Gene detail

Detailed information of XP_068746580.1 in Montipora capricornis

Genomic Location: chr3:72328151...72357242
NR annotation: XP_029201218.1, programmed cell death protein 4-like isoform X1 [Acropora millepora]
Species Montipora capricornis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_068890479.1

CCCAACAGTGATAAAAACAACAAACCCCCTGAAACCAGAAAGAAAACTCTGGTTTTAGCAGCTGTGTTGGTCGGGATTTTAAGGTGTTTTCAGTGCTCCATAAAGTTTCGTTTTACTCGCCCCAGCCAGCAGAGATTGCCGGCAAGGCTTTACTGCTTAGCATTCTATGCtaaacttcctttttttcgCTCTGGAACCGTGAAAATGGCAAGTTCCCCTTCCTCCAGCTCTGCAGAAACAATACCAACTGCATCCACAAAGAAGATGCGAGTGCGAAGTAAGTCCACGTCTGCCGTTGAAGATGTAAAGGAAGAAGCTCCCACACATACCCCAAACCAAGTGATCGATGGTGCGAAAAAAATCTTCAAGAATGGAATCAATTGCTCGAAGAACGGAGCCGAATCTTTGTTCGTGAGAAGCCCGAAGGACAAGCAGCACGATAGAAAATCTCGGAGCGGACTACGTGGTTTGCCGAAGAAAGGTGGAGCAGGAGGGAAGGGTACTTGGGGAGCCATTGGTGAATATTTAAGTGAAGAAGATCTTAAGGTCACAGATCAGCATGATCCAAACTATGAATCTGAGGAAGATGAAGATGAACCCTTTACCATGGAAGTGGTTGAGCCAGAGCTGACTGAAGAGGAGTTTAGCAAGAATGTCACTCCTATTGTGCAGGAGTACTTTGAGCATGGCGAAACTGATGATGTGGCGATGTCACTTTCTGAACTCAACATTTCTTCAAGCAAATATAAGGTTCCAGCAATAGCCATCAGTCTTGCTTTGGAGAAGAAgGCAACTCAGAGAGAGATGGCATCAATTTTGATCTCGGATCTCTATGGCAAACACCTTAGCCAACATGATATTGCAAAAGGATTCCAGCAGCTATTAGATGACCTTGATGATCTTTCTTTAGACACCCCAGAGGCACCTAAGtTTCTGGGAAAGTTCATTGCACGTGCCATCGCAGATGACTGTCTACCTCCAGCATTTGTCGCCAGTGTTGGAGAGCCTCCTTCTCAATCAAATCAGGAGAAAGCATTGACTGAAGCTAATGTGTTGTTGAGGATGAAACATGGAATGGTACGTTTGGATAGTGTGTGGGGCGTGGCTGGAGGACGACGCCCTGTAAAACTTCTTGTGAAAAAGATGGTGTTATTGCTCAAGGAGTACTTGTCTTCAGAAGATGTTGAAGAAGCAAGTCACTGTGTCCAAGACCTAGAAGTTCCTCATTTCTACCATGAACTGATATATGAGGCTATTGTTATGATGCTGGAAGATGGCCACGAACGAGTGATGCTATTGatgaaaaacctctttgacttCTTCTCAAAGACCAACATTGTTAAACCAGATCAAATTATAAATGGATTTGAGCATGTGTTTGACTCATTTGCGGACATTCAGCTGGACATTCCTAATGCTCATACCCTTTTGGAGAAATTTGCAGATATGTGTGCTCAGGATGGGATTATTCCAATCTCGTTGACTCTCAAAGTACCATCCAGGGGCCGAAAGCGTTTCGTAAGTGAAGGTGATGGAGGAATTGTCAAAGTTTAATTTGTCAGTATTTTAAGCCACGTAACAATCACGGAACTCGGTAGTAACAGTAAAGAAATCAAGATGGTTGACTGTAACagagattgtttttgtttgtatagAAATGACTGTGGGTTTTTCAAAAGGGTCCTCAATTCCTTATTAATCTTTGTAGGAAAATATGCAACGGTGGTGATCCCTGTTTTTAGAACAATTTTAACGATTGAAAGTAACttgtgagtttttttttttttttaagttgaacCCATGGCTTTTCCTGTCAGGGTTTGAGTTATCGGTGATTTTGTAAAAACAAGTGTGATAATTGCTATAATATTTCCAGCAACTTCATTTCCATGACCTTTTCCTTTCTCCATGTGGGCGGCGTCCTCAAATTAACGACATCGATCATGTCGGTAAAATACACCAgtgaaaaaaagtaaataaattttggaaaaattatCAA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q98TX3	Programmed cell death protein 4 OS=Gallus gallus OX=9031 GN=PDCD4 PE=2 SV=1
Q9JID1	Programmed cell death protein 4 OS=Rattus norvegicus OX=10116 GN=Pdcd4 PE=1 SV=2
Q61823	Programmed cell death protein 4 OS=Mus musculus OX=10090 GN=Pdcd4 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005810 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02847 all species →	MA3	MA3 domain	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR016024 all species →	Homologous_superfamily	Armadillo-type fold	Interproscan
IPR003891 all species →	Domain	Initiation factor eIF-4 gamma, MA3	Interproscan
IPR039778 all species →	Family	Programmed cell death protein 4	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12626 all species →	PROGRAMMED CELL DEATH 4	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0045892 all species →	Biological Process	negative regulation of DNA-templated transcription	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
K16865	PDCD4; programmed cell death protein 4	-	Proteoglycans in cancer	ko05205	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_068746580.1 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

