Gene detail

Detailed information of XP_068731501.1 in Montipora capricornis

Genomic Location: chr12:41350757...41353573
NR annotation: XP_015758366.1, PREDICTED: small nuclear ribonucleoprotein Sm D2 [Acropora digitifera]
Species Montipora capricornis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

rna-XM_068875400.1

ACCAACGGGAAGAACACGCGCCAGCGATTTGAATGGCTCAACGcgttcaaacgttttcttcgTTGTAGTAAGATATATCTTGGTTAACTATCTCCAACAATCCATCGAAtatcgagaaaaaaaaatggcatccTTaatgGGTAAACCGAAGAGCGAAATGACTCCAGAGGAGCTGACACAAAGGGAACAAGAAGAGTTCAACACGGGCCCTTTATCCGTTTTAACGCAATCTGTGAAGAACAATACTCAAGTCCTAATCAACTGTAGGAACAACAAGAAGTTACTCGCTAGAGTCAAAGCTTTTGACCGGCACTGCAACATGGTTCTTGAAAACGTTAAAGAAATGTGGACTGAAACGCCCAAGTCTGGCAAAGGTAAAAAGGCCAAGCCAGTAAATAAGGACAGATATATCGCCAAGATGTTTTTGAGAGGGGACTCTGTTATCCTGGTGCTCAGAAATCCCATGGCTGCCTCTGGGAAATAAACTATTGCGAACAAGCTTGGAATCCTGCTTAGTGATAAATTTTACTCATATCTTTGTTAACTCTCTGGACTTGCATCACACCACCTACTACAGTTTATACATATAAAACAGATGGGAGCGACATATGCATCTATCAATGTTAACCCcaaggaggggagggggggaccCCGGGCATATGTGGGGCGTTTGACTTTTCAGaagaatttttggtcaaaatccccaccaTGGGGCCCCAAAATGTGGTCAAATCAGGGAAGTAATGTCTACAGGTGCTCGTAATCTTTAAGAGAGACATTCTCCTTGTCAATGGATAGaaaatatttaataaaattCCAACGCTTGATTCTCTGACGAAAAGCGACTCGATATTATCAACAAGTGGTCAAATGCCCCACATAtgcctcccccccctcccctatcgggcttaacattgatagatgcATTAGAATACCTGTCCACAGTTTCTACTTGTAATGGGATTGTTAGGGACAAAGAATGTATCAATACACGTTTTTTGCCTACATATGTTGTGGTTGGTATTCCAAAGTTTATCCAAGAGCTGCATGTTAGTCTCATATTTTAGGACCAGGTTAAACATTACGTTATCGTGGTGTTGAACTATTAGGTTTGTCTCTGGAGGACTCTCAGTTAGGCAACTGATTCAAAAGTTGGGCCAAATTTAGAACTGAAGCTGTTTTCTGTCCTCTCTGCATAATGAATGGCCATGATTTCTTTTCATATTATCTAAACCTTGGGTTCTGAGATAAGTTTAAGGTTAAAATCCGTGTTGAATCAGATTTATTGGCCTGACTTTTCACACTTTATTCCTTGGTATGACAGGTAATTAAGATTTTGAACCTTTTTGGGCTGAGGTCAAAGTTGATTCccctaaaacaaagaaatggcggccatgtttaTGCCCCGACCCAATCCTCTGGTAATTGAACtcttttattatgcaaatgttttcttttgttttttttgcaaaacatggctgttgatcacgtgaaaaaaaaaccaacaatacTTTTCCCACatgggttttctttacaagtttgttgCTTTGGGATTTACCTCaagctaaaatttacaagtttgatttttgaatttgaggcttggtggtgaaatcagcTAGTCAGACATCATCATGCATAAGGGCTATCGTTTAGCCATAGATGGCCCTGTGATTGCATgcaataggcaactttcacgatagcatcatttgactacaactaccacaattcagtttgtttttcttttcttatttaattaaattttgtattcccagtggggtaaaaataacaatagctccaATTACCATGAGACAAGGAAAACCtaaaggattctggtacttgtagtcaaatggcatCATCATGCAAACGTGCTACTAAGTTAGGGACGCCTTGTCAAACTTGAAAGATTGTTTAtagtacatacatgtagtgtGTGGGAACTGCAGTAGACTTTGCCTTTATTGCTTGTGGAAAAAACATATTCAGTAAGCCACACAAGAAGTGAGGTGGCCAGGGAGAATAATTCATATCACCATTGTCACAGATACGTGTACCTGAATGCGCACGTTATGGATGAAACTAtggagaaaataatttcatgtaAAGTGGAATGTGTTGATGCCAAAGATGAACCAAGTCCAGGTAACTGCCTGATACAAGGTGAAATGGCAACTTCTCGGCTTAGGCCAAACAATGTAATGGCAGCTTCTCGCTTTTTGGTCCACACCATCCTTTTGTTCTGACGTCATTGCCCAATTCAAATTAACTGGCATCCAGTCCTTGTGCGACACGAGGCTTGGGCAGATGATGAGCAAAACTTAAGAAATGAAGAgaagactaaaaaaaaaaagacctttaAACCAATACACAAGGGAAATGTCACACAAGAGCATGCAAATTTCACCACATCCATTCAGCCACATGACCAACAAAAACTACtttgacataatttttttttgtcctatCTGTCAAGTGAATACCATACATTTGTTCCTTTAACCAGTCACAAACTGTCCCCTTGATTAATTAGGTCCATTATTTACTTGACGTCCGTAGTCAACTGGAGGTTTCCCCTCTTTGCTGCCATAAAGAGTTTGTCACAGGTTTACCCATGGAAGGTGTCTTgttaaataaaaggaaaataatattattcaa

