Special

MmuINT0089782 @ mm9

Intron Retention

Gene
ENSMUSG00000026840 | Lamc3
Description
laminin gamma 3 [Source:MGI Symbol;Acc:MGI:1344394]
Coordinates
chr2:31758950-31761316:+
Coord C1 exon
chr2:31758950-31759116
Coord A exon
chr2:31759117-31761127
Coord C2 exon
chr2:31761128-31761316
Length
2011 bp
Sequences
Splice sites
5' ss Seq
TGCGTGAGT
5' ss Score
7.55
3' ss Seq
CAACCTTCCATCTCTCCCAGCCT
3' ss Score
6.84
Exon sequences
Seq C1 exon
GTGCAAATGCAATGGTCACGCCAGTGAATGCGAACCCAATGCGGCTGGTCAGCTGGCTTGCCGCTGTCAGCACAACACCACAGGAGTGGACTGCGAGCGTTGTCTGCCCTTCTTCCAGGACCGTCCGTGGGCCCGAGGCACCGCCGAGGATGCCAACGAGTGTCTGC
Seq A exon
GTGAGTGTTTCTCAGGCAGCAGGCCTTGAAGCTAATGAGACTGACAGGAAACAATGCCCCAAACCACAGTGGGCTGCCTGTGCCCCTGGGTGGGCCTGGCATTCAGTGTGGGGTCCTTGGCTGGGCAGGAGAGTGAACATGATGTCTAGGGAGCACTTGAGCCCCAGTCCTCCCTCACAAGTCATTCCAGGATGAGTCCACCCAGAGAGGCGCCTGTGGTAGGAGGGCAGGAAGGTCCCCAAACTCCACTTAACCCTTTCTTAACTGTTCCAACCCTGGCAGCTAATGAAATCCAGTCTTCCACCCCCACCCATAGGATTCAGATCCGCCCACCCCAGTCTTTCCCACAGTCCCCCCGCAGTCCCCAGCAGCCCTTTGATGTTTCAGCTGTGTGTGGTGTGGCTCTGTCTGTTTAACCTCAAAGACATGCTGGTGAAGGAAGGAAGGGGCCCTGGAACCTTCTGCAAGGATGGTGGAGAGGGAAAAGAAGCCTTCCCAGTGTCTGTACCAGCCACTCCAGCATCCCACTTGCCCTGGTCCAGCCCATCTCCCTTCACGGTCCTCCTCTGCTTCCGGCTTCACTGTGTGGTGCCTGGAGCCAGGCACAGAATTCCACACACAGCCTCTCGCAGCTGACCTCCTGGGCTCGGGCCATAGCCTGCCAGAGCTGGGGGTGTTGAGGAGACAGCTTTTCCTTGAGATAGGACAGCTTTTTTTTCTGTCTGTAGGAGCTGCCTCAGGGCCCAACACAGTCCTAATGAGTTCCTCTTGGCTTGATCGGCTGCCTCCCCCAGGGAAGGTGTGCTGGCTCCCTGCTTGGGCCAAGTCTGTGCCTGTCTCTACGTGGGAGGGGAATGCTGAGAACTAGCCTGCTCCCCTGCCAAGCCCTTACCCCGGCCACCAGCCTGAAAGATGCAGGTTTCATGCCTGACCTTTCACCCCATGACTCCCAGCCCAGGCAGCCTCTGAGCCCTAAATCCCCCTTCTTTTGCATCCCTTTAATCCCTCTCTGCAGCCCTCTCCTCTGGGTGCCTGCTGTCTCCTCTCCTCTGTCTCCAGCCTCCAGTGAAGGGTCTGCAAAGAGTGCGAATACAGCTCTGTCCCTCCCCTAGTCCCCACCTCCACCCCCAGCCTCCTCCCCATAACTCCAGCCTCCTGGTAGCTCTGACTCAATCCGCTGGGCATCACACATCAGTTACCTCACTCTATCCCCTCCGTGGCCATCAGGAGGCGCGGTGCTCGCTCCCAGCAAGCCTCTTAGCATACACACACCAAGCAGATAATGCTTCCCTGGTCCAGAGTGTCTCCCCCTGGCTCCGATACACTTCTGGCTCCATGGTCCTCCTCTATTAAAACACCTCTCTGCCTCTGTCCGGGAAAACATTGTTTTGGAGAGTTTATTAATGAAGCCCACCTAGTTCTTAAAGAGCATCCTGTTTGGGAATACCAGATGATGGGGCTCTGTGTTCTGGGTCAAGTTGAGCCTAGACTCTGGCCCTTCCTCTTAGTCACTTGTCTTGTTGCTATGACAAAATGCTCCACAGAAGCAGGATAGGAAAGGAAAGGTTTGTTTGGGCTCACAGCGTGAAGGTACAGTCCCCTCACGGTGGGGACGCCATGATGGCAGGAAAGTGAAGCAGCTGGTCACATCACATCTACGGCCAGGAAGCAGGGAGAGATGAACGATGAGGATAATATATATTATCAGATCCCATTATAGATGGCTGTGAGCCACCATGTGGTTGCTGGGAATTGAACTCAGGACCTCTGGAAGAGCAGCCAGTGCCCCTAACCACTGAGCCATCTCTCCAGCCCCCAGTGCCATCCATTTTTAACGTGGGTCTTGCCATGTCAGCATACTGTAGAAATCACTGAACCTAGGAGAAACCTAGGAGGTTGACAGGATGAACCAAGCACACCCATCTTGGAGATGCCTCCTGCTTCAGAGAGCATAGTCTCTCAGCCCCAGCAGAGGCCATCACTCTTACACACAACCTTCCATCTCTCCCAG
Seq C2 exon
CCTGCAACTGCAGTGGGCACTCTGAGGAGTGCACGTTTGACAGGGAGCTCTATCGGAGCACAGGCCATGGTGGGCACTGTCAGCGGTGCCGTGACCACACAACTGGGCCACACTGTGAGCGCTGTGAGAAGAACTACTACAGATGGTCCCCGAAGACACCATGCCAACCCTGTGACTGCCACCCAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026840-Lamc3:NM_011836:4
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:
PF0005319=Laminin_EGF=WD(100=94.7)

							
A:
NA

							
C2:
PF0005319=Laminin_EGF=WD(100=84.4),PF0005319=Laminin_EGF=PU(13.3=9.4)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000028187f2010A





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000028187, ENSMUSP00000118745
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr9:131036333-131038863 
LOW PSI
HsaINT0090553
(LAMC3)
Human
(hg19)
chr9:133911720-133914250 
LOW PSI
HsaINT0090553
(LAMC3)
Rat
(rn6)
chr3:9308215-9310201 
Cow
(bosTau6)
chr11:101273579-101275657 
LOW PSI
BtaINT0084452
(LAMC3)
Chicken
(galGal4)
chr17:6068460-6068617 
LOW PSI
GgaINT0124012
(LAMC3)
Chicken
(galGal3)
chr17:6686068-6686225 
LOW PSI
GgaINT0124012
(LAMC3)
Zebrafish
(danRer10)
chr5:33851272-33857478 
LOW PSI
DreINT0088266
(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"