Gene detail

Detailed information of XP_068725092.1 in Montipora capricornis

Genomic Location: chr10:3797990...3803210
NR annotation: XP_029187661.2, U1 small nuclear ribonucleoprotein A-like [Acropora millepora]
Species Montipora capricornis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_068868991.1

ATAATAGGACATAAGGAAAGTGCGCGTGGAACGTTTTCTATCCATCGACCATGCTGATTTAGAGAACGATCATTTGGAAATCTGCGTAAATCTCTTTTAATTCAGACCATCAAGACTGCAAGCTGTTGCATTCCATTACGTTTAGTCCCCGATTTACCTTTTTACTACAATCTTTTAGCTCTCTGTCGCAAACTAAGGAGTGCGAGATATTTTGTCGACTCAGTTGACAGCATAGTCAACGCGCATTTGTTGACTGTAAACAGTTCTCAGATACAACAGCGTACGACGATGGAAAATCCACCGAACCAAACTATCTACATCAATAACCTTAACGAGAAGGTCAAGAAAGAAGAATTGAAGAAGTCTTTGTACGCGATCTTTTCACAGTTTGGGCCTATTTTAGACATTGTAGCACTCAAGACCCTCAAAATGAGAGGTCAGGCGTTTGTAGTGTTTAGAGACTTAACAAGTGCCACGAATGCACTACGTTCTATGCAAGGCTTCCCATTTTATGATAAACCAATGAGAATACAATATGCTAAAAGCAAGTCTGATGCCGTATCGAAACTGGAAGGAACATACATTCAACGTGAAAAGAAGCCCAGAGAAAAGCGAAAAGCTCCAGAGCAAGCTAAACCAGCCAAGCGCCAGCCTACTACCCAGTCTGCACCTGCAGCAGTGGCTCAGCCTGCAATGGCCCCAGTTGCACAAAATGTCATTCCAGCTGCAGTTCAACCTGCTGTGGTTGTACCAGAGTTGCCCAACAGTATTCTGTTCCTTACAAACCTGCCCAATGAGACTACGGAGCTGATGCTGTCCATGTTATTCAACCAATTTCCTGGATTCAAAGAGGTTCGTTTGGTACCTGGCCGTTCAGATATTGCCTTTGTGGAGTTCGAGAATGAAGTTCAATCTGGAACTGCTAAAGAAGCTTTACAGGGTTTCAGAATAACACCATCTCATGCCATGAAAATCTCTTATGCTAAAAAATGATTTTAGGTTTCTTGCAAGATAGTTTTGAAACTGGAAGTTAAGTTTTTGTTACACCCAATCAAACACATTACAAGAAGTTTCTGAGAGGCcagtttttaaaatgttcaaaatttctTCTGATTCTTTGTTGGTGCTACAATCTTGCAACTCAAAAGGGGATCTTTTAAAAGTTTGTGTTAAAACAGGCATTGATCAATCCAGAGAAACAAGAAAGGTCTTCACTTTAGTAAGGTAATTGATGGTATTGATGGTTTGCGTCTGAGATCACAGTGGCCATGTTTGAACAGAACAATGCATTAAAATGTCTTATGGGAATTTGAATCTATTATTATAGAAAACTTGTGGGGCGATTTTCTATTGATTTTTACACCAACTGGCCATCTCATCACAcagatgcaaaccaagaatatggATGCATGTCCTTGTAGTTTGATCATTTGCAGTTGCATTGCACAGAGGCTTCTGTTGTAAGTAGTTGTAAAAACGGTAAGAAACAGCATTGCACTCTGCTGCAAAcaatttaaaacttgaaaaccaCTCCGCGATAAgtcttttgaaatgtttttgacatttttcaTACTCATAACACAAATGTACAGCACTTCTTAAAGGAAGGGCTGTGTTTACAACTAAGGACTTTGCTTTTTAGCTTGGATTTTCTTGTCATATTATTTTTAGGGCAGTAAACGATTCCTGACTCATGTAAAAAACTGTTGCAAGGTGTAGATGGCAGGAAGTTAACAGGGTGCCTacctcaataggccattttcgaagtATCAacattcagcttgatagtgaggcagagaggacaaaaagaatagaaacaagttgcaattaagtgaaagatattagcatatcatccactttccttttaattggtctttgtcctctaaatcTCTTTTTCAAGCTAACTTTTATTGgtaatatatcaaaagtggccTATTCTTACAATGTCCAGACTGCAACAGTTATAAACAAAATGCTTTTTCCACTGACTGATAAAAATGTGGCAGTGAAAAACCTATTTTCTTATCAGTTTTGTTCTAACTCTGAGAAGCATGTGCAGTAAAAAAAAGATTTAGACAAGAAAGTAATGCAATGACATTCAATATGGTGTGGTAGTCAAGTTTTTTTGTAtcattgaaaaaaggaaaaaaatataattgGACATTGAGTAATGTGCAACagtacttttttctttcttaaagcATTGCACTTAGCTTCTTGCAGCATTGCACAAGGCTGTTATTATTTGTATGAAAGAGATTTTTCTAAGCTGATACACTGTACACATTGGCTGAAGTGAAAGAACATGGTTGTTAGGCTCTGGCTTTGAAGTTTGCTGGACCCTATCGAAGATACTACACATTTCTTATCCTTGAGGGAATTAAAAGGACCTTGGCCGATAGAAGCGATTAAACTTTTTGTCATGAATCTCTGTAATAAAAAAGCTTTATTAA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P43332	U1 small nuclear ribonucleoprotein A OS=Drosophila melanogaster OX=7227 GN=snf PE=1 SV=1
P08579	U2 small nuclear ribonucleoprotein B'' OS=Homo sapiens OX=9606 GN=SNRPB2 PE=1 SV=1
Q9CQI7	U2 small nuclear ribonucleoprotein B'' OS=Mus musculus OX=10090 GN=Snrpb2 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0007796 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00076 all species →	RRM_1	RNA recognition motif	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR000504 all species →	Domain	RNA recognition motif domain	Interproscan
IPR035979 all species →	Homologous_superfamily	RNA-binding domain superfamily	Interproscan
IPR012677 all species →	Homologous_superfamily	Nucleotide-binding alpha-beta plait domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10501 all species →	U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A/U2 SMALL NUCLEAR RIBONUCLEOPROTEIN B	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0003676 all species →	Molecular Function	nucleic acid binding	Interproscan
GO:0000398 all species →	Biological Process	mRNA splicing, via spliceosome	Interproscan
GO:0005685 all species →	Cellular Component	U1 snRNP	Interproscan
GO:0030619 all species →	Molecular Function	U1 snRNA 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

