Special

MmuINT0127135 @ mm9

Intron Retention

Gene
ENSMUSG00000023007 | Prpf40b
Description
PRP40 pre-mRNA processing factor 40 homolog B (yeast) [Source:MGI Symbol;Acc:MGI:1925583]
Coordinates
chr15:99140375-99145125:+
Coord C1 exon
chr15:99140375-99140466
Coord A exon
chr15:99140467-99145008
Coord C2 exon
chr15:99145009-99145125
Length
4542 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
ACACACTGCTGTGCCCACAGGAT
3' ss Score
8.63
Exon sequences
Seq C1 exon
GCTCTACTCCTTTGGACTTGTTCAAGTTCTATGTGGAGGAGTTGAAGGCTCGATTCCACGATGAGAAGAAGATCATAAAGGATATCCTTAAG
Seq A exon
GTGAGAGAGACCTGGGGCTACACATGGATAGACTGGGTGGAAGCCACATTCCCCGAACCAGGACTCCATAAGTCATGTTTTCCAGGAACCTGGCAGCTTGCATTGGGGATACAAATAGACACATTTTCTAGCAAGATGTAGTGATGCAGGTCAGCTTTCCAACTGAGGCAGGAGGATTGCCACGAGTTCAAAGCCAGTGTGAGGAAGAAAGTACCAACCAGGTTGAAATCCTGTATCAGAAAAATAGACTAAAAACCAAAGTAACAAATCATTGTTTTGCTCTTCTATGAGAAGCATTAGCCAGGGACAGGTGTTCCCAGGAAAGGTGATGTGGACCCCACCCTCAGGATGAGGAGATGGAGGGGTGGTGTGTTGTGACATAGGGGTGCTACAGGAGAAAGGCAATGGGTGGAAAGGGCACGCCAGCCCGAGGGGCAAGCATAGCATTTGTAAACTCGAATTCCCATATGCTAAGCTGCTGCCTGCCTGCTGCTGCTGCTGCCTGCCTGCCTGGAAGGGGTTTTGAAGAATTTGGAATTTGTTGCTAATACTTTACAATCTGGAGATTTCACATAAAAGCCTGTTTTGTTTTGGTTTTTGAGACAGGGTCTTATGTATTCCAGGCTGGCCCTGAACTCCTGATCCTTCTTTCACTTCCACATGCTGGGATTATAGTGTACACCACTGTGCCTGGCTTCACATAAAATCTTCAGTGTCTCTTGCCAGTGTGGATGATGTCAGCACTGGGCTCGTTCTGCAAGGCGCACCATGGACACTGGCTGAGATGCCATTGCCCTCTTAGAGGAGGACGGTGAGGCTTTCTTCACCTCACTACACCGTAGTGCTGGCAAGTGTCAGCTGCTGTTCACTAGTCCATGTGCCCTGTCATTTTCTCTACTGAAGAAATAGTTGTTCATGCTTGTCAAACTCTCAAGTGTAAGTGAAGGGATCGTTTTGTTCCAAAAGGAAAAAAATGTATTTCTTCATGGAAGTGAATACTATTTTAAATACATGTCTCTATTACTATCCTAATAGGAACTCTAATATCCTGATAGTAAACACTATTCTATTCTAGTAAATACTGTATGTATTAAGATACCATACAGTATGGTGACTAAAAGCAGGACCTAGGGGTAAAGAGTCCAGATTAGGGGCTTGAGAGATGGCTCAGTGGTTATGAGCACTGACTGCTCTTCCAGAGGTCCTGAGTTCAATTCCCAGCAACCACATGGTGGCTCACAACCATCTGTAATGGGAACTGATGCCCTCTTCTGGTGTGTCTGAAAAAAGAGAGTGTACTTACATACATAAAATAGATTAAGCCCTTAAGAACTTTTCTAAGCATTAGTTTGTCTCAGAAGTGGTAAGTGTTCCACCAAGGAACCCCCAGTTACCAAAGATAGCAACTGTGTCTCTTTCGTGGAGAGGGACATGGTACTGTTAGGCAGATTGCCTTACAAAGCCACAAATGTTGTATTGTAATACAGTCACCTGTTCAATATGGACTTAATAAACCAAGCACTGTGGCTCACACCTTTAATCCCAGGGCTTGAAGGCGAGGAGCAGGTGAGCTGCAGGTCAGCCTGGGCTGCACAACGGATCCTATCTAAAAACCTGAGTAAATTTCCCTAAGAGTTCAACGTTTCAAAGTTACTCTTCAGTGAGATGCATCATATTGTCCTGGGGTTTTCTCCTATTTCTCTGGAACCACATGCCCTCTAGAGCTTTACAAAGGGCTTTGGATTGAACTACACTTTTTAGCTCACCCATGTCTCTGGACTTGATCCCGGTACTCTCCGATTATCAGTGCTCTTTGATATAAAGGTTGGAGAACCACACCATGCCAGAGACTGGGTTAGAGGGATATAAGAGGGTAAGGGGAAGACCAGTCAGGCAGCTGTTAAGAATCTAAGTGGCAAAAAAGAAGAGCAAGACACTATAGGGATGCTGAGAAGAAAACAGCATCAAGGCCAAGTCTGGAGGTGACTCTTCCCCTATTTTCTAATAGAAAAGCTTGTATCTCTTTTGTGCCTTAGTGTACCATGTATAAGACTTTTATTAAAAAGATGGTTATAGTTGGTTGGGCATGATGGCAGATGCTTTTAATCCCATCACTTGGGAGGCAGGGGCAGGTGGGTCTCTGAGTTAAAGGCCAGCCTGGTCTAGAGTGAGCTCTAGGACTGCCAGGGCTACACAGAGAAACCCTGTCTTTTAAGATTTATTCATTTTATTTACATGAGTACACTGTCGCTGTCTTCAGACACACCAGAAGGGGGCATCTGATCCCATTACAAATGGTTGTGAGCCACCATGTGGTTGCTGGGAATTGAACTCAGGACCTCTGGAAGAATAGTCAGTGCTCTTAACCATCTCTCCAGCCTGAGAAACTTTGTCTTAAAAACGGTGAAAGTTGGGCTGGTGAGATGACTGAGTAGGTAAAGGTGTTCACCACCAATCCTTAGTTTGATCTCAGGAACCCATACTGGGAGGAAAGAACCAATTTCACATGTGCCATGGCACATGGGTGCCCACATATATACAAAATAAATGTTTAGACTCTGGATAGAACCAGTAAAATAAAATCGCCAGGCTGTTTTGTGAAGTGAATGGCAATTCTGTTGTTAAGTGTTAAAGATTGTAAGCAACGAGGGTTGAGCCATAAAGAGGTGCCTACAGAAGACAAGCATTCCAGTTGGGACGTGATCCTTTAAAGCAGCTTGGGCAGGGAGGAGTAAAGCCAATGAAGGATAGATGTCTATCCGAAGATAGCTAACATTTAGCTAGAGGAACTAGTGGCCTGATGGGTTTTATCTACCCAAAGCAACTGGTTATTTTGGACTTCTAGCCTTCGTTTGAGCTCCTAGCCATGGAGGCCTGATGATCTTAGAAGTTCCTGTGGCCGTCCATCCAGTCACATGAACTGTAGGGGCATCTCTCATCACCTAAGACTGCAGGGCCCTGAGCTTGGAGCAGGTAGAAGATTAGCGATGGGTACAGGAGAGCTGCTGCATTAGAAGAGTAGCCAGTTTGGCATGGGTTGGAAACTGCTAGGGAAGATGTAGGTCAGGTAAAAAGCTAGTGTAAGGGTAGTTCTCAGGAACATTAACACAGGGGAAGTGACCACAAACAGCCCTGGAGAGGAGAGTACTGCACACATCGCACAGTAGTCTGCTCTTTGGCCCGAAAACCTCTGCGAATTGCGGACAATCCATATATAAGAGATAAATAACAGCTAGAATTTTTTTTTTTTTTACCATTTTGTCAAGTGTCTTGCTTATAACAATCTCTTATTGTTTATTTCTTTTCCTTGTGCTGTGTCTAAGGAATTGAAACCGAGGGAAAGAACCAGTTAGTTAGCTTGAGACGCTAAAAGCAAGATAGAGGGATATTCTAAGTGAAGTGAGCTGTGTGCTCCTGGGGAGGAGAGTGAAGAAGATGTAGTCCAAGCCTTCCCAGGGGAAGGCCCGTACTAGGGAGATAAGGGCTGCCACGCAAGCACAAGGACCTGTGCTTGAGTCCTCAGCACCTACATAAAATCTGGGTATGCTTGCAACCCCAGCCTTGAGGCATGGCAGAGACATGATCCTGGCCTGATAGTTTAACAAAAACAGAAGGCTTCAGCTTCAGTGAGACTGAGGTTTCAAGGGAGGGAGACAGAGCTGTATACCCAGAGTCCTCTGGTTGTGACCTCACTCATAGAAAGGATGTGTTCAGGAAGGGCTGAGCCTTGACAGAGAAAAGACTCCTGGGAAAAAGCAATGTATACTCCTGCCATCAGCAGGCAGGAAGACTGGAGGAAGCCAGCTGTGTGAAAGGACAGGCAAGCTGGCCTGTGACACAGAATTCCATTTACCTATCAGCTTGGCCAAGTGAGATTCCTCTCCTGCACCTTAACTTCACTAGCACATGGAGGCTTTTTGGTGAGAAATACAGAACCTGGCTGTGTACTTAAGACAATGAACATGATTTAAATATTGATGGAGAGCTATACACTTGATGGCCAACATCTCTTCCTGGACCTATGCATTCAGGGTAGGTGTAGTGGCTGAAAGCAGATTTGGGATTTAGACCTGGGATATGTTAGAATAAGTGATTTCATTTTTCTGGTCTGCATAAAATTAGAAGACTGACCTAGTATGAGAGGATTAGTGGAGAAACGTGTCAAGCACTCAGCAGAGAACCTACTACCCAGTAAGCACCCAGAACATGAGGCAAAGGGTATAGACCAGATGTTAAGCATGCATGGCAGCTTCCATGAGCAGCAGGAAGGCCCAGCTGTGGCCAGAGGAACAAAGACCTAATTGTAATAACTCAGTCATCTATCAAGACGGAAGACACTTGCTGACTCTTTTGGCTCCATATGAATCCACACAGGTCGGATGGGGCCAGTAAGATGAAGACTTAGCATGGTTTCTAAGGTGTGTCACAAGTCTTATGGATCCTATTTGAGGGCAGAGGCCAGGCTTGAACACCTTGCAGCCTGATCCCTTTTGCCCACTGGCCTGTGGTGCCCCTGGCCTTCACACACTGCTGTGCCCACAG
Seq C2 exon
GATCGGGGCTTCTGTGTGGAGGTGAACACAGCATTTGAGGACTTCGCCCACGTCATAAGCTTTGACAAGAGGGCTGCTGCGCTGGACGCAGGCAACATCAAGCTGACCTTCAATAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000023007-Prpf40b:NM_018786:18
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0184614=FF=PD(17.9=32.3)

