Special

MmuINT0065098 @ mm9

Intron Retention

Gene
ENSMUSG00000055805 | Fmnl1
Description
formin-like 1 [Source:MGI Symbol;Acc:MGI:1888994]
Coordinates
chr11:103043956-103047043:+
Coord C1 exon
chr11:103043956-103044081
Coord A exon
chr11:103044082-103046934
Coord C2 exon
chr11:103046935-103047043
Length
2853 bp
Sequences
Splice sites
5' ss Seq
CAAGTATGC
5' ss Score
5.38
3' ss Seq
GCCTCTTCCTCATCCACCAGGCT
3' ss Score
8.66
Exon sequences
Seq C1 exon
ATATGACATGGAAAGCACAGACAGTGTGGCCTCTGGTGCAGAGAAGAGCAAGCCCCTGGACCAGTCTGTGGAAGACCTCAGCAAGGCACCTCCCTCATCTGTGCCCAAAAGTCGCCTGACCATCAA
Seq A exon
GTATGCAGGGCCCTAGATGGGTTGATAGGGGAATGGAGAACAGAGACCCCCGTTGCCACATGTAAACAGGGCCCTGAGGGTTGGCGGGAGGTGTAGTTCAGTATGGGGGAATCAGATGTGTTGAGTTTTCAGCTGGAGACACCAGAGGCTAGAATCTGAGGGGGACTGGAATAAGGAGGGGGTTTGGGGGCTGGTAGGACCCCTTTTGTACCTCTCTAACCCCTTGTTTCTCCCTGTGTGGCCTCCAGGTGCCCCCCTTCTCCCCGGTACGTACATAGGCACCTGGGGGCAGGTGCATGCTGGGGGTAGGTGCATGCTGAGGGCAGGTGCATGCTGGGTCCACTCTGTGGGTGGTGGGTTGGAAGAGCAGTCAGCTGACACTCCTGAGTTCAGGTACTGTGGACCAATCTCCTCATCCTGACATAGGATATCTTGCCATCTTGTTGGGATGCAGGGAGAGAGAAGGAGATAACCCTGGAGCATCAGTTTCCTCTGTTGGGTCTGAGGGACCAAATATATGTTTATTTACTTGTGTGTATATATGTGTAGTATGGTATATGGGCATGTGTGTGTGTGCCAATAGCTGATCAAGAAAAGCATGGCTTTTACTTGGGTGCTGAGGATTTGAACTCAGGTCTTCATGCTTACATAGCAAATGATCTTACCAACTGGCCATCCCCACAGCCATTCATTCATATATATATATATATATATATATATATGTGTATATATATATATATATATATACACACACATACATATATACATATACATATATGTATATATATGCATATAAACATACATATAAATATACATGTAAATGCATACACACACACACACTGTGTGTGTGTGTGTGTGTGTGTGTATAAGTGTGTATGTATGGCATTGGGACTTGAGTCCAGGGCTTCAGGCATTATAGGCAAGTACTCTTCCACTGAGCTACACCCCCTAGCCTTATTAAGCCCCAAGACCTTGCAATATCTTTCTTTCTTTCTTTCTTTTCTTTCCTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTCTCTCTCTCTCTCTCTCTTTCTTTCTTTTCCTTCCTTCCTTTCTTTCTTTCTTTCCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCATTTACATAGCAATCAGTTTTTCCGACACTTACTAAATAGCACATATTAGTGGCAAGTGCCCACAAGACAGGTAAATTCTGCTTTTGGGGACCTCAGTCTAGTGGGAAGTCAATTTACTGTGATAGATCATCGCAGAGCTGTGACCTGGATTTCTGAGAAGGGAGGTGCCCATTTCTTGGAGGGGGGGGGGGCTACCAGGAAGACTTTCCAGAGGAGGTGACACTGGAACTATGTCTGACAAGTGACACACTTGTGATAGGCAAGTGATGGGACAGAGGGGCAGCATGAACAAAGACTGAGACACATTTGAGCAATCTAGGAAAGGCTGATGTGGCAAAGCAGCCACGAGGGCCCAGTGGGAGAGGTGCGGCTGGCCAGTGTGGCAGGAAGAGTTACAGAACTGTCCAGAGGATGATGTGGAAGATATGGTTAGCAGCTCTCCAAAAATGAAAATCTCAAATAAGTTTTTGGGGGAGGGGGGTCAAGAAAATAGAATACCCAGTATGCTCCATACTAGGTGTCAGGCTGGAGCTAATCACATGATCCAAACTAGCCTGTGAAGAAGGTGTTCCTGAAGCTGAGGAAATGGCCCAGTTAGAAGACGCTTGCCTTGCGAAGCCCCGAGTTCAGTCCCCAGCACCCAAGTAAAGAGTTGGTTACAGTGGTTGTGTGCTTATAATCCCAGCACTGGAGAGGCAGACAGGAGATCCCTGGCAGCCGACCCTCACTGGTGGGTCCCAGGTCCCAGTGAGAGATCTTGTTTCAAAAGAACAGATTGGGGGCCGAGGAGACTGCTTGGTGGGTAAAGTGCTTCTGTGTCAGAGTGCAGGCCTGAGTTTGGGTCTCTAGCGCCCATGTAAAAATTGGGCACAGCGGCATGTACCTGGGTCCTCAGTACTGGGGAGATAGGAGGATAGCTGGGGCTTGGTGGCTTGCATATACAAAGGTGGTATCTACTATTGCTGGGTATGGTGATATATAGCTGTAAAGGAGGCCAGCCTGGGCTACATGAGACTCTGCCTCATTCACCCGACTCCCCCAATATGGAACTACTGTTGCCATTCACTTTACTGAAGTAGTAAGCTGGAATGTTCTTGAATCTAGGCACTTTGAGTTTAGTGTGCCTCTCAAGATGGAAGATGAGGCTGAGTGATTGTGAGCACCACCTTGTGGCGACATTACTGTTGTCTGGCTATTTCCAGGCTTGGTCCATCTATCCCTGGTGGGCTTTCCACTTGCAAGCTCTCCTCCTTCCTTCTCTCCCTCTCTACTTCCTGTCTCCCTCCCTCCTTTCCTTTTTGAGACAGGCTCTCATATAACCTAGCTCTCAAACTCCCTACTATGTAGCCCAGGCTGGTTTTGAGTTCCAGTCCTCTGCCCTTACTTCCCAAATACTGGAATTACAGGCATGTGCCATTGTGCCTGGCTCACAGCAGCCCTTTTAAAAAACCAAGTAATTTTAAGGGCCTTTGCTTCCTTGGCCCACCCTCACTCCCTCCCCCAGCATGCCTGCCCCTGGGGAAGGCAGCCTTCAGCTGGCCAGCTGAGTCAGGTAGATAGGAGACAGCAGCTTAGAGTTCCTAGATCGATCCCCCTCACTCCAAAAGGCATCTTACTGGTATGAGGAGCAGGAAGCTGGGGGTTGTGGGGAGGGTGTCTGACCCTGCTGCCTCTTCCTCATCCACCAG
Seq C2 exon
GCTGACCCCTGCCCACAGCAGGAAGGCGCTGAGGAATTCCCGAATCGTCAGCCAGAAGGATGATGTCCACGTGTGCATCATGTGTCTAAGAGCCATCATGAACTACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000055805-Fmnl1:NM_001077698:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.502 A=NA C2=0.011
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF063718=Drf_GBD=PD(6.8=23.3),PF063718=Drf_GBD=PU(6.1=11.6)

							
A:
NA

							
C2:
PF063718=Drf_GBD=PU(45.3=91.9)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000046296





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000046296f4968A
          









    
Other Skipping Isoforms:
ENSMUSP00000102642
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
chr17:45234201-45236135 
ALTERNATIVE
HsaINT0065118
(FMNL1)
Human
(hg19)
chr17:43311568-43313502 
ALTERNATIVE
HsaINT0065118
(FMNL1)
Rat
(rn6)
chr10:91265705-91268442 
ALTERNATIVE
RnoINT0061629
(Fmnl1)
Cow
(bosTau6)
chr19:45506520-45509324 
LOW PSI
BtaINT0063167
(FMNL1)
Chicken
(galGal4)
chr27:1397839-1399312 
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
chr3:37072255-37072379 
LOW PSI
DreINT0069060
(fmnl1a)
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"