Special

MmuINT0089764 @ mm9

Intron Retention

Gene
ENSMUSG00000026840 | Lamc3
Description
laminin gamma 3 [Source:MGI Symbol;Acc:MGI:1344394]
Coordinates
chr2:31771378-31774136:+
Coord C1 exon
chr2:31771378-31771602
Coord A exon
chr2:31771603-31773947
Coord C2 exon
chr2:31773948-31774136
Length
2345 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
ACAAGTGCCTTGCTCCTTAGGGA
3' ss Score
6.93
Exon sequences
Seq C1 exon
GCCAAGTGCTCTTGTGTGAAGTTCAGCTCACATCGGCCTGGCCCCAGCGTGAGCTTGCCCCTCCAGCCTCTTGGGTGGAGACCTGCTTATGTCCCCAGGGATACACAGGCCAGTTCTGTGAATTCTGTGCTCTGGGATACAAGAGAGAAATACCTCATGGGGGTCCCTATGCCAACTGCATTCCCTGCACCTGCAACCAGCATGGCACCTGTGACCCCAACACAG
Seq A exon
GTAAGTCCCCAGAATCCCATTCCAAAGCTCCCTGAGCTATGCAGACACGGTGGCATGAGGACTGGACCTCACAGATGGCCCTTGGGAGACATGGACACTGGCCTGTCCTTGCCCTGTTCCCTGGGACTTCGCCTATTATAACAAAAGTCCTGAGTGGAACCTAGGGGCCAGGGATTGTATGCACCTGAGGGGGCCTTCAGCCAGCCTCTCTTCAGGCATCTGCCCACGCCTCCTCCACCACCACCACACCCTGCAGGCCCTGGGAAAGGCCCCTCAGAGCCTTGCTTCCCAGCAGGTGCTATGAGAATTACCAGCACAGATAGCAACAGGAGAAAGACATTCAGAGAGTCGCACAGATGACAGGAACTCATGGGTGTTCACCCAAAGCCACAAGCCAAGTGTCCTCACTGCTTGGAAAAGTCACTTCTCTCCCCGAATGTCCCCATCTATACAGTACAGACAGCAGTAGTATACACTGCCCAGGCCATGGAGACAAAGTCCATGAAGGTCAGGAATTGTCTAGATATTTAAAAGAACAGAACGCTCTTTGCACTGAAGTTCAGGGGTAGCTGACGGAGTGAGCCGTGGGTGGGTTCTTTTCCTGGGAGAGACAGATAAATAATATAAAGGAAGGAATAAGATAGTCTCATCCCCTTCCTCCCTAATGTCTTCTCCTTGATTCCTGTAGACATGCAAGTGATATATTCTCCATTATTGTCCCATTTGTTTCCAAGTGGGGTGACCTCATGACCTGTAGGTGACAGAGCCACACCTCCCACCAGCGGTGGTGGCTGTCATTCAGTAGAGCTACTTCTCATACCTACAGAGATACAGAAACCTCTCCAGAGGTCATGTGACCAGGAGGCGCTAGGGGACAGACACAGGCCTTTTCACCTCTGTGTCACAGGCCTTTCGCCCTGCTGCCTCCCCAAGACAGGTGGAATCTCTGATACATAGAACATTGTCCATGGCTCCTGTGCCTGGCAGACATCACCAATTGAGCCTAGATGAAGCCTCGCAACCCTTTCCTGGATAATGCTCCCTGCAGCTCCTGTTGAGGAAACAGAATCTCCTCATGAGATTGAACTGATTTTTCACCCCCACGGAGCCCTTGACTTTGCCACAACTTTCCATTCGGTATAAGTAAGCCTTCGTCTGTAAAATGGGTAGAGCAGCTAGTCTAAGAATCAAGCCTGAGGGTGTGAGCTGAGGCAGGAATTCTCCCTGGCTCTAGGGAATGAAGTTCTCTTCCGTTCTCCTCACAGCCATGGCTGGACACTGCTGGTTGCCTCCTGTAGGGCCCCTCTTGGGTCCCCATGGTGAGTCACGACCCTAGGCTCTGAGCAGACTCCAGGGGTTGCTGGACTGGAGAAGGGGGTCTGTGGTATCCTCCGTCTTCCAGTACCAAGAGTTGCCATACCAATAGCATGTATATACTATAGGTCCTGTACAGAGTGAGCCCCCGAAAGACTGGAAGCCTGAGCCAGGGTCTCCCTTTAGGTGGGGCCCTCAAGGTGAAGAGGATTATTGCTGTGCCTTCCATTGGTCGGGAGAGCTGTGAGACAGGAATAGTGAACAGTGTCCAATTGTTGTCCCTGCCCACCCTTGCCCCCCACCCTGGCTCTGCCACCCCATCCATCCACTCCTGCCAGCATATTTGTGGTGTGGCCTCTGTTACCATCCATCCCAACTTCTAAGACAGGGATCTGAGGTGCAAGGTGGCCACCCAGCCAGTAGGTGGCAGAGCCACACCTCTTACCCACCGAGGGGCGGGTTAGAAGGTTTTCCCAGCTCACACACACAAACCTTAAGTGAACCCAGGCAGTCTGGCTCAGCCGGGATTTACCCCAAGCTCCTGTCTCTCTAGTCTACCAATGTGTGTCCTGCAACTCCTCCACCAGGATACTCACTGTCTAGGGTAGCAGTTCTCAATCTGTAAGTCGCAATGTCTTGGCAAACCTCTATCTCCAAAAATCTTTACATTACAATTCCTAGCTGTAGTAGCAAAATTACAGTTATAAAGTAGCAACAGAAAAATCTTTATGGTTGGAGGTCACCACATCATGAGGAACTGTGTTAAAGAGTCGCAGCATGCCGGGCAGTGGTGGCGCTTGCCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGGTGGATTTCTGAGTTTGAGGCCAGCCTAGTCTACAGAGTGAGTTCCAGGACAGCCAGAGCGACACAGAGAAACCCTGTCTTGAAAAACCAAAAAAAAAAAAAAAAAAAAGAATCGCAGCATTAGGAATTAGGAAGGTTGAGAACCACTGTTCCAGGGGCTTCTGGACTGAGATAGTGAACAAGTGCCTTGCTCCTTAG
Seq C2 exon
GGATCTGCCTGTGTGGCCACCACACCGAGGGTCCATCCTGTGAGCGGTGCATGCCAGGTTTCTACGGTAACGCCTTCTCAGGCCGTGCTGATGATTGCCAGCCCTGTCCGTGCCCTGGCCAATCAGCCTGTGCAACCATCCCAGAGAGTGGAGATGTGGTGTGCACACACTGCCCTCCTGGTCAGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026840-Lamc3:NM_011836:12
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:
PF0005213=Laminin_B=PD(19.3=34.2),PF0005319=Laminin_EGF=PU(28.3=17.1)

							
A:
NA

							
C2:
PF0005319=Laminin_EGF=PD(69.6=50.0),PF0005319=Laminin_EGF=PU(52.8=43.8)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000028187





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000028187f2010A
          









    
Other Skipping Isoforms:
ENSMUSP00000118745
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr9:133932535-133936421 
LOW PSI
HsaINT0090535
(LAMC3)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr11:101287608-101289327 
LOW PSI
BtaINT0084429
(LAMC3)
Chicken
(galGal4)
chr17:6071839-6072841 
ALTERNATIVE
GgaINT0124020
(LAMC3)
Chicken
(galGal3)
chr17:6689445-6690451 
ALTERNATIVE
GgaINT0124020
(LAMC3)
Zebrafish
(danRer10)
chr5:33897043-33918724 
LOW PSI
DreINT0088248
(lamc3)
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"