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000115869





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000023745, ENSMUSP00000113282, ENSMUSP00000122649
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr12:49637825-49641907 
ALTERNATIVE
HsaINT1028105
(PRPF40B)
Human
(hg19)
chr12:50031608-50035690 
Rat
(rn6)
chr7:140974064-140979080 
ALTERNATIVE
RnoINT0118347
(Prpf40b)
Cow
(bosTau6)
chr5:30375756-30379787 
ALTERNATIVE
BtaINT0118360
(PRPF40B)
Chicken
(galGal4)
chr7:35054160-35054331 
LOW PSI
GgaINT0048640
(PRPF40A)
Chicken
(galGal3)
chr7:37183514-37183685 
LOW PSI
GgaINT0048640
(PRPF40A)
Zebrafish
(danRer10)
chr9:4740925-4741009 
LOW PSI
DreINT0120525
(prpf40a)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
No suggested primer sequences

				
R: 
No suggested primer sequences

				
Band lengths: 

			

		

	





	
Functional annotations
(Submit an annotation)

	


There are 0 annotated functions for this event 


		










GENOMIC CONTEXT[edit]












INCLUSION PATTERN[edit]






SPECIAL DATASETS
  • Pre-implantation embryo development
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types






Retrieved from "https://vastdb.crg.eu/wiki/Special:VastDB"