Gene detail

Detailed information of XP_068745596.1 in Montipora capricornis

Genomic Location: chr3:47892913...47931458
NR annotation: XP_029206387.2, rRNA N6-adenosine-methyltransferase ZCCHC4-like [Acropora millepora]
Species Montipora capricornis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_068889495.1

TGTTTCAGATCGAAAGATGCTATTAAATCACAAAAATGCACTGCGTTGACATCGCACGAAGAGTCCACGTGTAAATTAAAATCAACGACAACAAATTAAAAAGCTCGCCTGATGCAGTGGCCATTCCCACAAGCAGGAGAGAAAACTCACGATAAAATGTTGACAAAGGCACAGATCATCCTGATCATCTTTGAGCTCTTCAAACGAGTATCCAAGAATTCAAACGACTGAAAGGAAGTGTTCCACTCAATATGAGAGCTTTCTGGTATAAGAGGTGAAATATGTCAACAAGGGAAAGAGAGAAATAGGAGTTTATTATATGGGAGAGATCGGACATCGACATGTTCAAGCCAAACGCAATATATGAAAAGTGGAATGAAATTAGCGCTATTGGTGGAGTCCTTAAATGCGTCCTTTAAGCTCCTTGTCAGGGCAGTGcagtctcccagatttttatactaatcatctctaatagagaaaagatacttagcaatgtaaagaCAAGGTAATAGAGGAAACAGCtcatttccggttgccgcccgcatctgaaaaacgcgcgtgcttactAGCGCTAGCGCCCTCGAGCTCGCGATCCGCTATATTGGAGACGTCTTGTGACTGCTACATTACCAACTATTCCACTTGTCTCTCCTGCCAGAAGGGCAGCCTGGGGAAAGTCGCTCGATTATTGATTTAGTTACTTGTTTAACATGCATTAAACTGGCGATCCTTTCGATCCAAATGACTGCTCCACAGGTAGCTAAAGAGAGATTTGGGCATGGATTAGaagtatttttgaaaaatgagtaTCTGGCAGAAGCCCCACACTGTCCACATGGGAAGGATTTCAAAGAACAATTGAAAAAAGACCCTCTCTATAAAGTGGACAGACGCCTTTTAAATGAAAGGTTCTTTGCTTGCTCAGCAGCCAGAGACAGAAAGGGCTGTGCATTTTTTCAGTGGGAAGGAGAGAAAATCTCGGAAACCAGGAAAAATGCTCATAGACAAATAGTGCAGGATTTCAGAGAACCATACAGACAGGCTTGTGATGGGTACAACAAATTGTTTGGTAATTTGGATGACAAGCGAAGACAAAATTGGTTGTTTTGTCATTCTTGTGACACCCTGTTGGtacttaaagaaaagaaaaaccacCTAGCACACGATTGTGAGGAATCTGGGGATTTATCCAAACCGACAATGATTTTgagaccaagagaaaatgagaagaCACAAGCACAATACTTCTTTTCAAGGAAGGCTACAGAATTTCTTGTGGATCTTGTGAAAGGTTTAGGTTTCAAGAATGTCATCTGTGTAGGTACTCCAAGGCTTCATGAGGAAATTCAATGCAGGCAATCACCAAGTGACCCCTTAGATAGTCTTCTCCTTGATATTGACTATAGATATGCTCAGTTTTTTCCACCCTCCAAATTTTGTTGGTACAACATGttcaatcatttcttttttggaaGCCATGTAAATGAGGAAACATTTCAGACGTTTCTCAGGAAGGAAGGACTACTCATGGTGATGGACCCTCCATTTGGTGGTTTAGCTGAAGTTCTTGCTGATTCTATTAAGACAATCTGGAATATTTGGAGGAAAGCATTTTCTTTTGAAAGTGACAAGGAGTTACCAACTATGTGGATTTTTCCATACTTTATGGAGCCACACATAAAAGCCGCCCTTCCTTCAATGACTATGCTTGATTACAAGGTTGACTATGATAATCATCCACACTTTAAAAGTAAGAAGATGAAAGGATCCAAACGGGGATCACCAGTGAGAATTTTTACCAACATCAATCCTACTGATGTAGTTTTGCCCTCATCTGAGGGTTACAGGTTTTGTGGTAAGTGCAAGAGATATGTTGCCCCTGAAAATATCCATTGTGTCAAATGCAACAGCTGCATGTCGAAGaacGGAAGGCAGTACATTCATTGCGAGATGTGTGGCACATGTGTTAAACCAGGTCTTCAGCACTGTATAACATGTGGTCGCTGTGAATTGGTTGGACACAGTTGTGAgagaCCACTCGAGGCAGGTACCTGTCACATATGCGGTGAACTGGGACACAAGAGAAGGAAGTGTCCAATGCGCTCTTCTGAGCCCCCAAGAAAGAGGAGGAAACAGGAAAACCCAGGTGAAGCCGCCAAAACTATTTTCCATAAGAAAAAGCCCTTCAAGGAACCTCCGAGAAAAACAATCCAGAAAAAGAAGATTAAGTAGAAATGCAATGTGCTGTGTGGGCTGAAGAAGTTCCATTAGCAAGATTTCTGTCGTCGTTTCagATTCCTGAATCAGGGACTTGTTGTCAGTGTGGTCATGTATTGACAGAGACACTTACCATTGCTGGAAAAAGGTTTTCAGATTACAGAGCTGAGTTATACACTCGCCTAGTGATACAAGAAAGTAAAAATCAAGCGCGGAAGCCACGAATGAGAAGAAATCTAGCAAAGCCTGGAAAGACCCTTAAGAGAGAAGAAAGCAAATCTTTGAATAACAGATTTCGAAgtggaagaaaaaggaaaagaattcGCCCATTGCTGTTGAAGCAAGAAGcgacaacaaaaagaaatacagaGAAGCTGACCGTACAAACATGTCAACCAACAGAGAAAAATGTTGACTCTGAACAGCCGAGAGATAAAAGCAAATCCCTCACATCAGCATTGGCTGAAATCAATAGAAGACTTCAGAACCAAAGCAAGCTATGGGTCTGCCTGGCCAGCGGCTTACCGATAAGTACAAACACGTGAATGTCCGCTGCCATTCATACTGAGATCCCAAGCATTCTGTCCGCGTCCTGAGGTGTCAGTCCACCCGGAGTAGCGTCATAGTTCGAATCTATCGGCACTTACCCTAAGTTATCCATTTTCACGAGTTGCGAGTGTGAAGGAACTTTCATGTTCTGTGTCGATAAGAACAATGCAAAGTAGTCCGGCTCTAAGAAGAATATTCCAGTACCAAAGCACGGTTCCCCGCGTGATACAGTTCGCCAAGCTTTACACTTGTGCGAGGTTGGGAATCTATATGTATTAACCGAAGCCATAAATTTCAAACTGAAGGCTAACGCaagtttatttgttctttttaatGTGGTCAACACGGAGGATGACATGCTTTGTCTAGTCCACTGGCTACTAGTCCTGGTTACTAGTCCTACGATTTTACGATTTTGCTAATATTTGGTCACCAAGACCTTTGACTTACCATGCGATGGATATTTTTAGGGTCCTCTTACTTATGCAGAACTTAACTTATGCAGAACATATTTTCTACGGTCTATGTATCATCCCTACGAATCAACTGGAGTAATATTGGATGGCCAATCATAGGGGTATTTCGAGGCCTTAGTTTGTTTGTATAAATTCTCACACAATAGTTATTTTTGGTGTATTAAGGTAAAAAATAGTAAATGGATAACTGGAAAAGGAGGGGAAATGTTAGTACCGTACAGTTACAATCATCAttataaagtattctcgtttgtct

