Gene detail

Detailed information of XP_068720359.1 in Montipora capricornis

Genomic Location: chr9:15443240...15468062
NR annotation: XP_020616032.1, nuclear pore complex protein Nup54-like [Orbicella faveolata]
Species Montipora capricornis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_068864258.1

CTAGTTGTTTTCTCTTCCTCTTTTTCGAGAGATTGtttcaaaagataaaatatgtccCTTTTTGGTTCTTCCAACCAACCTTCGACTGGTGGAGGGTTTGCATTTGGTACTCCTTCAACCACAGCTACAGCATTCGGTTTTGGAACAAGTCAGACTGGCAATACAGCCGGCAAGgtttttggtttgacaaatCCAAGTTTTGGTGGCTTCGGAGCAGCGACAACAACTTCTACTGGATCAGTATTTGGAACTAGCTTTGGCGTCAAAACAACTGCTTCCTCCACTTTTGGTTTTGGAACAACTACCAGTGTAGCGCCGTCTCTCGGAGGGGGACTAAGTACCGGATTTGGGGCAACTGGAGGCCTTGGTGGATCAACCTTTGGTCAGCAACCAACTGCAGTTGTCACAGGCCTTACGCAACCATCACAAGGAATTTTGGGCCGGAGCACACAGTCAGCACAAACACTGTTAGCTCAGCTAACAGCTGCTTTATCTCGGCCTCAGATTCATGGTGATGAAAGAGATGGCATCATAGCAAAACTAAATCAGTTACAGGCCTGCTGGGGAACTGGTAAAGGCTTCTACAACCAACAAGGAGCTGTGGACTTTTCACCACAGAATCCATTTTGTCGTTTTAAAGTTATAGGGTATAGTCGTCTTCCTACAGCCAGTAATGAAGATGGACACTTGTCTATTgagataaagaaaaaagaaagcgaGGTGCGTGCCTTGCAGCAAGGACTTGTGGATGCTCTGCACAAGTGCCTGGGCAGCAAAACCACTTTGATGGTGTGTATTGAAGGAATTAAACCTCTTCCTGAGGACAGGTCAGAAGTTATTTTGTATGTTGTTGAAAGGCATCCAAATGGATCCTCTAGAACTGTTCCAGCCACAGATGTCTTTACACACCTCAATCAGGCCAACATTAAGACTCAGTTGCAGAGCATTGGAATTGTCAATATCTACATGAAAACGAGTATGTCTCCATCACAGCTACAGCACTATCTTGAAAATCCTCCTGTTGGTATTGATTCACTTTTGTGGGAGCAAGCAAAGAAGGACAATCCTGATCCTCAAAGGTTGATTCCAATGGTAATAACTGGATTTAGTGAGCTAAAGAAGCGTCAAAAGCTGCAGGAACAGGAAACATTACAACACCAGAAGAGAACTGCTCTTATAACTGAGGAAATAACAGAGTTACAGCACAATCACGCTACTACCATGGCAAAACTTGCACAATTCAAAAGAAAACACTTGGAACTTAGCCATTGCATACTGGAGataatGATAAAGCAAGAATGTATGAGAAAGAGTGGGTACTCAGTTCAAGCTGATGAAGAACAACTGAGggttcaaCTTGAATGCTTGCAAGCTGAATTAAACGCACCATCTCAATTCAAGGCTCGTCTTAGTGAGATGATGTCACAGATTCGCTTACGACAGAGCCAAGCTGGCGAAAGGCTGGGGCCGGGGGATGGCAGATATGTTGTGGAAGGTGTGATGCAAGAGCAACTGAAACAACATCTTGAGCGACAGCAAGTTGGTCTGATGCATTTGATTGGGATCATAAAGGAAGACCTTCAAGATTTGGCTACTATAGAGCGCGGACTCACGGAACTTCCTTCCAATAGAAGCTAAGCTCAAGTGGGTCTGATGATGAAGTCTCTTTAACGCCAGGACAGAGTTAGCGAGGTTCAGGCCTTAGCACTAAACGCAGTGAAATACTACGAAAACAGCTTTAGGTTTTGTCGGCACCTCTCTTGCTTGTTAGCCCGATTCTAATAATTGGGCTCTGTTGTACGTCTGTAATGTATGCAAGTAATAATTGATACGAGgtttatgataataataataataataataataataataataataataataataataataataataataataataccaactttattcatttaattcaatgaaagagaAGGACACCAGAGGGTATCCCGCCcgcagccggatgtaattgactAGGATTCGATTTGATGAGggaagaaaaccggagtacccggagaaaaaccctcggggtcagattgagatcgactgaaactcagcccgcATACGACCCGATGCCAGGATTGAACCCGTGTCACCccagaggtgggaggcgcggttgatAACCGTTAAACCACCCCGACTCTACGAAACTATTATCAAGAGACTGAAGATGCGCTTTAAAGAGTACTTTGGGTCCGAAGAGTCTTGACAGATTTGGGACAAAACCTCTGGCCGGTATATTATCACGGTCTTGCGCATGTTCTAGCCGTAGCGAATGTTTATAAGCCAATCGGAAGCGACGTTGTAATACGCGCGTGAAATTTACACGTACTCGTGAAAATTTCGCTCAGCCCATAGCTCATTAGTGATTGTACGTGTAAAATTTTCCGCACGAATTATAACGTCACTTCCAATTCTTCTCACAAATGATGATATTTGTTACGGCTAGAACATGCGCAATACCGTGATACTCTCCCTTTAAATAACGTGCAAAGGGTTAAGACGCAAGTGTGAATGAGAAATGATAGAATCACGTGAAGTGATTTCTATCGTTTAAGACGCAAGTGATAAATTTGCCTTAAAAGCGCATCGTCAAGAATGCGCAATTTTCTGTTTTACCAGGTGTTACTCGTCATGGTAATATGTGGATACAAACTACATCAGCCAAAAAGAGGTTTAACTTTGCCTCATTGGCGTGCAGATTTTGTATTCATATTACAACAGCAAACTCAAGGTCTTGTGTCATTGTAAACCTAAGCTTAATTGTTCTTGATGACATCAGAACATTAAGCGTTTCCTGACTTATGATGACGTCAAAAGCTCGTATACTTAACTTCCAAGGCACGAGGTTTTATTTTTGAACATGAATTTTAGTATTgatgttaaaaacaaaaaatagcgTTGAAACTTACAAACAATATCATTAGTACTAACTACCTAATTGAAGCCGCAAAGCTTAATATTCTTGAATCATTGTGTAGTTATTTGCAAGACGTCTAAAGGTAGTGGGGGCGGCGTAAGTAGGGCAGCCCTTCATGAATGACACACTTACCGTAAATTGACCATTCAACACTACGTATCTCGTCTTAGCATGTGTCATCCATTCGTAACCTTATACATAAAGATCAAAAGCTCAAAAGATCGGATTGGAGCTTAGGCGTTCAGTAGGTGGTGATCAGTACTTGTTTGAAGTGTTCCTGTATCTGGAgaaaactaaattttaaaattggCTGCACTTTTGTCTGTTTTCTCCCCTACATTTACCCTTTTTGACATAAGGCAAACAAGATCGAGTACTTAAGTAAAACGAATGTCAAGtttgtttcttaaattttttgctgtttcaacAGCTTGCACCTGCTTTAGAAGTCATAAAACAACTGCGTTGTATGTCGGAAGTCTGAGAATTTTATTTGGCCTTCATTATGTTGTAGTCAACGCGTCATATTTGGTAATTTGGTAATGTACCAACTGAAAAGTGTAGTTTTAATGGACGTTAATAGTCTCAAATAAAGTCAAAATTGTTTCTGCGCGGAAATCTGA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q7Z3B4	Nucleoporin p54 OS=Homo sapiens OX=9606 GN=NUP54 PE=1 SV=2
Q8BTS4	Nuclear pore complex protein Nup54 OS=Mus musculus OX=10090 GN=Nup54 PE=1 SV=1
P70582	Nuclear pore complex protein Nup54 OS=Rattus norvegicus OX=10116 GN=Nup54 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006758 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13874 all species →	Nup54	Nucleoporin complex subunit 54	Domain	Interproscan
PF18437 all species →	Nup54_C	Nup54 C-terminal interacting domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR025712 all species →	Domain	Nucleoporin Nup54, alpha-helical domain	Interproscan
IPR040985 all species →	Domain	Nup54, C-terminal interacting domain	Interproscan
IPR024864 all species →	Family	Nucleoporin Nup54/Nup57/Nup44	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13000 all species →	NUCLEOPORIN P54	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005643 all species →	Cellular Component	nuclear pore	Interproscan
GO:0006607 all species →	Biological Process	NLS-bearing protein import into nucleus	Interproscan
GO:0006999 all species →	Biological Process	nuclear pore organization	Interproscan
GO:0017056 all species →	Molecular Function	structural constituent of nuclear pore	Interproscan
GO:0036228 all species →	Biological Process	protein localization to nuclear inner membrane	Interproscan
GO:0044613 all species →	Cellular Component	nuclear pore central transport channel	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
K14308	NUP54, NUP57; nuclear pore complex protein Nup54	-	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 XP_068720359.1 across 36 RNA-seq samples of Montipora capricornis. 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

