATAAAACATGTAATAAAGTGAATTGTTCTCAGTA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q1LZF1	Paired box protein Pax-6 OS=Bos taurus OX=9913 GN=PAX6 PE=2 SV=1
P55864	Paired box protein Pax-6 OS=Xenopus laevis OX=8355 GN=pax6 PE=2 SV=1
P26630	Paired box protein Pax-6 OS=Danio rerio OX=7955 GN=pax6a PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000410 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00292 all species →	PAX	'Paired box' domain	Domain	Interproscan
PF00046 all species →	Homeodomain	Homeodomain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001523 all species →	Domain	Paired domain	Interproscan
IPR036388 all species →	Homologous_superfamily	Winged helix-like DNA-binding domain superfamily	Interproscan
IPR001356 all species →	Domain	Homeobox domain	Interproscan
IPR009057 all species →	Homologous_superfamily	Homeobox-like domain superfamily	Interproscan
IPR043182 all species →	Domain	Paired DNA-binding domain	Interproscan
IPR043565 all species →	Family	PAX family	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR45636 all species →	PAIRED BOX PROTEIN PAX-6-RELATED-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0000978 all species →	Molecular Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	Interproscan
GO:0000981 all species →	Molecular Function	DNA-binding transcription factor activity, RNA polymerase II-specific	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:0048856 all species →	Biological Process	anatomical structure development	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 XP_068720302.1.

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

Expression pattern (RNA-seq)

Transcript abundance of XP_068720302.1 across 36 RNA-seq samples of Montipora capricornis. This gene has no row in the species' RNA-seq expression matrix, so every value below is shown as zero — the matrix simply does not cover this transcript. 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.

36Samples

0TPM > 0

1Conditions

0.0Max TPM

0.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
Polyps	36	0	0.00	0.00

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study
SRR12710846	Polyps	Polyps	OA3 day3	not recorded	SRP199550
SRR12710847	Polyps	Polyps	OA3 day3	not recorded	SRP199550
SRR12710848	Polyps	Polyps	OA3 day3	not recorded	SRP199550
SRR12710855	Polyps	Polyps	OA3 day9	not recorded	SRP199550
SRR12710857	Polyps	Polyps	OA3 day9	not recorded	SRP199550
SRR12710858	Polyps	Polyps	OA3 day9	not recorded	SRP199550
SRR12786896	Polyps	Polyps	OA3 day0	not recorded	SRP199550
SRR12786897	Polyps	Polyps	OA3 day0	not recorded	SRP199550
SRR12786898	Polyps	Polyps	OA3 day0	not recorded	SRP199550
SRR12807381	Polyps	Polyps	OA3 day0	not recorded	SRP199550
SRR12849113	Polyps	Polyps	OA3 day0	not recorded	SRP199550
SRR12904781	Polyps	Polyps	not recorded	not recorded	SRP199550
SRR12904782	Polyps	Polyps	not recorded	not recorded	SRP199550
SRR12904783	Polyps	Polyps	not recorded	not recorded	SRP199550
SRR12927880	Polyps	Polyps	E3 day0	not recorded	SRP199550
SRR12959182	Polyps	Polyps	E3 day0	not recorded	SRP199550
SRR12959183	Polyps	Polyps	E3 day0	not recorded	SRP199550
SRR12959184	Polyps	Polyps	E3 day0	not recorded	SRP199550
SRR12959188	Polyps	Polyps	E3 day21	not recorded	SRP199550
SRR12959189	Polyps	Polyps	E3 day21	not recorded	SRP199550
SRR12959190	Polyps	Polyps	E3 day21	not recorded	SRP199550
SRR12959201	Polyps	Polyps	E3 day15	not recorded	SRP199550
SRR12959202	Polyps	Polyps	E3 day15	not recorded	SRP199550
SRR12959203	Polyps	Polyps	E3 day15	not recorded	SRP199550
SRR12959214	Polyps	Polyps	E3 day9	not recorded	SRP199550
SRR12959215	Polyps	Polyps	E3 day9	not recorded	SRP199550
SRR12959216	Polyps	Polyps	E3 day9	not recorded	SRP199550
SRR12959227	Polyps	Polyps	E3 day3	not recorded	SRP199550
SRR12959229	Polyps	Polyps	E3 day3	not recorded	SRP199550
SRR12959230	Polyps	Polyps	E3 day3	not recorded	SRP199550
SRR12963484	Polyps	Polyps	E3 day0	not recorded	SRP199550
SRR27940191	Polyps	Polyps	not recorded	not recorded	SRP199550
SRR27940192	Polyps	Polyps	not recorded	not recorded	SRP199550
SRR27940193	Polyps	Polyps	not recorded	not recorded	SRP199550
SRR9129316	Polyps	Polyps	not recorded	not recorded	SRP199550
SRR9613519	Polyps	Polyps	not recorded	not recorded	SRP199550

Source: CnidoSite RNA-seq expression matrices (MCAPR_TPM, StringTie quantification over 36 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.