Special

MmuINT0114474 @ mm9

Intron Retention

Gene
NA
Description
NA
Coordinates
chr3:46246119-46251863:-
Coord C1 exon
chr3:46251739-46251863
Coord A exon
chr3:46251212-46251738
Coord C2 exon
chr3:46246119-46251211
Length
527 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGC
5' ss Score
8.05
3' ss Seq
CTGCGCTTCCCCTCTTGCAGGAA
3' ss Score
11.64
Exon sequences
Seq C1 exon
GCAGAGGCTGGGGAGCGAGCCAGAGGGGCGGGGGAGGAGCATGGTACCCCCCCAAAAAAGTGTGAAAGAGCAAACAGTGCTAGCCAGCGAGCTCCGGGTTCCTGCCGCCTGCAGTCCATAACCTG
Seq A exon
GTGAGCTTCAGTTTTCAGCCAGGATCGTCCCGGGCGCCTCTGGCCACCGGGGTGGGGGGTGGGGGGTGAGGGACGCGGCCCAGGCGGGCTCTCAGCCGCAGGGCGGGCGGCGTGGGTCGGGCTTCCTGCGCGGGACAGACGGGGGCCTGGGTTGCACGCCCCCCTCTGCCTTGCTCTCCCCAGGCTTGGCTGAAAGTTTAAGCCAGCAGAACACAGGAACACAGCACAGGGTCTGGGCCTGTTTGTGCTCCGAAACCAGCCACCAGCGCCTGGGATGGAGGCAGATGAAGGGCCTGTCCTGGCCAGCCACTTGTAAGTTGTTGCTGAGTTGGAAGGGAAGGAAAGCTGAGAGGTGAAGGCAGATTGCCAACTACCAGGAGAGGACATGGGTTTCTGGCTTTTTTTTTTTTTTTCTTTTGACTAGGTATTGCCTGGAAAGTGCAAGTGACCCTGTAGCTGGACCTCTAAGTGGTCTTTGGAGGCCACTGTGCAGGTCCTGAGTTTTGACTGCGCTTCCCCTCTTGCAG
Seq C2 exon
GAAGCTACAGCCTTGAGAGCTGCAGGCTTGTAGAGTTGGGGTCAAAAAAAGGAAATAAACCAAACAAGCCAAGAAGAAAAAGATGAGTCTGGAAGCTAAGTACCGTGCAGCTTCCCTCTACGTGGGTGACCTCCACGAAGATGTCACGGAGGACATGCTCTTCAGGAAGTTCAGCACAGTGGGGCCGGTGTTGTCCATCCGAATCTGCAGGGACCTGATTTCCCAACGTTCACTAGGCTACGCCTATGTCAATTTTCTCCAGGTTAATGATGCCCAGAAGGCCTTAGTCACCATGAACTTTGACGTGATCAAAGGTAAATCCATTCGTCTCATGTGGTCTCAACGGGATGCTTGCCTGAGGAGATCGGGAGTCGGGAATGTGTTTATCAAGAATCTGGACAAATCCATTGATAACAAAACCTTGTATGAACACTTCTCACCTTTTGGAACGATCATGTCTTCCAAGGTGATGACTGATGGAGAAGGCTCCAAGGGCTATGGCTTCGTGCACTACCAGGACCGGAGAGCGGCAGACAGGGCCATTGAGGAGATGAATGGCAAGCTGCTGAGGGAGAGCACTTTGTTCGTGGCCAGATTCAAAAGCCGTAAGGATCGGGAGGCTGAGCTCAGAGACAAACCAACCGAGTTCACTAATGTGTATATCAAAAACTTTGGAGATGACGTAGATGATGAGAAGCTCAGGGAAGTTTTCAGCAAATATGGCCAAACTTTGAGTGTTAAGGTGATGAAAGATGCCACTGGGAAGTCCAAAGGCTTTGGATTTGTGAGTTTTGATAGCCACGAGGCTGCGAAAAACGCAGTTGAAGACATGAATGGACAGGACATAAACGGGCAGACGATTTTTGTAGGCAGAGCCCAGAAGAAGGTAGAACGACAGGCTGAGTTAAAGGAAATGTTTGAGCAGATGAAAAAGGAAAGAATCCGTGCACGCCAGGCAGCTAAGCTCTACATTAAGAACCTGGATGACACCATCGATGATGAAACACTGCGCAAGGAATTTTCAGTCTTTGGGTCCATTTGCAGGGTTAAAGTGATGCAGGAAGCAGGGCAGAGCAAAGGCTTTGGCTTAATCTGCTTCTTCTCCCCGGAGGCAGCGGCGAAAGCAATGGCTGAGATGAACGGCCGCATCCTTGGCTCCAAACCCCTCAACATTGCACTGGGACAGAAGCACTGAGCCCAACATGATCCTACCTCGCAATCTGAGAAGCAGCTAGGAGAACGATACTGCTCTCCATCTTTCCGGTGCTATAAGGAAGGGTAATCTTGAAAAAACCCAGTGGCTGCTTAATTTACTGCAATCGTGCAAGGAAATGTCTATACGAAAACATTTCGTTTTATGTGAATGAAAAAAAAATGTACGTTAGAAGTTTGATTTGTTTTACAGAGCATATCTTCAAAAAAATTTAAAAATTCTTATTTTCTACTACTTAGAACCGTTTAGTTGGTTACATTCATATTACATTTTGAATTAAGTGAACCAAATGCTTGTCTCTATTGAATATTTTATTCTTTCAGGTTAATAACTGTGAGCTTTAATTTCTCCTATAAAAATTGCCCATAACAAATTTAATTTTTTTAAACTAACAAGAATCTTTTAACTTTTTTTTTTTTTTTTTTTTTTTTGCAATTCAAAATGTAGAAATTGGTAGCCAGAATGAAGTTAAATCACATATTGCACTTCTGAGTTAATCCATCCAAGCCAAAGTTCTAATATACATGCATAAACATATTCTGGTGTATTTGGTTTTATTCTATTTTAAGATGATGTTAGAGCTTTCTGGGGTTTGGTTTGGTTTGGTTCTTACACTTTTTGTATATTTGCTGTAATCTGCTTGGTGTTTTTTTTTTCTGCTTCCTTATGTTATATACATTTATCTATGCTGTTTATGGACATTTAACTTCATCTTAAATCAAATCACACCCATGTGGTTCAATGTGATGCAATTTTAGGCATTCACTAGATGCTGATGTTGTGAAAGTCATAGCTATGCAACTCAGAAACTCCATCTAATGTAAATCTTGAAAAAAATCTTCATGTTATAAAAATCTATCCTGGTTTTCAGAATATAAGTGCCTTATTTTTCTAAATCTCCACCTCCTTTTATTAGACTGTGTTAGCCCTGTATTAGACTGTGTTGCGTTTGCGTTTGCTCTTGGCCTTGGCTCATGTTCCGACAAATGTGAGGTTATGTTGCTTGATGTGTGTTTTAGCATGTGTTTTATTTGACACTCTTCCCACATGATGTATCTATTCTGTCCATAAAGTCTAACTCATTTTTACACATTTTTACAAAGACACTGTCATATTGGTGTTTCATATAGGCTACCTCAAATCTATCTGAAATAAGAGGTAAGAGTTATTTATTTACAACTTACTCATTATCTTAAAAATGTTACCAAAGGTTGGAAAACTCATGTTATTTCTTCTGCTTTCCATTCTTTCTGGTTCTTTCATTCTTCTCCATTTTTGATTGTTTGGTCATTTCTTATTACAATCTTTTAATTTATGTATTACAAATACATTTTTTCCTTAACAAAATTTTATGAGGAAAGTTTCATTTTGTGTTTATAAACCATATATACATATATACGTAGCAAGTTTTTCTAATCTCAATGAGAAAAGAAAACAGTTTAAAAAAAAGTAAAAAAAAAATATTTTCTACAAATACATTCTGCTGAAATCTGCCACATATTGTCCCTAACTTTTTATGTGTACACTAAGAGCTGATTTAGGAAAGGCGACATCAACAATTTTGTTTGAAATCATTGTTTTGTATTTGATGTTGTCAGATGCTCAAACGTAACTTACTCAAGGAATGACTTACCTATTACATTAGGGGCTTTTGACTTTGGCCAATGGGTTTTCCATGATTCCCAAACTCTTGAGAAATATGGGTGGCTTTGCAATGCTTCTCTTCTGGTCTTGACTTCTGCCAAGATAACTTGAAGGTACGCATTCTTCCCAACTCCTATTGATATGCTTCCAATTCTTTTCTGGAAAAATAAACTATAATTCAGGACTTAAAATCAATTTATTTTCATGTGTTGCCAAAATATCTTACAGATATTTCATAACAATAACATTTTCATTGTAAGTATAGGCAAATGCACATTTCCATATTGTCCAAGGACATAAATATTTTGTTAGGATCTGGCAGATTGAGCATAGTTATGATAAATAACCACTACTCTTTCATTGTATGGTTTTAATAGCTTCTTTTTTTTTAATTGTCAAATTTTTACCTGTGTCCATTGCATTAATATTTCAACACTTGTAAATTTAGTGTTTCAAGAACCTAAGCTATTTTTTCTCTTGAGTATTTATATCCACAGTTTTCTATCACATCAAAAACTATTTTAAACCTTACCAATGTTCTCACTTTGTTTACAGTTTGTAAAGCTGTCCCAAAGACAGATTTTGAACACAACTTTTTCAGTATCTCATTGAGATGACATTTTTTATTGTGATTTGTTCTAAACACTTTAAAATGTCTGTATATACACATGTAGATGTACATGTGTGTGGAGTATAAACATGGAGACAGGTAGGCAATCCATGTTGTCTTCTATTAATGTGTATGGCTCATATTATCAATATTTTTATAAACAAAACTTGTTTATATTTTGTGTAAAGAGTACAATAAAAGTTTTAGCTATGTCTTGCCTCTACACCATTAAGCAGCACATGTTTGGGTTAGTACTGATATAAACTGTATCAGAGCTGATATATACACTCAAATTCATTGGCTTGCAGAATCTCTACCTTGATGAGTATTTTCATCATCAGAAGTACCAGAAGTTGCCAGGACTGGAGAGTACAAAATGAAAACATTTTCTGGGAGATTTAATCTGCAAAAGTGTCCAGATAATTGAACAATGAAAACATCTCTCTTTTGTGCACAAATAATTGGTTAAATAGTTTACCATATGCATAGATATATTGTTATATCAGCTTAATAATGCAGTATCCTAATACCTTAGTAGAAATTGTATATTCCTAGTATTTAGCATAAAATTTGACAGTTCATTCTCTTTAATTTTTAAATATTATTCATTCTAAATTTGTGTGTATGTTTGTGCACATGTGTGAATTTGTGCATGCATCTGCATGTGTGTGTGTGTGCATGTGTGTTTCAACAATTACATTGTATCTTCCTAGTTAACAAGTTTTCACAAATTAAAAATTTCTGTAACTAAGTGCCTTGAATAAGAAAGACAATCTTTGCTTCATTAATAAATCAAAGCTAATCCAAACAGAAATGCCTTCAGCCAGTATCTCTACTCCTCCCCCACGTATACTCCCTATCTGTTGTATAGATGACTATGTTTTACAGATGATGTAACACATATGTGCCTTGTTCCAGTTTTCAAAAGTCACATGGAAATTGTTAAAATATAATTTAATGTTCTCTATATTCTTCAAATCCTAAAGAGACAATACTAAACATAATTTACCCCGTCAATGATGGATATGTCTGCGTTATTTATGTTCATTTCAATTATCTGTTTCTAAGTGTAGGTGTTTATATTTCATGCTTTTAAATGTTTCATAATTCTTTGACCTGAAATCTGGTTCTGTACGTATTCACAATAAAAGGATCAGTTATTCAGTAGCTGTTCTAACGTGTAGCCAGGTTTCATAAGAAACAGTTGACTGTTGTGTTAGTTCAGACAGTACTCAACGTGTGAAATCATTTAAAAAAATGTGAAAAAATGCATGATGCCTTATAAATCAAAGTTTGACAGGCCAATATTTGGGATGGCTTTCTTACGAACAGACACTAAGAATGATCATACCATCACTAGATGAGAGGGAACCTTAATGTGTGCTCGCTCTGTTCCTTTTCTTCTTCCCCTTCCCATTCAATAGCCTCCAACCTTTTACCTTGGAGGCTCCACTTGAGGGAGCTTGTCTACTCTTTATCATCACCCAAAGGCATGCTGTTCACAGCCAACCTGAGATAAGATTGGCATTCTAGGTGCCTTAAGATGGGGAATAACTTCCTCACATATGTGCTTGAGTGACTGCCTGCATGTGAAAACTATAGCAATTAAAAACATAAAATTCATCC
VastDB Features
Vast-tools module Information
Secondary ID
-Pabpc4l:NM_001101479:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
5' UTR





No structure available

		

			
Features


			

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

				
Domain overlap (PFAM):

					





						

							
C1:
NA

							
A:
NA

							
C2:
NA

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
NA





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000126224
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
chr4:134201246-134201717 
ALTERNATIVE
HsaINT1026022
(PABPC4L)
Human
(hg19)
chr4:135122231-135122872 
HsaINT0119443
(PABPC4L)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr17:24418140-24418790 
Chicken
(galGal4)
chr23:5432454-5432891 
Chicken
(galGal3)
chr23:5745492-5745628 
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CAGAGGCTGGGGAGCGAG

				
R: 
AATCAGGTCCCTGCAGATTCG

				
Band lengths: 
344-871

			

		

	





	
Functional annotations
(Submit an annotation)

	


There are 0 annotated functions for this event 


		










GENOMIC CONTEXT[edit]












INCLUSION PATTERN[edit]






SPECIAL DATASETS
  • 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"