Special

MmuINT0089576 @ mm10

Intron Retention

Gene
ENSMUSG00000015647 | Lama5
Description
laminin, alpha 5 [Source:MGI Symbol;Acc:MGI:105382]
Coordinates
chr2:180190905-180191372:-
Coord C1 exon
chr2:180191228-180191372
Coord A exon
chr2:180191046-180191227
Coord C2 exon
chr2:180190905-180191045
Length
182 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
TGATTGTTCTCTGCCCATAGGAG
3' ss Score
10.41
Exon sequences
Seq C1 exon
ATGCAGACCCAATGTAGCTGGACGTCGCTGTGATACCTGTGCCCCGGGCTTCTATGGCTATCCTAGCTGTCGCCCCTGTGACTGCCATGAGGCAGGCACCATGGCTAGCGTGTGTGACCCCCTCACAGGCCAATGCCATTGCAAG
Seq A exon
GTGAGCAGGGGCTTGTATCCCAGGCTCCTTACTACGTATCTGCTTCAGTTGAGCCATGGTCCTCCTCAGCAGCCTTCCTGGGCAGATGGGGCTTTCTGGAAGCTTTGGGGGACAAGGACAACTGGTCTATTGTCTGGCTCTCAGCACATAGCCAACTGGCCTTGATTGTTCTCTGCCCATAG
Seq C2 exon
GAGAACGTGCAGGGCTCAAGATGTGACCAGTGTCGCGTGGGGACCTTCTCCTTGGATGCTGCTAACCCCAAGGGCTGTACCCGCTGCTTCTGTTTCGGGGCCACAGAGCGCTGTGGGAACTCTAACCTCGCCCGCCATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015647:ENSMUST00000015791:36
Average complexity
IR
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:
PF0005319=Laminin_EGF=PD(51.0=51.0),PF0005319=Laminin_EGF=PU(44.9=44.9)

							
A:
NA

							
C2:
PF0005319=Laminin_EGF=PD(51.0=53.2)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000015791





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm9




Conservation


Human
(hg38)
chr20:62327670-62327865 
LOW PSI
HsaINT0090316
(LAMA5)
Human
(hg19)
chr20:60902726-60902921 
LOW PSI
HsaINT0090316
(LAMA5)
Rat
(rn6)
chr3:175567757-175567916 
LOW PSI
RnoINT0084022
(Lama5)
Cow
(bosTau6)
chr13:55418142-55418336 
LOW PSI
BtaINT0084205
(LAMA5)
Chicken
(galGal4)
chr20:8196249-8196755 
LOW PSI
GgaINT0011788
(LAMA5)
Chicken
(galGal3)
chr20:7828463-7828969 
LOW PSI
GgaINT0011788
(LAMA5)
Zebrafish
(danRer10)
chr23:9696668-9696765 
LOW PSI
DreINT0088047
(lama5)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
TAGCTGGACGTCGCTGTGATA

				
R: 
GTTAGAGTTCCCACAGCGCTC

				
Band lengths: 
257-439

			

		

	





	
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
  • Ribosome-engaged transcriptomes of neuronal types
  • Neural differentiation time course
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types





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