Gene detail

Detailed information of XP_032228652.2 in Nematostella vectensis

Genomic Location: NC_064040.1:7973156...7981279
NR annotation: XP_032228652.2, pre-mRNA-processing factor 39 [Nematostella vectensis]
Species Nematostella vectensis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

LOC5504457

ATGATGCAATGCGATCAATGCGTTTCTACTTTTCTCTCTTCCATCATGTCGGCTGCTACCGAACCAATGCAAGAACAATCCATGGAATATCAAAGCAATCATACCGGACTAGAGCCGAGCGAAGCTGAACTTAAAACGAATGGAGAACAAGATACAACATATGATAACGCAGGAAACGACGCCAAGATGTCTGAAGGGGAAGATGCAACGGCTAGCGTCAATGAGGTCGAAGAAGTCGTAAACGAGCAAGAACTAAAATATTGGAAGTCTGTGAAAGAGAATCCTTCAGATTTTACCAGCTGGACCTACCTTTTACAATTTGTCGAGCAAGAGAATAAACTCTCCTCTGCAAGAAAAGCATTTCAAACTTTTTTTAAGAGGTACCCATATTGTTATGGATACTGGAAGAAATATGCAGACATGGAACGAAAGAATGGCAATATTGAGGCTGCAAAGGAGGTATTTGAGCAAGGGGTGAAGGCCATTGCATGCAGTGTGGATCTATGGGTACACTATCTCAACTTTTCTTCTCAGGCAACCAAAGGCCAACCTGATGGCCCTGAAATCATGAGAAGATTGTTTGAGAGGGCAATTGCTACTGCAGGGCAAGACTTCCGCTCTGACAAGCTTTGGGATGCTTACATAGAATGGGAGAAAAGCCAGGGTCAGCTGCAAAGAGTAACAGCTCTCTACGACAAGCTCTTTACTGTGCCAACCCAGAATTACGCTCAACACTTTGAAAAATTCAAAGAGCACATCAACACTCACCCTGTAGCCAGTGTCCTGCAGACTGAGGAGCTGCTGAAGCTGCGAGCCGAGGTGGCTGCAGCTCCTCCTGGGGTGATCTCAGAGGCAGAGCCACAGGTAGCTGTACCTGACACCACTCTCCCAGTTGACCCAGAAGCTGATGAGGTAGCCCCTGGGACAGAGCTTGGACCGCCTGGTGAAGAACCTGGCATTGTTTTACCAGAGAATGATGCAGAGACTGTTGCCATTCGAGAGAAAGTGATAGCTGCGAGAACAGAGATCTTCAACAAGCTTGAAGATGAAATTCGCAAGTGCTGGGTGTTTGAGGACGCCATCAAGAGGCCTTACTTTCACGTTAAACCACTTGAGAGAGTACAGCTAAAGAACTGGAGAGATTACTTGGACTATGAAATTGCAAATGGCGAACACAGAAGGGTGGTGATATTGTTTGAGAGATGTGTGATTGCCTGTGCCTTATATGAAGACTTCTGGCAGAGATACGCTAGTTACATGGAGAATCACAGCATTGCAGAGTGTAGTTCTATATACACAAGAGCTTGTACCATCCATCTTCCACGCAAGCCAAACATTCATCTTGCTTGGGCAGCCTTTGAAGAGAAAAATGGGAACTGCAACAGAGCATCTGAAATCCTCAAAGACCTTGACAATGCTGTCCCAGGTCTTGTTTCTGTTAAGCTGCGGCGTGTCAGCTTGGAAAGGCGGGCAAACAACTTGGAAAAGGCAGCTGAGCTATTTGAGGAAGCTGTAGGAGAATCATCAGAGCAAGAAACCAAGTCTTTCTATGCTGTCAGATATGCAAGATTTCTAGCTAAGATAATGGGTGATTGTGAAAAGGCGTGCACCATTTTGAAACAAGCACTGGAAAATGATAAGGACAACAAGCGGCTCTACTTGCAGCTTCTCGATATCCGGCTGAATGAGTCACCTATTTTGGAGGATAAGGTTGAAGAGGTTTTTGAACTTGTGAAGAGCAGTGATCTTGATGAAGACACAAAGCAAGGGTTCTCTGAGAGAAGATTAGAATTTCTTGAAGACCACTGTTCTAGCATCACCAAGATACTATTGGCAAATGAGGCTCATGGCAAGCTGTACAAATCCAACCCGTCTGTTGTCGGCTCTGCCACTGCCAAGAAGAGAGCATCGGAGACAAGTGTTGAATCCAAAACAAAAGTTGCTAAAACAGAAGGTGCAACAGACACCGCACAGCATCTATACCCAGCAGCAGTAGAGAGCTATGATGCAGGATACTCTAGCGCATACAGCACCTCTGCAGCAGCCGCTACTGCCTACAGCTATGCCACCCAGACGCAGAACCAGTGGGCAGCATACAGTGCTGCAGCTCAACCGGCATATGCTTACAACCAGTGGTACTACGGACAAACGACACCTACTCTTTAG

