Gene detail

Detailed information of XP_068736080.1 in Montipora capricornis

Genomic Location: chr14:3114933...3149640
NR annotation: XP_029211457.2, pre-mRNA-processing factor 6-like [Acropora millepora]
Species Montipora capricornis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

LOC138032322

ATGGCGCTATTGAATAGGAAAAAGAAGTCTTTTATTGGAGTGCCAGCACCTTTGGGTTATGTTCCTGGCCTGGGCAGAGGTGCAACTGGTTTCACAACTCGATCAGATATTGGTCCTGCAAGGGATGCTACGGACATAACTGACGAGCGACATGGAAAACCGGGATTTGCAAACGAAAAGAAAACACAGAATGAAGATGATGATGAAGAGGATTTGAATGAAACCAATTATGATGAGTTTGCTGGTTATGGAGGAAGCTTGTTTTCAAGTTGTCCCTATGAAAAGGATGACGAAGAGGCAGATGCCATTTATGATTCTATTGACAGACGAATGGATGACAGAAGAAAAGAAAGGAGGGAGAAACGATTTAAAGAAGAAATTGAACAATATCGCCAAGAAAGGCCAAAGATTCAGCAACAGTTTTCTGACCTTAAGCGTAAGCTTGGGGAAGTCTCTGAAGACGATTGGGTGAACATTCCTGAGGTTGGAGATTACAGAAACAAAAAACAAAGAAATCCTCGAACAGAAAAGTTCACGCCTGTACCAGACAGTGTCTTGCATAGTGCTCTTATGACTGGAGAAAAAATGACATCCCTTGATCCACGGCAACAGAAATTTGGTGGATTTCAAACACCTTTTCCAGGAGGTATGACACCCAGTGGAATTGCTACTGGATTTTCCACTCCCTCAGCGGACCTTGATTTGATAAAAATTGGTGAAGCTCGCAAATCTCTTGTTGGTGTCAAGCTTGATCAGGCATCAGATTCTGTGAGTGGTCAGACAGTCGTGGATCCTAAAGGATATTTGACTGACCTACAAAGCTTAACACCCTCTGCAGGAGGCGATATCGGAGATATCAAGAAAGCTCGCCTCCTGCTCAAGTCAGTTATCACAACAAACCCCCAACATGGTCCTGGTTGGATAGCAGCTGCTCGGTTGGAAGAGGTCACTGGTCGTATGCAAGCAGCTCGAAATACAATCGTGAAAGGAACTGAAGTCTGTTCAAAGAACGAAGATGTGTGGCTTGAGGCCATTCGATTGCAGCCACCAGAATCAGCAAAATCAGTTTGCGCCCAAGCAGTTGGTCAGCTCCCACTATCAGTGCGACTGTGGATAAAAGCTGCAGCACTGGAAGAAGAGACCAAAGCCAAGAAACGAGTTTTCAGGAAAGCACTTGAGCAAATACCCAACTCAGTGAGGATCTGGAAAGCGGCAGTAGAGCTGGAAGGACCGGAGGATGCGCAGATCATGTTGAGCAGAGCAGTGGAATGTTGTCCCACGAGTGTAGAGCTCTGGCTTGCTCTTGCTCGACTGGAAACTTACGAAAATGCGAGAAAGGTCTTAAACAAAGCACGCGAAAATATCCCAACCGATCGCCAGATCTGGATAACAGCAGCTAAGCTCGAAGAAGCGAATGACAACCTTCCTATGGTGGAAAAAATCATTGACAGAGCTGTGACGTCTTTAAGGGCAAACGGCGTCGAAATCAACAGAGATCAGTGGATTAAGGATGCAGAGGAGAGCGAGAAAGCTGACAGTGTGGTCACATGTAGAGCTATAATCAACACTGTAATCGGCATTGGGGTGGAAGAAGAAGACAGAAAACACACGTGGATGGATGATGCTGACAGTTGTGTTGCTAATGTCGCTTTCGAGTGCGCAAGAGCTATCTATGCACATGCTCTGTCAGTTTTTCCCAGCAAGAAGAGCGTCTGGTTGCGTGCTGCACACTTCGAAAAGAATCATGGGACAAGAGAGTCTTTGGAGTCCTTGTTACAGAATGCAGTTAAGCACTGCCCGAAAGCAGAAGTTTTGTGGCTGATGGGTGCAAAATCCAAGTGGCTGGCTGGTGAAATTTTTGAAGCTCGTTCCATCTTAGCCTTGGCGTTTCAAGCGAATCCCAACAGTGAGGAAATTTGGCTGGCTGCCGTGAAGCTGGAGAGTGAAAATAATGAGGATCAGAGAGCGAGAAAACTTTTACAGAGAGCAAGATTAAACGCCTGCACGCCAAGGGTGATGATGAAGTCGATCAAGTTAGAATGGGTTTTACGAAACCTTTCGGAGGCAGAGAAGTTATTAGACGAAGCTGTTCAGAGATACCCAGATTTCGCCAAGTTGTGGATGATGAAGGGCCAAATACACCAAGAACAGAATCACATTGACAGCGCTAGAGAAGCATATAAACTAGGGACCAAGAAATGTCCCCGGTCCATTCCAATCTGGCTGTTGCTTGCAAGACTTGAAGAAAAATCAGGTCAGGCCACAAAAGCAAGATCTGTATTGGAGCAAGCCCGTCAGAAAAACTCGAAGTGCCCTGAACTATGGCTTGAGGCGGTTCGGATAGAAACTAGAGGAAGCCGAAAAGAATTCGCGCGGACTTTAATGGCGAAAGCTATGCAAGAATGTCCTACTTCCGGGATCTTATGGGCAGAAGCTATTTTCATGGAAAGTCGACCTCAACGAAAGACGAAAAGCGTGGATGCACTGAAGAGATGCGAACATGATCCTCATGTGCTGTTAGCAGTGGCTAGGTTGTTTTGGAGCGAAAGGAAAATAAACAAGGCAAGGGAGTGGTTTAACAGAGCTGTTAAACTCGACCCAGACCTCGGCGATTCATGGGCGTGTTTCTACAGATTTGAGTTGCAGCATGGAACCGAGGCCCAGCAAGAAAGTATTATGCAACGGTGCGTGATGGCCGAACCGCATCACGGAGAAAGTTGGTGTGCAGTATCCAAAGCCATTCCGAATTGGAGACTTCGAACAAAGGATATTCTTCCCAAAGTAGCCAAGTCTTTGAAACCTATTGAGAAGGAATAA