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9H5U6	rRNA N(6)-adenosine-methyltransferase ZCCHC4 OS=Homo sapiens OX=9606 GN=ZCCHC4 PE=1 SV=3
D3ZV31	rRNA N(6)-adenosine-methyltransferase ZCCHC4 OS=Rattus norvegicus OX=10116 GN=Zcchc4 PE=3 SV=1
E1BGQ2	rRNA N(6)-adenosine-methyltransferase ZCCHC4 OS=Bos taurus OX=9913 GN=ZCCHC4 PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005309 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF10237 all species →	N6-adenineMlase	Probable N6-adenine methyltransferase	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR039846 all species →	Family	Zinc finger CCHC domain-containing protein 4	Interproscan
IPR041370 all species →	Family	Methyltransferase EEF1AKMT1/ZCCHC4	Interproscan
IPR037275 all species →	Homologous_superfamily	Zinc finger, CTCHY-type superfamily	Interproscan
IPR017921 all species →	Domain	Zinc finger, CTCHY-type	Interproscan
IPR001878 all species →	Domain	Zinc finger, CCHC-type	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13493 all species →	ZINC FINGER CCHC DOMAIN-CONTAINING	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005730 all species →	Cellular Component	nucleolus	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0008988 all species →	Molecular Function	rRNA (adenine-N6-)-methyltransferase activity	Interproscan
GO:0031167 all species →	Biological Process	rRNA methylation	Interproscan
GO:0008168 all species →	Molecular Function	methyltransferase activity	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	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
K25177	ZCCHC4; rRNA N6-adenosine-methyltransferase ZCCHC4	EC:2.1.1.-	Ribosome biogenesis	ko03009	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_068745596.1 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

