Special

MmuINT0091668 @ mm9

Intron Retention

Gene
ENSMUSG00000009207 | Lnp
Description
limb and neural patterns [Source:MGI Symbol;Acc:MGI:1918115]
Coordinates
chr2:74408992-74411683:-
Coord C1 exon
chr2:74411595-74411683
Coord A exon
chr2:74409034-74411594
Coord C2 exon
chr2:74408992-74409033
Length
2561 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGA
5' ss Score
9.21
3' ss Seq
TATTTCTGTCTCTAAAACAGGCA
3' ss Score
8.07
Exon sequences
Seq C1 exon
CTGTGACTTCTTTTGGACAACTCATGATATTTATTATTGTGCCAAGTTTCTGCAAATAAAAGATGGGTGGATTATTTTCTCGATGGAGG
Seq A exon
GTAAGAAAACTTTTTCTGTATTGCTAATTTTTAAAATCTAACAAAAAGTATTACAAAGATTTTCACAAAGTTATCCTTTAGAGTATACTTTTGAATGAGTTTGAAATGATGTATTTAATTCCATTTAAGTCCATTAGAATTACTTCTTTGGATATTATTTTGGTAGTTCTATTTATTTTATGGGTATCTAATATGTCTAGTAATTTATTTTTATTTATGTATTTTATACAAGTAGTTTTCTTACAACAGTTTCATACTGCCCAAGTTCCAAGTTTATTCTAAAAGTAGTTGAAATTAAAAATTTTATACCATACTTACGGTTTTTGTATACTATTCTATCTATCTAATCTGTCTGTCTGTCTCTTTTAGAGACAGGGTTTTACTGTGCAGCCTTGAACTCAGAAATTTGTCCTGCCTCTGCTGGTATTAAAGGAATTTTTGTTTGTTTTGTTTTGCTTTTTTATTAGCATGTCACATAAATTTACTGATACCACATTAAATATGCTTTTGAGAGTTATAGGTAGAACAAAATTAAAAATGCAGATTTTATTAGATAAGCCTTTAGAGAAAGTATCTCAAATTTAGAGATATAAAATATAAATTATATTGATAAATACTCTTCTAATGTAAGAAGAGATAATGTAGTCTAAGATAAACTAATTACCTTATTCTTTATCATAATAATAGAGTCTAGTAATACTTGGTAAATAATTTAGCTTCTGACTTGTTAGATCCATGTTTTAGATTTGTGTTATATTGACTTTCTTTCTCTTTTAAAAAATCCCCCCCAAACAAATCCACAGGTAAAAACAACATATTTATTGTATATTAACATGATGTTTTAAAGTGTATACATTACATTGTTTAGCTATAGCTAATTAACATATGCATTAACTCATAATTATATTTTTTGTTGTGAGAAACATTCCCTCTGTTAGCATTTTTCAAGAATATAGTATATAGGGCTAGAGAGATGGTTAAGTGGTCAAGAGTACCTGTTCTTGCCAAGGACTAGAGTTGAGTTCCCAGTGCCCACATCAGGTCATTCACAACTGCCTGGGGCTCCAGTTTCAAGGATCTGGCACCTCTAGCCTCCCATGATACCTAAATTCGCATTCGCGGAACTACACACAGAAACATATGTATATGCATACTTTAAAATGAAATAAACTCACAAAAAGAGTATAGTTATCTTTATAAGCTGTAGTCACAACGTAGAACTTGCTATGTATTTTGTATCCCTTGACCCCCAAAGCTTTCAGCTCTTCAACTCTCTACCTCCAGTTCCCTTAGATTTCTTACTTTCTACTTGATGGGATCTCATTTTTTCATTCCACAGATGAATGAAGTGACTCCTCTTTAAAAGTCTTTGACAGAGCCAGGTGGGGGGTGCGGGCACGGTGGGGGTGGGGGAAGGGGCGCTGTTTATGCCTTTAGTCCCGCACTTGAGAAAAGGAGGCAGGTGAATCTCTGTTAAGTGAGAGGTCAGCCTGGTCTGCAAAGTGGGTTCCAGGACAGCTAGGGATGTTGTTACACAGGGAAACCCTAACTCAAAGAACAAAATAAAACAAAAACAAAAACAAAAAATTTTGACAGACTGAGATTTAATTTATTTTTTTTTTAATTTGGTTGAATTATATGAAGTTGCTGATATTCTGCTTTGACATACAAAAATGGCAATTTTTCATGATTCAATCTTACATTATCAACTCTTGTAGGGATATAATACTGTTATAAATATTTTCTCAATTGCCATTTGAACCATTCTGGCTTATATAGAAATACCTTTGGCAAATAATCTCTGCTATTAGAAAGTATTCCTATATACTCTTTAACGATTTCATTTTTCAAAAGCTGTGTACTTAGGGCTAGAGAGATGGCTTAGAGGATAGAGCACTGATTGTTCTTCTGGAGGCCCTGGCTCCATTTCCAGGACCTCGTTGGTAGCTCACAGCCAGCTATGACTCCAGCTACAGGAGATCCAGTGCCCTCTTCTGGCCTCTTTGGCACCAGGGATGCACATGTTATATAGATACACACAGCCACATATCTATAATCATTTAAATCAATCAATCAATCAATCAAACAAACAAATGAAAAAAATCCCCTCTGGAACTTTGGGAATCACAGGAAGATAGTCTATTTTTTAATTTTTAAAATTTATTTTTTACCTCCAGAGCCCCGTGGGGCGTCACTGCTGAAACCAGTTGGTAGCTGCTAGCACAGAGCCTGGGCACTACTGAACTAGACTCTCTTTATTTAGTTCCTCAATCTTTTGGTATATGAATCCCTTTGGGTGAAAATATGTTTCTCTCTATAAAAATCTGTTGAGGTTAAGACTGGTAAAAGTAGAGCTATCAAAAGTCAAAAGTTATTTCAAGAATCTTACATAGTTTGGTAATTGTAGTTTTTCAATTATAGTTATGAACAGATAGCTTGGTAACATTGAGAAACCTAGTTGAGAATTAAAATGGTCTTTAAGGACTACATAAGTGTGTTTTTAACAAAATGTTTGTTGTAACAACTTTTAATGCCAGGTCTTATTTCTGTCTCTAAAACAG
Seq C2 exon
GCAAAACCTTCAACAGTAGAAGTTCTAGAAAATATAGATAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000009207-Lnp:NM_027133:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion (1st CDS intron)





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
PF136871=DUF4153=PU(8.7=64.3)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000066891





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000099737, ENSMUSP00000107624, ENSMUSP00000120494, ENSMUSP00000122488, ENSMUSP00000123058
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr2:175993224-175995557 
ALTERNATIVE
HsaINT0087118
(LNPK)
Human
(hg19)
chr2:176857952-176860285 
LOW PSI
HsaINT0087118
(KIAA1715)
Rat
(rn6)
chr3:61486155-61488669 
ALTERNATIVE
RnoINT0085901
(Lnpk)
Cow
(bosTau6)
chr2:20946982-20948572 
LOW PSI
BtaINT0081321
(KIAA1715)
Chicken
(galGal4)
chr7:15872638-15873776 
ALTERNATIVE
GgaINT0049396
(KIAA1715)
Chicken
(galGal3)
chr7:17484285-17485426 
ALTERNATIVE
GgaINT0049396
(KIAA1715)
Zebrafish
(danRer10)
chr9:2025433-2026437 
LOW PSI
DreINT0089798
(lnpa)
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"