Transcript

rna-XM_068879979.1

gccgtccgccattttggagacgATTGCTGATTCTTGGATCAGACAATCGAGAAAGTTTGCCTTGTAAACGAAGAATGGCGCTATTGAATAGGAAAAAGAAGTCTTTTATTGGAGTGCCAGCACCTTTGGGTTATGTTCCTGGCCTGGGCAGAGGTGCAACTGGTTTCACAACTCGATCAGATATTGGTCCTGCAAGGGATGCTACGGACATAACTGACGAGCGACATGGAAAACCGGGATTTGCAAACGAAAAGAAAACACagaatgaagatgatgatgaagaggatTTGAATGAAACCAATTATGATGAGTTTGCTGGTTATGGAGGAAGCTTGTTTTCAAGTTGTCCCTATGAAAAGGATGACGAAGAGGCAGATGCCATTTATGATTCTATTGACAGACGAATGGAtgacagaagaaaagaaaggagGGAGAAAcgatttaaagaagaaattgaacAATATCGCCAAGAAAGGCCAAAGATTCAGCAACAGTTTTCTGACCTTAagCGTAAGCTTGGGGAAGTCTCTGAAGACGATTGGGTGAACATTCCTGAGGTTGGAGATtacagaaacaaaaaacaaagaaatcctCGAACAGAAAAGTTCACGCCTGTACCAGACAGTGTCTTGCATAGTGCTCTTATGACTGGAGAAAAAATGACATCCCTTGATCCACGGCAACAGaaatttggtggatttcaaACACCTTTTCCAGGAGGTATGACACCCAGTGGAATTGCTACTGGATTTTCCACTCCCTCAGCGGACCTTGATTTGATAAAAATTGGTGAAGCTCGCAAATCTCTTGTTGGTGTCAAGCTTGATCAGGCATCAGATTCTGTGAGTGGTCAGACAGTCGTGGATCCTAAAGGATATTTGACTGACCTACAAAGCTTAACACCCTCTGCAGGAGGCGATATCGGAGATATCAAGAAAGCTCGCCTCCTGCTCAAGTCAGTTATCACAACAAACCCCCAACATGGTCCTGGTTGGATAGCAGCTGCTCGGTTGGAAGAGGTCACTGGTCGTATGCAAGCAGCTCGAAATACAATCGTGAAAGGAACTGAAGTCTGTTCAAAGAACGAAGATGTGTGGCTTGAGGCCATTCGATTGCAgCCACCAGAATCAGCAAAATCAGTTTGCGCCCAAGCAGTTGGTCAGCTCCCACTATCAGTGCGACTGTGGATAAAAGCTGCAGCACTGGAAGAAGAGACCAAAGCCAAGAAACGAGTTTTCAGGAAAGCACTTGAGCAAATACCCAACTCAGTGAGGATCTGGAAAGCGGCAGTAGAGCTGGAAGGACCGGAGGATGCGCAGATCATGTTGAGCAGAGCAGTGGAATGTTGTCCCACGAGTGTAGAGCTCTGGCTTGCTCTTGCTCGACTGGAAACTTACGAAAATGCGAGAAAGGTCTTAAACAAAGCACGCGAAAATATCCCAACCGATCGCCAGATCTGGATAACAGCAGCTAAGCTCGAAGAAGCGAATGACAACCTTCCTATGGTGGAAAAAATCATTGACAGAGCTGTGACGTCTTTAAGGGCAAACGGCGTCGAAATCAACAGAGATCAGTGGATTAAGGATGCAGAGGAGAGCGAGAAAGCTGACAGTGTGGTCACATGTAGAGCTATAATCAACACTGTAATCGGCATTGGGGTGGAAGAAGAAGACAGAAAACACACGTGGATGGATGATGCTGACAGTTGTGTTGCTAATGTCGCTTTCGAGTGCGCAAGAGCTATCTATGCACATGCTCTGTCAGTTTTTCCCAGCAAGAAGAGCGTCTGGTTGCGTGCTGCACACTTCGAAAAGAATCATGGGACAAGAGAGTCTTTGGAGTCCTTGTTACAGAATGCAGTTAAGCACTGCCCGAAAGCAGAAGTTTTGTGGCTGATGGGTGCAAAATCCAAGTGGCTGGCTGGTGAAATTTTTGAAGCTCGTTCCATCTTAGCCTTGGCGTTTCAAGCGAATCCCAACAGTGAGGAAATTTGGCTGGCTGCCGTGAAGCTGGAGAGTGAAAATAATGAGGATCAGAGAGCGAGAAAACTTTTACAGAGAGCAAGATTAAACGCCTGCACGCCAAGGGTGATGATGAAGTCGATCAAGTTAGAATGGGTTTTACGAAACCTTTCGGAGGCAGAGAAGTTATTAGACGAAGCTGTTCAGAGATACCCAGATTTCGCCAAGTTGTGGATGATGAAGGGCCAAATACACCAAGAACAGAATCACATTGACAGCGCTAGAGAAGCATATAAACTAGGGACCAAGAAATGTCCCCGGTCCATTCCAATCTGGCTGTTGCTTGCAAGACTTGAAGAAAAATCAGGTCAGGCCACAAAAGCAAGATCTGTATTGGAGCAAGCCCGTCAGAAAAACTCGAAGTGCCCTGAACTATGgcTTGAGGCGGTTCGGATAGAAACTAGAGGAAGCCGAAAAGAATTCGCGCGGACTTTAATGGCGAAAGCTATGCAAGAATGTCCTACTTCCGGGATCTTATGGGCAGAAGCTATTTTCATGGAAAGTCGACCTCAACGAAAGACGAAAAGCGTGGATGCACTGAAGAGATGCGAACATGATCCTCATGTGCTGTTAGCAGTGGCTAGGTTGTTTTGGAGCGAAAGGAAAATAAACAAGGCAAGGGAGTGGTTTAACAGAGCTGTTAAACTCGACCCAGACCTCGGCGATTCATGGGCGTGTTTCTACAGATTTGAGTTGCAGCATGGAACCGAGGCCCAGCAAGAAAGTATTATGCAACGGTGCGTGATGGCCGAACCGCATCACGGAGAAAGTTGGTGTGCAGTATCCAAAGCCATTCCGAATTGGAGACTTCGAACAAAGGATATTCTTCCCAAAGTAGCCAAGTCTTTGAAACCTATTGAGAAGGAATAAACACGAAACCACGAAACCGCCAGTGTACGAAAAGGAAAAATCAACTCGAATGCTTCGTGTGGGGAGTGCCCCCCTCGAACACAAAGTTCTTGTGTCAAGTAGTATGTCACCTGAATCGCCCGAATAAACCGTGTGTATCATTTTGGAGTGATCAAATCCCGAAACTTTGCCTTGGACCACTCAAGCCTAGATCCGCCTCGTACGAGATTTTGATTCCACCGGAAACCGGTGCCTTTCTTTTAGCACTTTCATTTGTCGTTCTCTCCTTGCTCGCGAGGAAACAAAATGAAGACATCGCTCGAGATTGAGAAGTGATTCGGAGATAGCAACTTTCGTAGTTTCTGGCAAGGACCCTGGAAATAACGTTCTAGGAAAGAACTGCGCTTTCTATTTGTGTAACTtgtgtttttgtcttttatttcacTACTGTACTCTGTAAATGAaactttcttgaaaaaaaaaagtctgtaTAATCca

