Gene detail

Detailed information of XP_068744802.1 in Montipora capricornis

Genomic Location: chr3:27065910...27080132
NR annotation: XP_029193964.1, protein lin-54 homolog [Acropora millepora]
Species Montipora capricornis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_068888701.1

ATTGTGGGATGATTTTCTTTCCCTGGCAAAAGCGCGTGATTTTGAACAACAACATGTCCGCAAAGTGGAGTTAATTGAATATCTTCACTACGTAGTTTTTATGGGATTTTTTCATGGAAACGACGCTTGCTTTAGACGCCGTTTAAGATCAATGTATCTTGCAGGGAATTTCAACTTGTATGGAGAAAATAATTACAGTCAAGCAAGAACCTATTGATGATGCATATCCTTCACCGCCATCAACCACAACAGCATCAACCACTGTTTCTACTGGAACAACAACAGTACTAgttcaaaattcaacaacaaGAACTACCAGTGTAGTTAGCTTGGGCACAGCAACAGTAACGTCAGGGAGCATTACAGGGGCTGCTACCGTGGCAGCAGCTCCTGAACCTCAGATATTCTTCATCCAACCAAAACCTGAACTGCAAAAAGCACAATGTACTGTGGTCTCAGTCATGCAAGGTGGCACTGGAACAACAACCAATACAAGGACAGTAGCTACAAATGCCCAGTCCAAACCACCTGTAGTCGTTATTTCAGGTAGCCCGATCAAGCTAACGCCTCTGTCACGCGCAGGGGCAGCTCTAGGTGGTGCACAGGCAAACTCTGGTACAGGCAACAACATAACATGCACATTGGTTCATGTTCAGCCATTTAATGCAGCAACCAAGCAACACATTGCTCCAAAAGCTGGGGGCTCCCCAAACAAGGCACCTGTTCCGCTTCAAATTCAAAAACTTGTACCAATCAGTGTTGCAGCAAGTTCGTTGGCTAAAATACAACCCGGAACAACACCACAGTTTACTATGGCTGCTCCAGCAGCTTCAACTACAAATGTGCGTCACATTGCGCCTAAAGTAAGCATTGTGCCGGCTGTGCCAGGTGCTCAGACTGTCCGTTTAACAACACCAGCCATGCAAGTCAGAAATATTGCACCAGCTGAGAAACCAGCTCAAGTTCCCCAACAGCTGGCACCCAAGCCTATTGTGACTCAGGCATCTAGTGCAGCACAACAGCCAAGGCTTATTGTCCCAGCATTACCTTCCAACATGTCACAAATATCTGGTGTAACTGGTGCAGCAGCCACAGGAAATGTGCAGTTTCCTCATGGAGTTATCAGTGGAGGGGTTGTTTATCTCCCTCAGCAAGCCCTAGCATCTGGTGGTGGTTTCCCTATTGCAGTCCCTATGCAGACCAGTGCATTGAATACAGGCACCCAATCAGGGATGACTGTTAATGGGAATTCACCTGAATCATCTCCACCAAGTAGACCACGCAAGCCCTGCAATTGTACGAAATCACAGTGCCTCAAACTGTACTGTGATTGTTTTGCAAATGGAGAATTCTGCAACAATTGTAATTGCGTGAATTGTTCCAATAATATGGAGCgtgaaaaggaaagaagtaaAGCGATCAAGGCTTGTTTGGACAGAAATCCTCAGGCTTTTCATCCGAAAATTGGAAAAGGAAGGGGTGATGCTGACAGGCGACATAATAAAGGTTGTCATTGTAAACGATCAGGCTGTCTCAAAAACTATTGTGAATGTTATGAGGCCAAGATTTTGTGTACAAATCTTTGTAAGTGCACAGGATGCAAGAATTTTGAAGAGAGTCCAGAGCGAAAGACGTTAATGCATTTAGCAGACGCTGCAGAGGTTCGCGTGAAACAACAGAATGCTGCCCGCACAAAACTCGAATCTCAAATAGAGGACCTGCCATCTAGACCGACGTTTTTGTCAAACTCTGGAGAGAGACTCCCGTTTTCGTTTGTCACGGACGATGTTGTTAAGGCAACTTGTCAATGTCTGCTGGCCCAGGCTTCCAATGGTGAAAGTGAGGGGAAACCTCAAGCAATGATTGAAAAGTTGGTTTTAGAAGAATTTGGACGCTGCTTGTTATCAATCATTCACACAGCCAATGGGACCAAAGaatGAGCCTTGTTGGTGACGTGCTAATCTGTGGAATCCACATTTTTCATCCTTGTTGGGATTTTAATCATTCTGTTCAAACTTGGACAGAATTTTTATCCGGTACATAGTAGTGTAAATAGTGATTTGACAATGTTTTTGACTGTTAAGCATTTTCAACGTTAACTGTACGTGTAAAAATAACGTTCTGCTTTATTAGCCCCACCCTCGTCGTCTCCAAGAGCAGGTTCGTTGTCGAAGAAGAGGGCCAATATCCGAAGAAACAATGGGAAGAACGTCGACGAAGCAATAAGAAACGAGCTTACCCTGCCTTATCTTTCCATTTCTTCTCCTTCCCGTTTCCACAAACCACTTTGGTCGCAAGCAGGACTGCACTAATCGAGTGAGCGTGCAATCCGCTGTCCTCACGAAATGAGGGGTACCTGCAGTCGATATTCGCATATTCGGGAAATAGGAAAATATCAAGGACGTTAAAAATAAAGTCTACCTGAGAGCGTTTTTCTGTCAATTGTCGTCGAAATAAACCGCTTTTAGGCCATTACAGCGTTATTGCAATGCAACGAAACTTAATTGAAGAGCCCACTTCCCTCGTCTCGTATTATCATTACGGCAAAACAAAATACCACTGGAGCGAAAAATTGTGACCTTTCAGATAAGTCTCTTTCCCGACTTTAGATTTAATACGAAGACAAGGTGGAGTTTCAAGAACTTAATTGCGTTGCTAAAAGTAActcaaaggttttaaaaaattctactGTCGACTTAAAATCGCTCTTTTTGGATTGGACTTAAGCGCGTTGGATTTAATTTAAATtcgaataatattttattttcttagtATCTATCCTTAAATAAAAGCGTCTGTAGagacaacctcgtccccagggcgagGTTGTCTTTAGAGACTTAAACCGAAA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q5RBN8	Protein lin-54 homolog OS=Pongo abelii OX=9601 GN=LIN54 PE=2 SV=1
Q641Z1	Protein lin-54 homolog OS=Rattus norvegicus OX=10116 GN=Lin54 PE=1 SV=2
Q571G4	Protein lin-54 homolog OS=Mus musculus OX=10090 GN=Lin54 PE=2 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006380 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03638 all species →	TCR	Tesmin/TSO1-like CXC domain, cysteine-rich domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR005172 all species →	Domain	CRC domain	Interproscan
IPR028307 all species →	Family	Lin-54 family	Interproscan
IPR033467 all species →	Domain	Tesmin/TSO1-like CXC domain	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12446 all species →	TESMIN/TSO1-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006355 all species →	Biological Process	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
K21776	LIN54; protein lin-54	-	Cellular senescence	ko04218	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_068744802.1 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