30TPM > 0

1Conditions

308.7Max TPM

207.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
Polyps	36	30	207.85	308.74

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR12959203	Polyps	Polyps	E3 day15	not recorded	SRP199550	308.74
SRR12959202	Polyps	Polyps	E3 day15	not recorded	SRP199550	303.61
SRR12959201	Polyps	Polyps	E3 day15	not recorded	SRP199550	301.05
SRR12904781	Polyps	Polyps	not recorded	not recorded	SRP199550	293.30
SRR12959216	Polyps	Polyps	E3 day9	not recorded	SRP199550	290.77
SRR12959182	Polyps	Polyps	E3 day0	not recorded	SRP199550	288.57
SRR12959230	Polyps	Polyps	E3 day3	not recorded	SRP199550	285.76
SRR12959184	Polyps	Polyps	E3 day0	not recorded	SRP199550	285.30
SRR12959183	Polyps	Polyps	E3 day0	not recorded	SRP199550	283.53
SRR12959214	Polyps	Polyps	E3 day9	not recorded	SRP199550	281.30
SRR12959229	Polyps	Polyps	E3 day3	not recorded	SRP199550	278.73
SRR12959215	Polyps	Polyps	E3 day9	not recorded	SRP199550	274.02
SRR12904782	Polyps	Polyps	not recorded	not recorded	SRP199550	273.34
SRR12786896	Polyps	Polyps	OA3 day0	not recorded	SRP199550	273.30
SRR12786897	Polyps	Polyps	OA3 day0	not recorded	SRP199550	272.84
SRR27940193	Polyps	Polyps	not recorded	not recorded	SRP199550	272.28
SRR12786898	Polyps	Polyps	OA3 day0	not recorded	SRP199550	269.71
SRR12959227	Polyps	Polyps	E3 day3	not recorded	SRP199550	268.51
SRR27940191	Polyps	Polyps	not recorded	not recorded	SRP199550	239.66
SRR12904783	Polyps	Polyps	not recorded	not recorded	SRP199550	238.63
SRR12710847	Polyps	Polyps	OA3 day3	not recorded	SRP199550	216.81
SRR12710846	Polyps	Polyps	OA3 day3	not recorded	SRP199550	215.49
SRR12710848	Polyps	Polyps	OA3 day3	not recorded	SRP199550	214.17
SRR12710858	Polyps	Polyps	OA3 day9	not recorded	SRP199550	213.84
SRR12710857	Polyps	Polyps	OA3 day9	not recorded	SRP199550	208.81
SRR12710855	Polyps	Polyps	OA3 day9	not recorded	SRP199550	205.27
SRR12959190	Polyps	Polyps	E3 day21	not recorded	SRP199550	168.64
SRR12959188	Polyps	Polyps	E3 day21	not recorded	SRP199550	165.85
SRR12959189	Polyps	Polyps	E3 day21	not recorded	SRP199550	165.20
SRR27940192	Polyps	Polyps	not recorded	not recorded	SRP199550	125.40
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
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.