Special

MmuINT0089730 @ mm9

Intron Retention

Gene
ENSMUSG00000026478 | Lamc1
Description
laminin, gamma 1 [Source:MGI Symbol;Acc:MGI:99914]
Coordinates
chr1:155066052-155070888:-
Coord C1 exon
chr1:155070789-155070888
Coord A exon
chr1:155068860-155070788
Coord C2 exon
chr1:155066052-155068859
Length
1929 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAGT
5' ss Score
9.66
3' ss Seq
TGTCCACTTCCTGTCTACAGGAC
3' ss Score
11.08
Exon sequences
Seq C1 exon
GCTTCGCAGGCTGCTCAGGAGGCTGAGCTCAATGCCAGAAAGGCCAAAAACTCTGTCAGCAGCCTCCTCAGCCAGCTGAACAACCTCTTGGATCAGCTAG
Seq A exon
GTAAGTAACAGAAGGGTTGCTGCAGCCACCGCTTGCAGGGCTGAGTCCACTGATGCAGAGTCACATTCTCTAAAAGCATCATTAAGGCATTCATATTAATGTTTTGTTTAGCTCTTGCTTATTTAAAGACACCTTGTACACAGTGTCTTGCTTGGCAGAACCTTGTAAGGGCAGCTTGCATCGGCGCGACACTGATAGGCTGTCGATTCTAGAGTGAAGGCGAATGGGACTCTATTAAGTTCAAGTACTTAGGTGCCTTCCCTGGGGCTGAGATGAGCTGCCAGCTAGGGATGCCACTATGGCCAAGGTCCAGCCTACAGTTAAACAGCCATTTCCTCTTAGTTCTGCCTGCTGGTGGAGCGTCTTTAAGGGATTTGAAGAGAAAGGCTCAGTGGGAGAATAAAATAATACTTGAACCTGACTGCACTTCAGAGCTCAGAATTCTCTCCACTTGCCAACCAAAGAACAATTTGATGAAGTGAAAACTTTCACACCAAACAAGAGAAAAGCTTTGTTTTGTCTTATCTTGTTTCAGGGACATATAAGCGCTGAGCTCTCAATTTAACCCAGTGTGGTAGAGAACTGAGCTTTCTTAGGACCTCCATTACGAGAGAGTCATATAGCCACCAAAGACTGGGGATGGATTCTTTTATGTTTTTTTTTTTCTTAAAGGGAAGAGAGATAATATTTTATCTGTCTCAGAGACCAATAATAATAAATTATGTGCCTAGAATGAAAGCAAGCTAAAGCAGGGGCTTTACACCTTCTTTATCCGTTAGGTTGTATAAATGCATGCAAATAATTCTTGACCGTCTGTACTTGCTGGTTTTGTGTCAACTTGACACAGGCTGGAGTTATCACAGAGAAAGGAGCTTCAGTTGAGGAAATGCCTCCATGAGATCCAGCTGTAAGACATTTTCTCAATTAGTGATCAAGGGAGGAGGGCCCTTGTGGGTGGTATCATCCCTGGGCTGGTAGTCTTGGCTGTATAAGAGAGCAGGCTGAGCAAGCCAGGGAAAGCAAGCCAGTAAAGAACATCCCTCCATGGCCTCTGCATCAGTTTCTGCTTCCTGACCTGCTTCAGTTCCAGTCTTGACTTCCTTTGGTGATGAACAGCAACATGAAAGTGTAAGCTGAATAAACCCTTTCCTCCCCAGCTTGCTTCTTGGTCATGATGTTTGTGCAAGAATAGAAACCCTGACTAAGACACCATCTGAGAGTTGGTGAGGTAGACTGGGCTCAGGAAACTGCTTGTCTTTCTGTATGATTTTATTTTCTATAGAGCATCTTCTTCCAAAAGAAACTATTATTTTTTTCTTGATATATTTAGAGCAAAGCTTTGCTTACAGATCTCGGCATTTTAACCTTGGTCGTTTTTCATCAAAAGGTTGCTAGTGGTGTGTAACGCCTACAAGCAGAAAGTGACCCCCAAACGGCCCCATTTGAATCCCAGGAGTTGAGGATGTATGCTTCTATCTTAGAGACTTTGGCATTCTTTGACGATACTGAAATGGACCACAGATTACACCTAGATTACACATAGAAACCTGCAGAGGATTGAGTCTTACCAAGTCACCTTCTTCAGCATAAGCGAGGTCTAAGACATGGTGCTTATACATTTAGAAACACATCCTCCGAGGGCTAGAGAGATGGCTCAGTGGATAAAAGCACTAGCTGCCAAGTTGGACAACCCGAGTTCAATCCCTGGAAACCTCATAGTGGAAAGAGAACCAAGTCCTGCAAGTTGTCCTCTGACATCCACACACATGCTATGGCATTCATGCAGACACGCATGTACACACATGTGCATAGTGATAAGTAATAAATATCAAATTAAAATATTGTGTGAACAAAGCTTTGTCAAAAAAGAAATCTGTCCTAGTATTAATGATACACGCTACTTCTCCTCTGTCCACTTCCTGTCTACAG
Seq C2 exon
GACAGCTGGACACAGTGGACCTGAACAAGCTCAATGAGATCGAAGGCTCCCTGAACAAAGCCAAAGACGAAATGAAGGCCAGCGACCTGGACAGGAAGGTGTCTGACCTGGAGAGCGAGGCTCGGAAGCAGGAGGCAGCCATCATGGACTATAACCGGGACATAGCAGAGATCATTAAGGATATTCACAACCTGGAGGACATCAAGAAGACCCTACCAACCGGCTGCTTCAACACCCCGTCCATCGAGAAGCCCTAGTGGCGAGAGGGCTGTAAGGCAGTGTCCCTGACAGGGGACCCTGTGAGGCCTCGGTGCCTTGACACAAAGATTACACTTTTCAGACCCCCACTTCTCTGCTGCTCTCCATCACTGTCCTTTTGACCCAAGAAAAGTCAGAGTTTAAAGAGAAGCAAGTTAAACATCTTTAACCAGGAACAAAGGGTTTTGCCTAATAAAGTCTCTCCTCCACTTCTGTCAGCACCCTACCGGAACTTTCCCTTGTTTGCCTGAAGTCACGGCATCTTCCAGGGGCCTACCCACATCATGTGAACCTTTTAATGCCAGGGCAGACCCAGCCCCCTCCCCTCTCTCAACACCAGCAGGACCTATCTCAGTACTCATGTTTCTATGAAGGAAATCTTTGGCTCCTCATCGTAGCATTGAGATGGCCAGTATGTCCGCTCTGCATCTTCTGCCTCCTCTTTGAAAGGAAATAAACATCCTGTGCCAAAGGTATTGGTCATTTAGAATGGTGATGGCCATCCATCAGACATGCTGGCTGGCTGAGCATAGGACACAGAGCCATCGTGGGTGACAGCGTAGTTACATGTGGGTCCCCAGGAGAACATGGCTCAAAGATGCTTAGGGTTTCCTCCTGTTTTCATTGACTAGGAAGATGAATGTTTCCCAAATCCTCAGGCAGCTGATAAAAAGTCTGGATGGGCAGCTCGCACGCACCACTACGTGAGGTAGCTTTTGATATTTTTATAAGCAGGACTTAATGCAGAAGAAACAGATGTGATAACCCACTCAAGTTTTTTTCCCCAAGTAGTACTAATTCTTGAAGCTTTGTTAGTGTTAGTCTTGGAACTGTTGGTAAGATATCTGTCAAAACAGTTGTCCTCTAAGGTCTTGACCAATGAAAGAAGAGCAAATCTCCTTTTCCCCATATTTTCTGGGAAGTGGCTGTAATTGGGATGTAACCGCTCTCATTAGGATTCCATGAGTGCATTTCTTTTTCTCTTTTTCTTGGAGAGAGATGTGACATTTGGCCCTTAGCTCCATTCTCTTCTGATGTTTCCGTTCTTTCTAGAACTCTTCAGAGCACATCGTTGTTTGCCAGGTCCTGGTGGCAAACACCCGCTCTCAGTGTTTCTCAAGGCTGCCAACCCCATCTAGTTCCTGCACTTTGTGGCTCTGCCCACTCCAAGCCTTTCCTCTGTGTGGAGAGGGAAGATCCATGCGTGGCATTTCCTAGTGGGCTTCTCAACCTCTGATCCTCAGCTCGGTGGTCTCCTTAAGACCACACTGTGACAGTTCCCTGCCACACATCCCCTTCCTCCTACCTACCTGCCTCTGAGATTCATATTTAGCCTTTAACACTATGCAATTTTGTACTTTGCGTAGCGGGGGAAAGAAACTATTATCTGACACACTGGTGCTATTAATTATTTGAAATTTATATTTTTTGTGTGAATGGATTTTGTTTATCATGATTATAGAGTAAGGAATTTATGTAAATATCCCCGGTCCTCCTAGAACGGCACTGTCTGCTCACGTCTCTGCTCAGTTGTCCCTCTCACTGGCACAGGAACCTGTACCATGCCTGGTCACGTCGTGCCTAGTCCCCAGTGTTTTGCTCCACCTCTGCCTTGTGTTTGCAGCACCTTCACTGTCTGACGGGAAGCCTGCTCACCTCCACAACCTGACCGAAGAGGGCCCTCTTCCCCGTGGCTCTGACCATCTGAGCTGCAGCTCCTCAAGGTTCTCATGCCTGCCCCGGAGCAGTAGCCAAGCTGACAGGGTAAAGGGATTAGGAACGTTTGTTTGTGGAACCTTCCCACACGGGTCAGTTTTCTAAGGGAGCATGTGATGACTGAACACTTGAGGGCATCAGCACCGTGCTACTGATGACAGAGGGGAGGCTCTGTTCAGCCTGTCTCCATCTCGGAGATTGCCACAAAATCTCAGCTTGGCATCCTCCGAGGCCTTTTGTGCCACGGCAGAGGCGTGGCCTCACCAAGTTCAGTGCTGATTGGCTAGTTCCTCTATTCCGAGCTCACCACCTTAACATTTTGGTCACAGTTGCAAGAAAATGGCTGAAACAGACCACCACCAGCATTCTTTGGGTCAACTCCACTCCAGCAGGCCCGAGGCGCTGGTGGGTGGGGTGTTTTGGTTTGTTTTCTCCAGCTTTTGTGGTATATTTTTAAACAGAATTTTATTTTTTAAAATGAAAGTTATTTACAAGATGATACCTTATTACACTCCTTCGACACAGCCATTGCTTTATTGTATAGTTCCAATAACCTGTATTTTATGTAATGAAATGGACAGAATGGCTGCTGTAGAATGCGGGGTGCCGCACAGAACAGATTGTTTTATCCCTCCCCCGCCCCCGCCCATGGAATTTTCCTTTGATTCCAACTGTGGCCCTTTTCAATGTGCCTTCACTTTAGCTGTTTGCCTTAATCTCTACAGCCTTCCCCCCTCAGGGAGGGCAATAAAGCGCAACACTTGGCATTTTTTTATGTTTAAAAAGAAAACAGTATTTTATTTATAATAAAATCTGAATATTTGTAACCCTTTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026478-Lamc1:NM_010683:27
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.529 A=NA C2=0.439
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
PF115703=E2R135=PD(22.2=48.5),PF118393=DUF3359=PD(1.6=3.0)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000027752





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:183140504-183142533 
LOW PSI
HsaINT0090503
(LAMC1)
Human
(hg19)
chr1:183109639-183111668 
LOW PSI
HsaINT0090503
(LAMC1)
Rat
(rn6)
chr13:70659549-70661518 
LOW PSI
RnoINT0084177
(Lamc1)
Cow
(bosTau6)
chr16:65660403-65662353 
LOW PSI
BtaINT0084364
(LAMC1)
Chicken
(galGal4)
chr8:7497388-7497766 
LOW PSI
GgaINT0035400
(Gga.52643)
Chicken
(galGal3)
chr8:7835189-7835567 
LOW PSI
GgaINT0035400
(Q5ZIH4_CHICK)
Zebrafish
(danRer10)
chr2:35994395-35995482 
LOW PSI
DreINT0088231
(lamc1)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
AGCCAGCTGAACAACCTCTTG

				
R: 
TCTTTGTGTCAAGGCACCGAG

				
Band lengths: 
358-2287

			

		

	





	
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"