Gene detail

Detailed information of g13810.t1 in Montipora capitata

Genomic Location: Sc0000487:29646...61279
NR annotation: XP_029211457.2, pre-mRNA-processing factor 6-like [Acropora millepora]
Species Montipora capitata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

g13810.t1

atggcgctattgaataggaaaaagaagtcttttattggagtgccagcacctttgggttatgttcctggcctgggcagaggtgcaactggtttcacaactcgatcagatattggtcctgcaagggatgctacggacataactgatgagcgacatggaaaaccgggatttgcaaatgaaaagaaaacacagaatgaagatgatgatgaagaggatttgaatgaaaccaattatgatgagtttgctggttatggaggaagcttgttttcaagttgtccctacgaaaaggatgacgaagaggcagatgccatttatgattctattgacagacgaatggatgacagaagaaaagaaaggagggagaaacgattcaaagaagaaattgaacaatatcgccaagaaaggccaaagattcagcaacagttctctgaccttaagcgtaagcttggggaagtctctgaagacgattgggtgaacattcctgaggttggagattacagaaacaaaaaacaaagaaatcctcgaacagaaaagttcacgcctgtaccagacagtgtcttgcatagtgctcttatgactggagaaaaaatgacatcccttgatccacggcaacagaaatttggtggatttcaaacaccttttccaggaggtatgacacccagtggaattgctactggattttccactccctcagcggaccttgatttgataaaaattggcgaagctcgaaaatctcttgttggtgtcaagcttgatcaggcatcagattctgtgagtggtcagacagtcgtggatcctaaaggatatttgactgacctacaaagcttaacaccctctgcaggaggtgatatcggagatatcaagaaagctcgcctcctgctcaagtcagttatcacaacaaacccccaacatggtcctggttggatagcagctgctcggttggaagaggtcactggtcgtatgcaagcagctcgaaatacaatcgtgaaaggaactgaagtctgttcaaagaacgaagatgtgtggcttgaggccattcgattgcagccaccagaatcagcaaaatcagtttgcgcccaagcagttggtcagctcccactatcagtgcgactgtggataaaagctgcagcactggaagaagagaccaaagccaagaaacgagttttcaggaaagcacttgagcaaatacccaactcagtgaggatctggaaagcggcagtagagctggaaggaccggaggatgcgcagatcatgttgagcagagcagtggaatgttgtcccacgagtgtagagctctggcttgctcttgctcgactggaaacttacgaaaatgcgagaaaggtcttaaacaaagcgcgcgaaaatatcccaaccgatcgccagatctggataacagcagctaagctcgaagaagcgaatgacaaccttcctatggtggaaaaaatcattgacagagctgtgacgtctttaagggcaaacggcgtcgaaatcaacagagatcagtggattaaggatgcagaggagagcgagaaagctgacagtgtggtgacatgtagagctataatcaacactgtaatcggcattggggtggaagaagaagacagaaaacacacgtggatggatgatgctgacagttgtgttgctaatgtcgctttcgagtgcgcaagagctatctatgcacatgctctgtcagtttttcccagcaagaagagcgtctggttgcgtgctgcacacttcgaaaagaatcatgggacaagagagtctttggagtccttgttacagaatgcagttaagcactgcccgaaagctgaagttttgtggctgatgggtgcaaaatccaagtggctggctggtgaaatttttgaagctcgttccatcttagccttggcgtttcaagcgaatcccaacagtgaggaaatttggctggctgccgtgaagctggagagtgaaaataacgaggatcagagagcgagaaaacttttacagagagcaagattaaacgcctgcacgccaagggtgatgatgaagtcgatcaagttagaatgggttttacgaaacctttcggaggcagagaagttattagacgaagctgttcaaagatacccagatttcgccaagttgtggatgatgaagggccaaatacaccaagaacagaatcacattgacagcgctagagaagcatataaactagggaccaagaaatgtccccggtccattccaatctggctgttacttgcaagacttgaagaaaaatcaggtcaggccacaaaagcaagatccgtattggagcaagcccgtcagaaaaactcgaagtgccctgaactatggcttgaggcggttcggatagaaactagaggaagccgaaaagaattcgcgcggactttaatggcgaaagctatgcaagaatgtcctacttccgggatcttatgggcagaagctattttcatggaaagtcgacctcaacgaaagacgaaaagcgtggatgcactaaagagatgtgaacatgatcctcatgtgctgttagcagtggctaggttgttttggagcgaaaggaaaataaacaaggcaagggagtggtttaacaggtatggcgtttaa