26.0Max TPM

8.8Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
Polyps	36	29	8.77	26.04

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR12904783	Polyps	Polyps	not recorded	not recorded	SRP199550	26.04
SRR27940191	Polyps	Polyps	not recorded	not recorded	SRP199550	25.53
SRR12904781	Polyps	Polyps	not recorded	not recorded	SRP199550	18.59
SRR27940193	Polyps	Polyps	not recorded	not recorded	SRP199550	18.44
SRR12904782	Polyps	Polyps	not recorded	not recorded	SRP199550	17.63
SRR12959230	Polyps	Polyps	E3 day3	not recorded	SRP199550	15.73
SRR12786896	Polyps	Polyps	OA3 day0	not recorded	SRP199550	14.66
SRR12786898	Polyps	Polyps	OA3 day0	not recorded	SRP199550	11.67
SRR12786897	Polyps	Polyps	OA3 day0	not recorded	SRP199550	11.17
SRR12959182	Polyps	Polyps	E3 day0	not recorded	SRP199550	10.62
SRR12959203	Polyps	Polyps	E3 day15	not recorded	SRP199550	10.29
SRR12959202	Polyps	Polyps	E3 day15	not recorded	SRP199550	10.07
SRR12959183	Polyps	Polyps	E3 day0	not recorded	SRP199550	9.88
SRR12959184	Polyps	Polyps	E3 day0	not recorded	SRP199550	9.53
SRR12959201	Polyps	Polyps	E3 day15	not recorded	SRP199550	9.12
SRR12959190	Polyps	Polyps	E3 day21	not recorded	SRP199550	8.26
SRR12710857	Polyps	Polyps	OA3 day9	not recorded	SRP199550	8.26
SRR12959214	Polyps	Polyps	E3 day9	not recorded	SRP199550	7.80
SRR27940192	Polyps	Polyps	not recorded	not recorded	SRP199550	7.60
SRR12710855	Polyps	Polyps	OA3 day9	not recorded	SRP199550	7.54
SRR12959215	Polyps	Polyps	E3 day9	not recorded	SRP199550	7.22
SRR12959216	Polyps	Polyps	E3 day9	not recorded	SRP199550	7.06
SRR12959188	Polyps	Polyps	E3 day21	not recorded	SRP199550	6.80
SRR12959229	Polyps	Polyps	E3 day3	not recorded	SRP199550	6.48
SRR12959189	Polyps	Polyps	E3 day21	not recorded	SRP199550	6.39
SRR12710858	Polyps	Polyps	OA3 day9	not recorded	SRP199550	6.36
SRR12710847	Polyps	Polyps	OA3 day3	not recorded	SRP199550	6.35
SRR12710846	Polyps	Polyps	OA3 day3	not recorded	SRP199550	5.48
SRR12710848	Polyps	Polyps	OA3 day3	not recorded	SRP199550	5.28
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
SRR12959227	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.