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q3SZF8	Small nuclear ribonucleoprotein Sm D2 OS=Bos taurus OX=9913 GN=SNRPD2 PE=3 SV=1
P62316	Small nuclear ribonucleoprotein Sm D2 OS=Homo sapiens OX=9606 GN=SNRPD2 PE=1 SV=1
P62317	Small nuclear ribonucleoprotein Sm D2 OS=Mus musculus OX=10090 GN=Snrpd2 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0008540 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01423 all species →	LSM	LSM domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR047575 all species →	Domain	Sm domain	Interproscan
IPR010920 all species →	Homologous_superfamily	LSM domain superfamily	Interproscan
IPR001163 all species →	Domain	Sm domain, eukaryotic/archaea-type	Interproscan
IPR027248 all species →	Family	Small nuclear ribonucleoprotein Sm D2	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12777 all species →	SMALL NUCLEAR RIBONUCLEOPROTEIN SM D2	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003723 all species →	Molecular Function	RNA binding	Interproscan
GO:0008380 all species →	Biological Process	RNA splicing	Interproscan
GO:0030532 all species →	Cellular Component	small nuclear ribonucleoprotein complex	Interproscan
GO:0000387 all species →	Biological Process	spliceosomal snRNP assembly	Interproscan
GO:0005682 all species →	Cellular Component	U5 snRNP	Interproscan
GO:0005685 all species →	Cellular Component	U1 snRNP	Interproscan
GO:0005686 all species →	Cellular Component	U2 snRNP	Interproscan
GO:0034715 all species →	Cellular Component	pICln-Sm protein complex	Interproscan
GO:0046540 all species →	Cellular Component	U4/U6 x U5 tri-snRNP complex	Interproscan
GO:0071011 all species →	Cellular Component	precatalytic spliceosome	Interproscan
GO:0071013 all species →	Cellular Component	catalytic step 2 spliceosome	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
K11096	SNRPD2, SMD2; small nuclear ribonucleoprotein D2	-	DNA replication proteins	ko03032	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_068731501.1 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

83.4Max TPM

40.7Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
Polyps	36	30	40.68	83.36

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	83.36
SRR12959230	Polyps	Polyps	E3 day3	not recorded	SRP199550	64.33
SRR12959190	Polyps	Polyps	E3 day21	not recorded	SRP199550	62.36
SRR12959227	Polyps	Polyps	E3 day3	not recorded	SRP199550	62.04
SRR12959201	Polyps	Polyps	E3 day15	not recorded	SRP199550	59.75
SRR12959202	Polyps	Polyps	E3 day15	not recorded	SRP199550	59.43
SRR12959188	Polyps	Polyps	E3 day21	not recorded	SRP199550	56.17
SRR12904782	Polyps	Polyps	not recorded	not recorded	SRP199550	55.72
SRR12959189	Polyps	Polyps	E3 day21	not recorded	SRP199550	54.92
SRR12959203	Polyps	Polyps	E3 day15	not recorded	SRP199550	54.05
SRR12710855	Polyps	Polyps	OA3 day9	not recorded	SRP199550	51.05
SRR12904783	Polyps	Polyps	not recorded	not recorded	SRP199550	50.34
SRR27940191	Polyps	Polyps	not recorded	not recorded	SRP199550	50.09
SRR12786898	Polyps	Polyps	OA3 day0	not recorded	SRP199550	48.52
SRR12786896	Polyps	Polyps	OA3 day0	not recorded	SRP199550	48.46
SRR12710857	Polyps	Polyps	OA3 day9	not recorded	SRP199550	48.15
SRR12786897	Polyps	Polyps	OA3 day0	not recorded	SRP199550	47.12
SRR12959215	Polyps	Polyps	E3 day9	not recorded	SRP199550	45.57
SRR12959184	Polyps	Polyps	E3 day0	not recorded	SRP199550	45.17
SRR27940193	Polyps	Polyps	not recorded	not recorded	SRP199550	44.66
SRR12959214	Polyps	Polyps	E3 day9	not recorded	SRP199550	44.19
SRR12710858	Polyps	Polyps	OA3 day9	not recorded	SRP199550	44.13
SRR12959182	Polyps	Polyps	E3 day0	not recorded	SRP199550	41.37
SRR12959216	Polyps	Polyps	E3 day9	not recorded	SRP199550	40.96
SRR12959183	Polyps	Polyps	E3 day0	not recorded	SRP199550	40.29
SRR12904781	Polyps	Polyps	not recorded	not recorded	SRP199550	37.90
SRR12710848	Polyps	Polyps	OA3 day3	not recorded	SRP199550	35.53
SRR12710847	Polyps	Polyps	OA3 day3	not recorded	SRP199550	35.46
SRR12710846	Polyps	Polyps	OA3 day3	not recorded	SRP199550	34.76
SRR27940192	Polyps	Polyps	not recorded	not recorded	SRP199550	18.81
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.