Special

MmuINT0089452 @ mm9

Intron Retention

Gene
ENSMUSG00000024421 | Lama3
Description
laminin, alpha 3 [Source:MGI Symbol;Acc:MGI:99909]
Coordinates
chr18:12623870-12626869:+
Coord C1 exon
chr18:12623870-12624030
Coord A exon
chr18:12624031-12626760
Coord C2 exon
chr18:12626761-12626869
Length
2730 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGCT
5' ss Score
6.52
3' ss Seq
CAACTCTGTTCCCTTTGCAGCAT
3' ss Score
10.64
Exon sequences
Seq C1 exon
GTAGAACTGCAGCTTCGTCTGCGGGTCCCACAGGTTGGCCACTACGTGGTCCTGCTGGAGTATGCCACGGAGGTGGAGCAGCTTTTTGTGGTGGACGTGAATCTGAAGAGCTCAGGGTCTGCCTTGGCAGGCCAGGTGAACATATACAGCTGCAAGTACAG
Seq A exon
GTAGCTAATCACCCCACAACCCCAAATTCCTCCACCAGGGAAGTCTGCCTGGAACTTGGGGGATTCGTACACTGGACTTTTGACGCAGCCTTTGAAAACTAGCAGGCAGCTAGTTGTAAGGTCCAACATTATCCCCAGCCTGGTATTGGGAGCCTCTCTGTGGGTGGCAGCATTGTGAAATTATGTAACAGGTGCACCTCTCCCTGCACGCCCCCCCCTTTAGAACCCAACAAATTAGTGATTGGTGATTGCTGTGTGCAAAAAACAATAGCAGAAACTTTTAGATTCACCCTAATGAACTTTTTGCCCAAGAGTGCTAATTGCCAAGGGCTTACTAGAAATGATTTTCTTTGCATAATAGTTCAAGAGCATTCTTTAATTAAAGAATCAGCACAAAGGATATTTGTAGAGGAGACTAAAATGTAAAATTAATGACACCAGAAGTTGTAGCCCTTGATACAGCAGGTAGAAGAAAGCTACAGTAAACACACCAGTTCTTAGTCACAGCCTTCAACGTTTTGTTAACCTGGCTTTTATGTTGCTCTGATCAAACACAAGATAATTTGAAGTAGCCGACCACCTTCCTGGATGTGAAAAATTTTAAAAAGGTGTGCAAAGAGTAGATTTTAGCATTGTACCATGGGCACTGTTGTGGGGCCTGATCAAATGCCTGCTGAATTAGCTGTGCTCCTAACGATCCTAAAAAGCCATCTCTGAGGACTTTGTTACTGGAACAAAGATCACAAACAATGAGTCATATTTGGATTTGTGTATGGTGTTGAGGATCAAACCCAGTGCCATGTGCATGCTGAGCACTCTCCCACTAGTGCATGGGAGCACTTTCCCACTAGGCCTGTGTCCTCAGCTCTGTATATGAACATTAAGGGCATACAGTGATCCTAGGGTAGTTTCTCAGAACCATCTATCACTATCTGAAAATATGAATTTCATGTACAGTTGGCATCAGTATCACTGTAAAGTGTTTGCCCCAATGGGTAGGCCCTGTGTGCTGGAGTCCTGGGTGCGTCGGCCACAGGCCTTCAACCTCTATCCATCTGAGCTCACCTTCCACTTCAACTTTTAAACTTCTTGCATCTTTCAGCTCACAGTCTTGACTCTCATTTCTCACAATCTAAGAGAAGTTGGCTAGGGGACAGAAGAATATTCATAGTTATTCTGGTGACTCTAGATGACCTCAGAAAAGCTCCAGGTTGGGGATAGTTTATATTTTGGGAAGATAGGGGCTTGTTATGCAACCCAGTGTGGTTTTAAATCCATGATCTTCCTGCTTCAACGTCCAGGCTGCTAGGGTTATAGCCATGCGCCATCCTCCCTGGCATGGCAGAAGGATTACAAAGCCAAAGAAAGAAAGGGCCCTTACAGGACGCCATGCAGGTTTTATGATTAGCACTGGGGGACATTGGGTGATGTTCTAGAATCTTTAGCACATGACAACAACTAAGCATGTTTAGCAAACCCGTCATTAGAATTCTAGGACAGCATCATATTAGACGATTGCCTACTTCATACTAAGCCACTCCCAGGAAAGTCCCATTGTATATTTTTACTTGGCCAAGGTCTTTCCTTTTTTTTTAATGCTTCAGTTGTCACAGGGGTCAAGTGAAAGGGAACTGACTATAGCGTGGGAATCTAAAACACAGGAATTATTCCCTATAAAGGCCTATGTTAAGTGAAAGGCCTGCTCGGCATTGCACTGTCTCCTGCTGATGTTTGACCATACTCCTGCATGTCTCACATGATTTCTAACCACTTTGTTAGAAAGACAACCTCTCAGCAAAATAGTGACATCATTTAGAACACTACTTTTCAGAATAATAATGCAGTGATAGACAAATCAACCCTTTTTGCCACAGCGAGGTGATCCTTAATGACTAAACCAATGGCCATCTGCTTCTTAGAAAGAACTTTTAAAAGGATGATGATAAAACTAAACGCAAGTGAATCCCAGGGTAGCACTTCAGTCCAGGACGGCTTCAGCTGTACTTGCGTGTTGACTGCCAAGTTCCTATATATCTACCCAATCTGTGTTCGATTCTTTGCATATTTTATCTTCTTTTAGTCAGTACCTAAATCTCCTTGACTCAATGACGTCAGGTGTGCATTAGGGATGGCCATGTTGTCTTCATCCACTTCCCGCTCCAGTTCATATGTATCCAGGGGAAATGGCATCAGCCTGCTTCCTAAGCTTAAGCATGCTTTCCCACCAGAGCCAGACTCCATGGGGCAAAACTCTGACTTTTTAAGAATGGTTTCAAATTTGTCTCTCACTCGATGGAATGGAAGGTGGGGACCAGAGGTAGAAGTTCTTAGAAGGGACTGAGGAAGAAAACAGACTCAGACTTGGCCTTGCAGACAGTCAGTCTGGCTTGTCCTTCCCCCATGTTAGTAAAGCCAGCTGTGCCTACTGATGGGCATGGGATGGTCATAGCTGGGCAATCTGAATTATGAATGGTCCAATGAACGTTGGTAAACTTCTAAGAGATTGAACCGCCACTCTCTAGCCACTTTTAAAAGATCACAGTGGTGAGAACATTCCAGAATGAATTTGGGGGATCATTCAAACCATAGTAGGCTGCACCCCCTCGACTTCTCATGCAGGAAAATCGACTCTGGTTCGCCCAGTTATAAAGAGGGAAAGCAGACCAGCAGCCAGGTGCACAGCAAGGGAGACGCCAGTGTCAGGCTAAGACAACTCTGTTCCCTTTGCAG
Seq C2 exon
CATCCCGTGCAGGAGTGTGGTGATTGACAGCCTGAGTCGCACGGCTGTACATGAGCTGTTGGCAGATGCAGACATTCAGCTCAAGGCGCACATGGCCCATTTCCTTTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024421-Lama3:NM_010680:24
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:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000089703





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000089703f1552A
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr18:23833989-23836980 
LOW PSI
HsaINT0090228
(LAMA3)
Human
(hg19)
chr18:21413953-21416944 
LOW PSI
HsaINT0090228
(LAMA3)
Rat
(rn6)
chr18:3821010-3823484 
LOW PSI
RnoINT0003552
(AABR07031193.1)
Cow
(bosTau6)
chr24:33215653-33219460 
LOW PSI
BtaINT0084082
(LAMA3)
Chicken
(galGal4)
chr2:102837147-102839022 
ALTERNATIVE
GgaINT0098643
(LAMA3)
Chicken
(galGal3)
chr2:106332480-106334355 
ALTERNATIVE
GgaINT0098643
(LAMA3)
Zebrafish
(danRer10)
No conservation detected
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"