Transcript

rna-XM_032372761.2

tgtggtgtttttttttcatccccaTGATGCAATGCGATCAATGCGTTTCTACTTTTCTCTCTTCCATCATGTCGGCTGCTACCGAACCAATGCAAGAACAATCCATGGAATATCAAAGCAATCATACCGGACTAGAGCCGAGCGAAGCTGAACTTAAAACGAATGGAGAACAAGATACAACATATGATAACGCAGGAAACGACGCCAAGATGTCTGAAGGGGAAGATGCAACGGCTAGCGTCAATGAGGTCGAAGAAGTCGTAAACGAGCAAGAACTAAAATATTGGAAGTCTGTGAAAGAGAATCCTTCAGATTTTACCAGCTGGACCTACCTTTTACAATTTGTCGAGCAAGAGAATAAACTCTCCTCTGCAAGAAAAGCAtttcaaactttttttaagaGGTACCCATATTGTTATGGATACTGGAAGAAATATGCAGACATGGAACGAAAGAATGGCAATATTGAGGCTGCAAAGGAGGTATTTGAGCAAGGGGTGAAGGCCATTGCATGCAGTGTGGATCTATGGGTACACTATCTCAACTTTTCTTCTCAGGCAACCAAAGGCCAACCTGATGGCCCTGAAATCATGAGAAGATTGTTTGAGAGGGCAATTGCTACTGCAGGGCAAGACTTCCGCTCTGACAAGCTTTGGGATGCTTACATAGAATGGGAGAAAAGCCAGGGTCAGCTGCAAAGAGTAACAGCTCTCTACGACAAGCTCTTTACTGTGCCAACCCAGAATTACGCTCAACACTTTGAAAAATTCAAAGAGCACATCAACACTCACCCTGTAGCCAGTGTCCTGCAGACTGAGGAGCTGCTGAAGCTGCGAGCCGAGGTGGCTGCAGCTCCTCCTGGGGTGATCTCAGAGGCAGAGCCACAGGTAGCTGTACCTGACACCACTCTCCCAGTTGACCCAGAAGCTGATGAGGTAGCCCCTGGGACAGAGCTTGGACCGCCTGGTGAAGAACCTGGCATTGTTTTACCAGAGAATGATGCAGAGACTGTTGCCATTCGAGAGAAAGTGATAGCTGCGAGAACAGAGATCTTCAACAAGCTTGAAGATGAAATTCGCAAGTGCTGGGTGTTTGAGGACGCCATCAAGAGGCCTTACTTTCACGTTAAACCACTTGAGAGAGTACAGCTAAAGAACTGGAGAGATTACTTGGACTATGAAATTGCAAATGGCGAACACAGAAGGGTGGTGATATTGTTTGAGAGATGTGTGATTGCCTGTGCCTTATATGAAGACTTCTGGCAGAGATACGCTAGTTACATGGAGAATCACAGCATTGCAGAGTGTAGTTCTATATACACAAGAGCTTGTACCATCCATCTTCCACGCAAGCCAAACATTCATCTTGCTTGGGCAGCCTTTGAAGAGAAAAATGGGAACTGCAACAGAGCATCTGAAATCCTCAAAGACCTTGACAATGCTGTCCCAGGTCTTGTTTCTGTTAAGCTGCGGCGTGTCAGCTTGGAAAGGCGGGCAAACAACTTGGAAAAGGCAGCTGAGCTATTTGAGGAAGCTGTAGGAGAATCATCAGAGCAAGAAACCAAGTCTTTCTATGCTGTCAGATATGCAAGATTTCTAGCTAAGATAATGGGTGATTGTGAAAAGGCGTGCACCATTTTGAAACAAGCACTGGAAAATGATAAGGACAACAAGCGGCTCTACTTGCAGCTTCTCGATATCCGGCTGAATGAGTCACCTATTTTGGAGGATAAGGTTGAAGAGGTTTTTGAACTTGTGAAGAGCAGTGATCTTGATGAAGACACAAAGCAAGGGTTCTCTGAGAGAAGATTAGAATTTCTTGAAGACCACTGTTCTAGCATCACCAAGATACTATTGGCAAATGAGGCTCATGGCAAGCTGTACAAATCCAACCCGTCTGTTGTCGGCTCTGCCACTGCCAAGAAGAGAGCATCGGAGACAAGTGTTGAATCCAAAACAAAAGTTGCTAAAACAGAAGGTGCAACAGACACCGCACAGCATCTATACCCAGCAGCAGTAGAGAGCTATGATGCAGGATACTCTAGCGCATACAGCACCTCTGCAGCAGCCGCTACTGCCTACAGCTATGCCACCCAGACGCAGAACCAGTGGGCAGCATACAGTGCTGCAGCTCAACCGGCATATGCTTACAACCAGTGGTACTACGGACAAACGACACCTACTCTTTAGCTTGGCTAGTTTTAACAGTTAATTTCAGAAACGTTGtacatagttttttttttgtaaaaaaaaagtgcataAAATGCAAGATCAATGACAAAAGTTGGTGTTCTACTGTACAAAGTTAAAGATGTTGTAGACAGACAGGAAACTGCATAATAAAACATGGTTTATTGACAA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q86UA1	Pre-mRNA-processing factor 39 OS=Homo sapiens OX=9606 GN=PRPF39 PE=1 SV=3
Q4KLU2	Pre-mRNA-processing factor 39 OS=Xenopus laevis OX=8355 GN=prpf39 PE=2 SV=1
Q8K2Z2	Pre-mRNA-processing factor 39 OS=Mus musculus OX=10090 GN=Prpf39 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003066 (this species only)