No KEGG orthology assignment for XP_068725092.1.

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

Expression pattern (RNA-seq)

Transcript abundance of XP_068725092.1 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

92.2Max TPM

55.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
Polyps	36	30	55.40	92.15

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	92.15
SRR12959202	Polyps	Polyps	E3 day15	not recorded	SRP199550	90.44
SRR12959201	Polyps	Polyps	E3 day15	not recorded	SRP199550	88.84
SRR27940192	Polyps	Polyps	not recorded	not recorded	SRP199550	85.08
SRR12786898	Polyps	Polyps	OA3 day0	not recorded	SRP199550	84.21
SRR12786896	Polyps	Polyps	OA3 day0	not recorded	SRP199550	82.06
SRR12959189	Polyps	Polyps	E3 day21	not recorded	SRP199550	81.41
SRR12786897	Polyps	Polyps	OA3 day0	not recorded	SRP199550	81.35
SRR12959190	Polyps	Polyps	E3 day21	not recorded	SRP199550	80.33
SRR12959227	Polyps	Polyps	E3 day3	not recorded	SRP199550	76.43
SRR12959188	Polyps	Polyps	E3 day21	not recorded	SRP199550	75.12
SRR12904783	Polyps	Polyps	not recorded	not recorded	SRP199550	72.02
SRR27940191	Polyps	Polyps	not recorded	not recorded	SRP199550	71.97
SRR12959216	Polyps	Polyps	E3 day9	not recorded	SRP199550	71.51
SRR27940193	Polyps	Polyps	not recorded	not recorded	SRP199550	70.93
SRR12904782	Polyps	Polyps	not recorded	not recorded	SRP199550	70.36
SRR12959215	Polyps	Polyps	E3 day9	not recorded	SRP199550	69.46
SRR12959214	Polyps	Polyps	E3 day9	not recorded	SRP199550	67.89
SRR12959184	Polyps	Polyps	E3 day0	not recorded	SRP199550	67.29
SRR12904781	Polyps	Polyps	not recorded	not recorded	SRP199550	67.21
SRR12959183	Polyps	Polyps	E3 day0	not recorded	SRP199550	65.96
SRR12959182	Polyps	Polyps	E3 day0	not recorded	SRP199550	65.39
SRR12710855	Polyps	Polyps	OA3 day9	not recorded	SRP199550	48.21
SRR12710858	Polyps	Polyps	OA3 day9	not recorded	SRP199550	44.82
SRR12710848	Polyps	Polyps	OA3 day3	not recorded	SRP199550	42.86
SRR12710846	Polyps	Polyps	OA3 day3	not recorded	SRP199550	42.58
SRR12710847	Polyps	Polyps	OA3 day3	not recorded	SRP199550	42.19
SRR12710857	Polyps	Polyps	OA3 day9	not recorded	SRP199550	40.37
SRR12959229	Polyps	Polyps	E3 day3	not recorded	SRP199550	32.38
SRR12959230	Polyps	Polyps	E3 day3	not recorded	SRP199550	23.71
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.