Transcript

g13810.t1

ATGGCGCTATTGAATAGGAAAAAGAAGTCTTTTATTGGAGTGCCAGCACCTTTGGGTTATGTTCCTGGCCTGGGCAGAGGTGCAACTGGTTTCACAACTCGATCAGATATTGGTCCTGCAAGGGATGCTACGGACATAACTGATGAGCGACATGGAAAACCGGGATTtgcaaatgaaaagaaaacacagaatgaagatgatgatgaagaggatTTGAATGAAACCAATTATGATGAGTTTGCTGGTTATGGAGGAAGCTTGTTTTCAAGTTGTCCCTACGAAAAGGATGACGAAGAGGCAGATGCCATTTATGATTCTATTGACAGACGAATGGAtgacagaagaaaagaaaggagGGAGAAACGATTCAAAGAAGAAATTGAACAATATCGCCAAGAAAGGCCAAAGATTCAGCAACAGTTCTCTGACCTTAAgCGTAAGCTTGGGGAAGTCTCTGAAGACGATTGGGTGAACATTCCTGAGGTTGGAGATtacagaaacaaaaaacaaagaaatcctCGAACAGAAAAGTTCACGCCTGTACCAGACAGTGTCTTGCATAGTGCTCTTATGACTGGAGAAAAAATGACATCCCTTGATCCACGGCAACAGaaatttggtggatttcaaACACCTTTTCCAGGAGGTATGACACCCAGTGGAATTGCTACTGGATTTTCCACTCCCTCAGCGGACCTTGATTTGATAAAAATTGGCGAAGCTCGAAAATCTCTTGTTGGTGTCAAGCTTGATCAGGCATCAGATTCTGTGAGTGGTCAGACAGTCGTGGATCCTAAAGGATATTTGACTGACCTACAAAGCTTAACACCCTCTGCAGGAGGTGATATCGGAGATATCAAGAAAGCTCGCCTCCTGCTCAAGTCAGTTATCACAACAAACCCCCAACATGGTCCTGGTTGGATAGCAGCTGCTCGGTTGGAAGAGGTCACTGGTCGTATGCAAGCAGCTCGAAATACAATCGTGAAAGGAACTGAAGTCTGTTCAAAGAACGAAGATGTGTGGCTTGAGGCCATTCGATTGCAGCCACCAGAATCAGCAAAATCAGTTTGCGCCCAAGCAGTTGGTCAGCTCCCACTATCAGTGCGACTGTGGATAAAAGCTGCAGCACTGGAAGAAGAGACCAAAGCCAAGAAACGAGTTTTCAGGAAAGCACTTGAGCAAATACCCAACTCAGTGAGGATCTGGAAAGCGGCAGTAGAGCTGGAAGGACCGGAGGATGCGCAGATCATGTTGAGCAGAGCAGTGGAATGTTGTCCCACGAGTGTAGAGCTCTGGCTTGCTCTTGCTCGACTGGAAACTTACGAAAATGCGAGAAAGGTCTTAAACAAAGCGCGCGAAAATATCCCAACCGATCGCCAGATCTGGATAACAGCAGCTAAGCTCGAAGAAGCGAATGACAACCTTCCTATGGTGGAAAAAATCATTGACAGAGCTGTGACGTCTTTAAGGGCAAACGGCGTCGAAATCAACAGAGATCAGTGGATTAAGGATGCAGAGGAGAGCGAGAAAGCTGACAGTGTGGTGACATGTAGAGCTATAATCAACACTGTAATCGGCATTGGGGTGGAAGAAGAAGACAGAAAACACACGTGGATGGATGATGCTGACAGTTGTGTTGCTAATGTCGCTTTCGAGTGCGCAAGAGCTATCTATGCACATGCTCTGTCAGTTTTTCCCAGCAAGAAGAGCGTCTGGTTGCGTGCTGCACACTTCGAAAAGAATCATGGGACAAGAGAGTCTTTGGAGTCCTTGTTACAGAATGCAGTTAAGCACTGCCCGAAAGCTGAAGTTTTGTGGCTGATGGGTGCAAAATCCAAGTGGCTGGCTGGTGAAATTTTTGAAGCTCGTTCCATCTTAGCCTTGGCGTTTCAAGCGAATCCCAACAGTGAGGAAATTTGGCTGGCTGCCGTGAAGCTGGAGAGTGAAAATAACGAGGATCAGAGAGCGAGAAAACTTTTACAGAGAGCAAGATTAAACGCCTGCACGCCAAGGGTGATGATGAAGTCGATCAAGTTAGAATGGGTTTTACGAAACCTTTCGGAGGCAGAGAAGTTATTAGACGAAGCTGTTCAAAGATACCCAGATTTCGCCAAGTTGTGGATGATGAAGGGCCAAATACACCAAGAACAGAATCACATTGACAGCGCTAGAGAAGCATATAAACTAGGGACCAAGAAATGTCCCCGGTCCATTCCAATCTGGCTGTTACTTGCAAGACTTGAAGAAAAATCagGTCAGGCCACAAAAGCAAGATCCGTATTGGAGCAAGCCCGTCAGAAAAACTCGAAGTGCCCTGAACTATGgCTTGAGGCGGTTCGGATAGAAACTAGAGGAAGCCGAAAAGAATTCGCGCGGACTTTAATGGCGAAAGCTATGCAAGAATGTCCTACTTCCGGGATCTTATGGGCAGAAGCTATTTTCATGGAAAGTCGACCTCAACGAAAGACGAAAAGCGTGGATGCACTAAAGAGATGTGAACATGATCCTCATGTGCTGTTAGCAGTGGCTAGGTTGTTTTGGAGCGAAAGGAAAATAAACAAGGCAAGGGAGTGGTTTAACAGGTATGGcgtttaa