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q91YR7	Pre-mRNA-processing factor 6 OS=Mus musculus OX=10090 GN=Prpf6 PE=1 SV=1
A1A5S1	Pre-mRNA-processing factor 6 OS=Rattus norvegicus OX=10116 GN=Prpf6 PE=1 SV=1
Q2KJJ0	Pre-mRNA-processing factor 6 OS=Bos taurus OX=9913 GN=PRPF6 PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004674 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF06424 all species →	PRP1_N	PRP1 splicing factor, N-terminal	Domain	Interproscan
PF14559 all species →	TPR_19	Tetratricopeptide repeat	Repeat	Interproscan
PF13181 all species →	TPR_8	Tetratricopeptide repeat	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR011990 all species →	Homologous_superfamily	Tetratricopeptide-like helical domain superfamily	Interproscan
IPR003107 all species →	Repeat	HAT (Half-A-TPR) repeat	Interproscan
IPR010491 all species →	Domain	PRP1 splicing factor, N-terminal	Interproscan
IPR019734 all species →	Repeat	Tetratricopeptide repeat	Interproscan
IPR045075 all species →	Family	Pre-mRNA-splicing factor Syf1-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11246 all species →	PRE-MRNA SPLICING FACTOR	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0006396 all species →	Biological Process	RNA processing	Interproscan
GO:0000398 all species →	Biological Process	mRNA splicing, via spliceosome	Interproscan
GO:0000244 all species →	Biological Process	spliceosomal tri-snRNP complex assembly	Interproscan
GO:0046540 all species →	Cellular Component	U4/U6 x U5 tri-snRNP complex	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
K12855	PRPF6, PRP6; pre-mRNA-processing factor 6	-	Spliceosome	ko03041	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_068736080.1 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

87.8Max TPM

25.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
Polyps	36	29	25.40	87.79

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR12959227	Polyps	Polyps	E3 day3	not recorded	SRP199550	87.79
SRR12904783	Polyps	Polyps	not recorded	not recorded	SRP199550	52.55
SRR27940191	Polyps	Polyps	not recorded	not recorded	SRP199550	52.50
SRR12959203	Polyps	Polyps	E3 day15	not recorded	SRP199550	39.90
SRR12904782	Polyps	Polyps	not recorded	not recorded	SRP199550	39.76
SRR12959184	Polyps	Polyps	E3 day0	not recorded	SRP199550	38.20
SRR12959201	Polyps	Polyps	E3 day15	not recorded	SRP199550	37.65
SRR12959182	Polyps	Polyps	E3 day0	not recorded	SRP199550	37.36
SRR12959183	Polyps	Polyps	E3 day0	not recorded	SRP199550	37.20
SRR12959202	Polyps	Polyps	E3 day15	not recorded	SRP199550	36.91
SRR12786898	Polyps	Polyps	OA3 day0	not recorded	SRP199550	36.56
SRR27940193	Polyps	Polyps	not recorded	not recorded	SRP199550	35.52
SRR12786896	Polyps	Polyps	OA3 day0	not recorded	SRP199550	34.50
SRR12786897	Polyps	Polyps	OA3 day0	not recorded	SRP199550	33.29
SRR12959216	Polyps	Polyps	E3 day9	not recorded	SRP199550	32.08
SRR12959214	Polyps	Polyps	E3 day9	not recorded	SRP199550	31.99
SRR12959230	Polyps	Polyps	E3 day3	not recorded	SRP199550	31.60
SRR12904781	Polyps	Polyps	not recorded	not recorded	SRP199550	30.29
SRR12959215	Polyps	Polyps	E3 day9	not recorded	SRP199550	29.56
SRR12959229	Polyps	Polyps	E3 day3	not recorded	SRP199550	27.08
SRR12959189	Polyps	Polyps	E3 day21	not recorded	SRP199550	18.27
SRR12959190	Polyps	Polyps	E3 day21	not recorded	SRP199550	17.34
SRR12959188	Polyps	Polyps	E3 day21	not recorded	SRP199550	14.89
SRR12710857	Polyps	Polyps	OA3 day9	not recorded	SRP199550	14.74
SRR12710847	Polyps	Polyps	OA3 day3	not recorded	SRP199550	14.62
SRR12710858	Polyps	Polyps	OA3 day9	not recorded	SRP199550	14.07
SRR12710848	Polyps	Polyps	OA3 day3	not recorded	SRP199550	13.39
SRR12710855	Polyps	Polyps	OA3 day9	not recorded	SRP199550	12.75
SRR12710846	Polyps	Polyps	OA3 day3	not recorded	SRP199550	12.20
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
SRR27940192	Polyps	Polyps	not recorded	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.