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF05843 all species →	Suf	Suppressor of forked protein (Suf)	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
IPR008847 all species →	Domain	Suppressor of forked	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR17204 all species →	PRE-MRNA PROCESSING PROTEIN PRP39-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0000243 all species →	Cellular Component	commitment complex	Interproscan
GO:0000395 all species →	Biological Process	mRNA 5'-splice site recognition	Interproscan
GO:0005685 all species →	Cellular Component	U1 snRNP	Interproscan
GO:0030627 all species →	Molecular Function	pre-mRNA 5'-splice site binding	Interproscan
GO:0071004 all species →	Cellular Component	U2-type prespliceosome	Interproscan
GO:0006396 all species →	Biological Process	RNA processing	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	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
K13217	PRPF39, PRP39; pre-mRNA-processing factor 39	-	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_032228652.2 across 48 RNA-seq samples of Nematostella vectensis. 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

16Conditions

104.2Max TPM

73.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole 6 week old aboral regenerate · regenerate 96hpa	3	3	67.42	73.66
whole 6 week old aboral regenerate · regenerate 144hpa	3	3	57.15	69.87
whole 6 week old aboral regenerate · regenerate 0hpa	3	3	68.79	70.28
whole 6 week old aboral regenerate · regenerate 2hpa	3	3	78.65	85.61
whole 6 week old aboral regenerate · regenerate uncut	3	3	59.85	65.37
whole 6 week old aboral regenerate · regenerate 4hpa	3	3	83.71	104.21
whole 6 week old aboral regenerate · regenerate 120hpa	3	3	69.93	72.73
whole 6 week old aboral regenerate · regenerate 36hpa	3	3	81.09	91.79
whole 6 week old aboral regenerate · regenerate 24hpa	3	3	78.26	84.08
whole 6 week old aboral regenerate · regenerate 20hpa	3	3	81.79	89.66
whole 6 week old aboral regenerate · regenerate 16hpa	3	3	68.94	75.21
whole 6 week old aboral regenerate · regenerate 72hpa	3	3	73.76	82.15
whole 6 week old aboral regenerate · regenerate 60hpa	3	3	77.58	85.78
whole 6 week old aboral regenerate · regenerate 48hpa	3	3	80.82	87.18
whole 6 week old aboral regenerate · regenerate 8hpa	3	3	70.48	78.39
whole 6 week old aboral regenerate · regenerate 12hpa	3	3	71.13	78.55

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

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR6320836	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	73.66
SRR6320863	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	73.22
SRR6320837	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	55.39
SRR6320847	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	69.87
SRR6320838	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	54.88
SRR6320841	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	46.71
SRR6320846	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	70.28
SRR6320840	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	69.93
SRR6320839	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	66.17
SRR6320861	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	85.61
SRR6320842	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	78.74
SRR6320848	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	71.59
SRR6320844	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	65.37
SRR6320843	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	59.73
SRR6320845	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	54.46
SRR6320849	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	104.21
SRR6320872	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	74.55
SRR6320873	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	72.37
SRR6320882	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	72.73
SRR6320850	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	72.50
SRR6320883	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	64.57
SRR6320855	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	91.79
SRR6320851	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	88.35
SRR6320852	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	63.12
SRR6320854	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	84.08
SRR6320856	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	77.68
SRR6320853	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	73.03
SRR6320859	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	89.66
SRR6320857	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	84.58
SRR6320860	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	71.13
SRR6320880	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	75.21
SRR6320881	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	67.96
SRR6320858	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	63.66
SRR6320862	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	82.15
SRR6320865	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	69.61
SRR6320864	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	69.53
SRR6320869	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	85.78
SRR6320866	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	75.21
SRR6320867	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	71.74
SRR6320870	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	87.18
SRR6320868	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	80.90
SRR6320871	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	74.37
SRR6320875	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	78.39
SRR6320874	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	74.89
SRR6320876	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	58.15
SRR6320879	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	78.55
SRR6320877	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	72.31
SRR6320878	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	62.52

Source: CnidoSite RNA-seq expression matrices (NVECT_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.