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
PF14559 all species →	TPR_19	Tetratricopeptide repeat	Repeat	Interproscan
PF06424 all species →	PRP1_N	PRP1 splicing factor, N-terminal	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR011990 all species →	Homologous_superfamily	Tetratricopeptide-like helical domain superfamily	Interproscan
IPR045075 all species →	Family	Pre-mRNA-splicing factor Syf1-like	Interproscan
IPR003107 all species →	Repeat	HAT (Half-A-TPR) repeat	Interproscan
IPR010491 all species →	Domain	PRP1 splicing factor, N-terminal	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:0000244 all species →	Biological Process	spliceosomal tri-snRNP complex assembly	Interproscan
GO:0000398 all species →	Biological Process	mRNA splicing, via spliceosome	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
GO:0006396 all species →	Biological Process	RNA processing	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 g13810.t1 across 48 RNA-seq samples of Montipora capitata. 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.

48Samples

48TPM > 0

3Conditions

138.9Max TPM

57.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole organisms · ambient pH treatment	21	21	59.59	133.62
whole organisms · low pH treatment	15	15	59.09	138.90
whole organisms · extra low pH treatment pH treatment	12	12	52.10	112.76

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11452246	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	133.62
SRR11452252	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	127.88
SRR11452243	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	112.09
SRR11452237	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	110.11
SRR11452250	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	106.60
SRR11452242	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	102.68
SRR11452234	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	96.54
SRR11452233	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	81.81
SRR11452232	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	70.20
SRR11452228	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	63.04
SRR11452230	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	62.59
SRR11452222	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	57.51
SRR11452231	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	53.27
SRR11452259	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	19.55
SRR11452254	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	15.01
SRR11452260	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	12.85
SRR11452251	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	7.15
SRR11452262	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	5.50
SRR11452240	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	5.33
SRR11452263	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	4.53
SRR11452217	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	3.47
SRR11452245	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	138.90
SRR11452249	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	125.88
SRR11452238	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	112.33
SRR11452236	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	111.76
SRR11452247	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	95.37
SRR11452241	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	87.91
SRR11452221	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	54.40
SRR11452224	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	52.02
SRR11452223	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	48.99
SRR11452258	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	18.19
SRR11452255	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	16.30
SRR11452253	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	10.37
SRR11452216	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	6.23
SRR11452218	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	5.05
SRR11452229	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	2.60
SRR11452248	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	112.76
SRR11452235	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	106.69
SRR11452244	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	100.88
SRR11452239	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	97.72
SRR11452225	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	60.32
SRR11452227	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	53.32
SRR11452226	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	52.24
SRR11452256	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	18.66
SRR11452257	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	11.19
SRR11452219	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	4.10
SRR11452220	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	4.00
SRR11452261	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	3.29

Source: CnidoSite RNA-seq expression matrices (MCAPI_TPM, StringTie quantification over 48 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.