Special

MmuINT0089644 @ mm9

Intron Retention

Gene
ENSMUSG00000002900 | Lamb1
Description
laminin B1 [Source:MGI Symbol;Acc:MGI:96743]
Coordinates
chr12:32008327-32009185:+
Coord C1 exon
chr12:32008327-32008530
Coord A exon
chr12:32008531-32009040
Coord C2 exon
chr12:32009041-32009185
Length
510 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
TATTTATTCTTCATGTTTAGGTC
3' ss Score
9.73
Exon sequences
Seq C1 exon
ACCTGTGGAACACCTCCAGGGGCTGACTGTTCTGAAAGTGAATGTGGTGGCCCCAACTGCAGAACTGACGAAGGAGAGAAGAAGTGTGGGGGGCCTGGCTGTGGTGGTCTGGTCACTGTGGCCCACAGTGCTTGGCAGAAAGCCATGGATTTTGACCGTGATGTCCTGAGTGCCCTGGCTGAAGTCGAACAGCTCTCCAAGATG
Seq A exon
GTGAGTCAGTGGATGGCCTCAGGTTTCGCTGTTTGTTGGCTTGCAGTTGTAGGGAGGGTCTGAAAAGGAGTCAGTTCCACATCACTAAATTCACTGTCCAGTGTAAAGCTGATGTTTCTGTGTGGTCAAAAAGGTGATGGTGAGGTTCTTAATCACTTAATCAGACCGGGAATTTGCTTTCTCTCCATGGGAATAGCATGTATGTTAGGAGAAAGCAGCGTAAATCTTAGATAAGCCATATGCGTGAACAAAGTTGAGCACGGTTCTAGAGTGACATTCTCCTCAGTCCACAAGCTGTTTTAGAGCCAAAACACAGCTTTGAACACATTTCAAACGCTAGCCCTAAGAATATTGAACAGGAATGTGCATATTGAGTGCTTAAGTCTACATAAAAGCATCATATTTTAACAGACAAATTTGCTTCTAAGTTTGTTGCCATCAGCTTGTTTGACCCTGCTTTAGAGAGAGCAAGCTGGTTTCATAGATGGCTTATTTATTCTTCATGTTTAG
Seq C2 exon
GTCTCTGAAGCAAAAGTGAGAGCAGATGAGGCGAAGCAGAATGCGCAGGATGTCCTGTTAAAAACAAATGCTACCAAAGAAAAAGTGGACAAGAGCAACGAGGACCTGCGGAACCTCATCAAGCAGATCAGAAACTTCCTGACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000002900-Lamb1:NM_008482:27
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.324 A=NA C2=0.531
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000002979





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000132778
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr7:107931501-107932173 
ALTERNATIVE
HsaINT0090386
(LAMB1)
Human
(hg19)
chr7:107571946-107572618 
ALTERNATIVE
HsaINT0090386
(LAMB1)
Rat
(rn6)
chr6:50590490-50591015 
LOW PSI
RnoINT0084091
(Lamb1)
Cow
(bosTau6)
chr4:49271633-49272123 
LOW PSI
BtaINT0084274
(LAMB1)
Chicken
(galGal4)
chr1:14686357-14686739 
ALTERNATIVE
GgaINT0112338
(LAMB1)
Chicken
(galGal3)
chr1:15864576-15864958 
ALTERNATIVE
GgaINT0112338
(LAMB1)
Zebrafish
(danRer10)
chr4:25756476-25756809 
DreINT0088126
(lamb1b)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GAACACCTCCAGGGGCTGA

				
R: 
CAGTCAGGAAGTTTCTGATCTGCT

				
Band lengths: 
342-852

			

		

	





	
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






Retrieved from "https://vastdb.crg.eu/wiki/Special:VastDB"