Special

MmuINT0065121 @ mm9

Intron Retention

Gene
ENSMUSG00000036053 | Fmnl2
Description
formin-like 2 [Source:MGI Symbol;Acc:MGI:1918659]
Coordinates
chr2:52985887-52989492:+
Coord C1 exon
chr2:52985887-52986010
Coord A exon
chr2:52986011-52989445
Coord C2 exon
chr2:52989446-52989492
Length
3435 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAG
5' ss Score
9.65
3' ss Seq
TGTTTTTGTTTTCTGTTTAGCCT
3' ss Score
7.81
Exon sequences
Seq C1 exon
TCTCCTTCCCATAAATCAAAGAGGCAGCAGCAAGAGTTAATTGCGGAATTAAGAAGGCGACAAGTTAAAGATAACAGACATGTATACGAGGGAAAAGATGGCGCCATTGAAGACATTATCACAG
Seq A exon
GTAAAGGGTATTTCGTCTTTGTGGTCTATAGTGATCACACTGCCTCGTGGACGTGGGGCCACATACACATGTTCCTTTTGGTAACAGTTTAATTTGGTTAATGAGATGTAGAATTATGCAGCAAGATTGTAAACTAGGGTTAGAAGTACCTTCTGATAGTGTTTGCCATCCAACACCCTGAACAATCTTGTCCATTCTGTGAGGACCTTTAGGTAGTCTTCCCTAAGTTCCCTATTGGTTTGATTTGTTATAATTCACCATTTCCTCCTTGTGTCCACTCCTTATTGCTTGCCCAATAGAAATAATGCAAGAGAATCCATTTTCTGTACTAACAGTTAATGTAGGTTTCTCTGGCATGCTCTTTAAAAACCTCAAAATAACAAAGCCAACAGGAAGTTAGTATTTTTGGTTTGATGAATTTTTAGGATTCTCAGAACTGGGGACATAGCTTATTTATTTATTTATTTATTTATGTTTGTTTGTTTTCCCAGCTTAATATTTTTCTTGAACCAATTCTCCAGGGTTTTATATTGCCTCTTATTGATGAGGGTGGTAACTTAGGCTGCTGGACTATTTAGCAGTAAATGACTTTTGTTCAATGTCTTTTCCACATGAAATCTGTTTATCAGTTAAGATACTTCAGACATTTTTCTCTTATGGTAAGGTTTAAAAATATGTTCAAGTATAGACAGTTATATGATGCATGTGCAGGTGTTCTTTACCATTCTCAACACTAAGCAACAAAGTCAGTCCTGTTAAGTGTAAGTGCTAGGCCTCTAGTCTCTCAGGACTCAATCCTCAGGTCCTCAGGCATTCCCTAGAACCTCATTTGGAAATATTCAAGTATGCATCTTTTAAACTTGAGGATGGATACTTATAAAACAAAGCCAAATTATAATCATATTAATCTTTATCATACTCAGAAGTAAACATTCCTTAATATTAAATTTGTAGCTATTCATATTTCCCAAATTCTAGTTTGTCAAAAATATAATTGATTCATTGCACCTTCTTGTAGCTTACTCAAAATCGTGAATAGGGATATCAAGGTTCTACAAGCACAGACTCTTGATCATTTTAAGCACAGGAACATTAAGCAGAATGTCGATTAGATTTTTAAAGTCAAAAAAGGACTCCTTGGCTGTTATTAAAGAAGCATAAATGAGTGACTAGTAAAAAAATGGCAATTTCTCCTCACGGAGCACACGTGGTGTCAACATCCACTATGCAGTGGCTTGCAGAGCCCCCTTGTGGGTTAGTTCTCTGCCTCCTCTGCACAGGGAAGTTCTACTCTGCATGGCCTATGAAGGTGAACACCTAAGTGTCACACCAAGACTAACTTGAGACCAGGAAAGCATCCAACTTCGTACATTAAGAACTCATAGGCAGACCATAGTGGGACCTTCTCTAATCCTGGTACTGAGGATGTTGGAGGAAGGACGATCGGGAGTTAAAGGTCATCCTTGACTTGAGTGCAATTCAGCTCCTGCCTTAAAGACAAGAGAATGAAACTGCCCTCCATACCCATGACATCTTATAAAATGGACAGTGTAGATTCGCCTGTATCTCAGAATAGTTTTTCCCCAGTCCTTTTCACTCCTCGTTTCCCAACCCCGAAGTCGCAGACTTGCTTCTGACTTTAATGCCCTCTCCCACCCTTCCTCTTCCATTAACCATGAACTAATGCAATAGCCGCTGGCTTTTCACTCGTGTGTTGTCTGGCTGTTATTCTCAATGCAGTGCTGAAGACTGTGCCCTTTACCGCTCGCACCGCCAAGCGTGGCTCTCGGTTTTTCTGCGAACCTGTTCTCACTGAAGAATACCATTACTAAACTATTGCTCTTTGTCACCTGATACTATTAAAAGGTCACTACAGGTTTTTTTTTTTTTTAAAACCTCTTATCTCCCCTCCTGCACCCCTTATGTACACCCTCCATGTCTTAGGACAAACCACTATGCTAGCGTGGAATGCTATCTTCATTTTACATTTTCTGTTGTCTTCGTGCTGCATGGTTTTGTATTTGTCATGACTATACACTCACTGCCATCTTCAGTATATGTATGTATGTATGCATGCATGTATGTATGTATGCATGTATGTACCACATTCCTGCAACCATATGGATGTGGGTGACAGTTAATAGAACCAGTAGAATAAACAGTAAATGATTTGGGGACTCTTATCTTTTAAATGACAACAAACAGTAACTACAAAGACCACTATTCACTGAGTGTTTACTGTGCTCGAGTAGGTTGACTGAGAACACACCCTTCTCTATGCTAACATAGTAATAAAATGATTAAAAGGGGCAGGAAACAGTGACATGATCCGGCAGGTTAAGGTGCCTGCCAACTAAGATCGAGCCCCTGTAGCCAAGTGGTGAAGGGAAAGAAGCTGTTCTCATTTCCTCACCAGAGCCATGGCCCATGCTGCTCCCGGCAATAAAAATACAGATCGTCTACACTCTGAAAATGAGAGACGTTTTAAAGCCACACTAAAGACCTCTGCAAATTGGCCCTTTTCAGGTCTTCTACAGTCCTAAGTGTGCTAGAACTCAATATGAGCTTTATGCTGGGGACGCTTTTAACAATAAACCTTGACAATGCTGACCATAACCCAGCAGTTCATAGCCCATGTCCCCAAAACACTACCCTAGGCAGGTGACCTCTATTCACTGTCATGCCCTATTTCAGCTGTCAGCAGTTCCATATTAAGAGCAGAGATGCAAGGCAGGAGGTGCAAGCAAAGGCTAAGGCGCTCCCCATCTTTCTTATACTCTTTACTGGCAACTGTTCCATGTCAAACTCCTCTGCTTGGCAGGGTGGCAGCACAAATGCAGATAGTATACTTACTATTGAAAGGTTGCATTTTTTTCATAGAATTTAAAAACAAAGCGGGGAGATGTAAGATTTGTCCAGGTAGTGTCCTGGGGTAGTATTTGTTAAAAACGGAGTAGATATGTCTATGCATAGTTGCTTAGAAAAGAGACAAAGAACGTATTTCTAATTTTCGATAGACATGGACTATCTCCTGTGCTGAGGTTAATATGGAACTGGGTGTTTTGTGGCACAACTATTCTATGGATTATATTTGCTAGGTGTTCTTGTCTTTGCATCAAAAGATCTGTCATTGCCTGCTCTGCCTTGTTCTTAACCAGTGCTCATTAACTGGCTGAAAACTTTCATCTGCTCAACTGTTTGTTGTTGGATTGTCTGTCTTTCTGGAGCCAATCTTCAAAGCAGCTTGACCCTGGGCGATCAGGGCTGGGTGGGAAGACACTTGTCCTTCCCAGTTTAACCTAACACAACCTGTAGTAAAGGCTATGCCCTCTGTTAGCTAACATGCCCAGCATTGTTAAACACTAAGTTGAGTTGCTTTCTGTTTTCATCCCATTTTTACTTAACCATCATTTTGTGTTTTTGTTTTCTGTTTAG
Seq C2 exon
CCTTAAAGAAGAATAATATCACTAAATTTCCAAATGTTCACTCGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000036053-Fmnl2:NM_172409:25
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.569 A=NA C2=0.366
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0028516=Citrate_synt=PD(25.8=95.2),PF145131=DAG_kinase_N=PD(20.5=71.4)

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000047260





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000117822, ENSMUSP00000118658
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr2:152640915-152647795 
ALTERNATIVE
HsaINT0065139
(FMNL2)
Human
(hg19)
chr2:153497429-153504309 
ALTERNATIVE
HsaINT0065139
(FMNL2)
Rat
(rn6)
chr3:38674274-38675679 
ALTERNATIVE
RnoINT0061650
(Fmnl2)
Cow
(bosTau6)
chr2:43653052-43656625 
ALTERNATIVE
BtaINT0063179
(FMNL2)
Chicken
(galGal4)
chr7:35040705-35043746 
ALTERNATIVE
GgaINT0047766
(FMNL2)
Chicken
(galGal3)
chr7:37170058-37174530 
ALTERNATIVE
GgaINT0047766
(FMNL2)
Zebrafish
(danRer10)
chr9:4767305-4778737 
ALTERNATIVE
DreINT0069081
(fmnl2a)
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"