43.0Max TPM

23.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
Polyps	36	30	23.40	43.00

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR12959229	Polyps	Polyps	E3 day3	not recorded	SRP199550	43.00
SRR12786898	Polyps	Polyps	OA3 day0	not recorded	SRP199550	40.87
SRR12786896	Polyps	Polyps	OA3 day0	not recorded	SRP199550	39.65
SRR12786897	Polyps	Polyps	OA3 day0	not recorded	SRP199550	38.27
SRR27940191	Polyps	Polyps	not recorded	not recorded	SRP199550	33.10
SRR12904783	Polyps	Polyps	not recorded	not recorded	SRP199550	33.08
SRR12959227	Polyps	Polyps	E3 day3	not recorded	SRP199550	32.42
SRR12959183	Polyps	Polyps	E3 day0	not recorded	SRP199550	32.14
SRR12904781	Polyps	Polyps	not recorded	not recorded	SRP199550	30.85
SRR12959182	Polyps	Polyps	E3 day0	not recorded	SRP199550	30.66
SRR12959214	Polyps	Polyps	E3 day9	not recorded	SRP199550	30.52
SRR27940193	Polyps	Polyps	not recorded	not recorded	SRP199550	29.85
SRR12959215	Polyps	Polyps	E3 day9	not recorded	SRP199550	29.83
SRR12904782	Polyps	Polyps	not recorded	not recorded	SRP199550	29.29
SRR12959203	Polyps	Polyps	E3 day15	not recorded	SRP199550	29.18
SRR12959184	Polyps	Polyps	E3 day0	not recorded	SRP199550	28.06
SRR12959201	Polyps	Polyps	E3 day15	not recorded	SRP199550	27.93
SRR12959202	Polyps	Polyps	E3 day15	not recorded	SRP199550	27.54
SRR12959230	Polyps	Polyps	E3 day3	not recorded	SRP199550	27.25
SRR12959216	Polyps	Polyps	E3 day9	not recorded	SRP199550	26.99
SRR12959188	Polyps	Polyps	E3 day21	not recorded	SRP199550	25.93
SRR12710847	Polyps	Polyps	OA3 day3	not recorded	SRP199550	22.91
SRR12959189	Polyps	Polyps	E3 day21	not recorded	SRP199550	22.43
SRR12959190	Polyps	Polyps	E3 day21	not recorded	SRP199550	22.09
SRR12710846	Polyps	Polyps	OA3 day3	not recorded	SRP199550	21.18
SRR12710858	Polyps	Polyps	OA3 day9	not recorded	SRP199550	19.64
SRR12710848	Polyps	Polyps	OA3 day3	not recorded	SRP199550	19.11
SRR12710855	Polyps	Polyps	OA3 day9	not recorded	SRP199550	18.11
SRR12710857	Polyps	Polyps	OA3 day9	not recorded	SRP199550	17.16
SRR27940192	Polyps	Polyps	not recorded	not recorded	SRP199550	13.49
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.