29TPM > 0

1Conditions

23.1Max TPM

10.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
Polyps	36	29	10.81	23.06

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR12786897	Polyps	Polyps	OA3 day0	not recorded	SRP199550	23.06
SRR12786898	Polyps	Polyps	OA3 day0	not recorded	SRP199550	22.46
SRR12786896	Polyps	Polyps	OA3 day0	not recorded	SRP199550	21.24
SRR27940191	Polyps	Polyps	not recorded	not recorded	SRP199550	19.31
SRR12904783	Polyps	Polyps	not recorded	not recorded	SRP199550	19.19
SRR12904782	Polyps	Polyps	not recorded	not recorded	SRP199550	18.54
SRR12904781	Polyps	Polyps	not recorded	not recorded	SRP199550	17.89
SRR27940193	Polyps	Polyps	not recorded	not recorded	SRP199550	16.95
SRR12959202	Polyps	Polyps	E3 day15	not recorded	SRP199550	15.58
SRR27940192	Polyps	Polyps	not recorded	not recorded	SRP199550	15.54
SRR12959203	Polyps	Polyps	E3 day15	not recorded	SRP199550	15.48
SRR12959184	Polyps	Polyps	E3 day0	not recorded	SRP199550	15.32
SRR12959201	Polyps	Polyps	E3 day15	not recorded	SRP199550	14.73
SRR12959183	Polyps	Polyps	E3 day0	not recorded	SRP199550	14.48
SRR12959182	Polyps	Polyps	E3 day0	not recorded	SRP199550	13.62
SRR12959216	Polyps	Polyps	E3 day9	not recorded	SRP199550	12.94
SRR12959215	Polyps	Polyps	E3 day9	not recorded	SRP199550	10.64
SRR12959214	Polyps	Polyps	E3 day9	not recorded	SRP199550	10.48
SRR12710846	Polyps	Polyps	OA3 day3	not recorded	SRP199550	9.60
SRR12710847	Polyps	Polyps	OA3 day3	not recorded	SRP199550	9.32
SRR12959227	Polyps	Polyps	E3 day3	not recorded	SRP199550	9.31
SRR12959188	Polyps	Polyps	E3 day21	not recorded	SRP199550	8.79
SRR12710848	Polyps	Polyps	OA3 day3	not recorded	SRP199550	8.53
SRR12959189	Polyps	Polyps	E3 day21	not recorded	SRP199550	8.45
SRR12959229	Polyps	Polyps	E3 day3	not recorded	SRP199550	8.33
SRR12710857	Polyps	Polyps	OA3 day9	not recorded	SRP199550	8.24
SRR12710858	Polyps	Polyps	OA3 day9	not recorded	SRP199550	7.44
SRR12710855	Polyps	Polyps	OA3 day9	not recorded	SRP199550	6.98
SRR12959190	Polyps	Polyps	E3 day21	not recorded	SRP199550	6.68
SRR12807381	Polyps	Polyps	OA3 day0	not recorded	SRP199550	0.00
SRR12849113	Polyps	Polyps	OA3 day0	not recorded	SRP199550	0.00
SRR12927880	Polyps	Polyps	E3 day0	not recorded	SRP199550	0.00
SRR12959230	Polyps	Polyps	E3 day3	not recorded	SRP199550	0.00
SRR12963484	Polyps	Polyps	E3 day0	not recorded	SRP199550	0.00
SRR9129316	Polyps	Polyps	not recorded	not recorded	SRP199550	0.00
SRR9613519	Polyps	Polyps	not recorded	not recorded	SRP199550	0.00

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.