Special

MmuINT0065320 @ mm9

Intron Retention

Gene
ENSMUSG00000039735 | Fnbp1l
Description
formin binding protein 1-like [Source:MGI Symbol;Acc:MGI:1925642]
Coordinates
chr3:122263751-122266857:-
Coord C1 exon
chr3:122266753-122266857
Coord A exon
chr3:122263880-122266752
Coord C2 exon
chr3:122263751-122263879
Length
2873 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
TGGACCATTTTTGCCTGTAGGCC
3' ss Score
7.79
Exon sequences
Seq C1 exon
AGTAAAAAGAAGTTTGAAAGAGAATGTAGAGAAGCGGAGAAAGCACAGCAGAGTTATGAGAGGTTGGATAATGACACCAATGCCACCAAGGCAGATGTTGAAAAG
Seq A exon
GTAAGGACTCTAAACTCGCTATAAAACAGTATTACTACTGGAGCGTAGTCATTGCGTACAGCCAACAATCCTACTTTGATAACCAAATATTACATGCATGGAAAGAAGGCACACCTTTTGCGTCATTATTGTATCTAAAGCTAAAATATGCAAATGTTGTTTACTTGGTCTGAGAAGGAAAAAATGATAACATAATGCCTTAGTTGCATTCATAATGCTCAGGATAAACTGGCTGCTAGGGGTTTTTTCTTCCTTATTCCTAAATTGAATAAAAAGACTGAGATACAGCCCGAGTATGCTAATTGGGTGTGACTCAGTAGTCCTCTTCAGCAGCTCTACAGAATGTAAGCATTGAGCTATCACCATGGTACCTGGTTACTCAATGAAATTCTTGTCACTGATTCTGAGCTGGCTATTCTGTAGCGTAATTTGCTGAGAGATTGATTGGTCTTGTAACTGCTGTTTCCTAGTTTCTCCTCTGTTAGTTGATAGGGTTCAGTTAGCTCCCACCCCACCCCATCTTTATTATTTCCTTATATAGGCTGTACTCATCTCTGTTTCACATTTTGAGTTACATAAACAAATGTCAAATACATTTTTAAATAATAGTTTTGAATAATAATTCTGAAACTGACTGTAACACTGGTGTGTCTGATCTTGATTACCTCCCTTATCTGAGCACTGAGTTCTTGCTAATATGACGTGAGTGTTTATGATCTAGGCAACCATGTTTGAACTGACTCCCATGGCTGAGTTCATGATTATCTTGTCTTTACATGTGTATTGGTATGAGAATGTGCCTCTTATAACTTAAAGACTGTATTTAAAATTTGTATGGACATCTTTATCTATTATGAGCTTTGATCCTGCTATTTAAGTTTTTATATCCTAATTTTGATTATATGATTTCCTTTCCAGCATTATGCCATATTCATAATTGAAGAATGTGTTACTCGATAGTATTGTGAGTAACAGCACTATTTTGTACATGGGACATGTCTCAAAGTTGACATTCACCTTTAAACACTTCTTTGAGTCATTATCAAATAATGGTTATTCAAATTTGTGTCACAGGCAATTGAAAGTTACTTGTTTAGTGGATTCACATTTAACCCTTTAATTTGTCTACAAGGATTAGCTTTACATAGTCACTAAGCATCGGGAAACCGAGATATAAGACGGCTGCTAGTTAGTTTATCCTAACTTTCAAGATTTCAGTGTTCATGGTTTAATGTTCAGTTATTTGAAATCTCTTTATTATTAGAAAATTAGACTAGGCTTCAATTGTTTGAGCTTGTAGCCTTATTCTTTTTTATTCGCTGCCGAAACCTCCATCCTAGCTGGGACCTGGAGGAGTGTCCCCTGGCAGGTCAGGAGGACTTGAGGCTAGGACTCGGAATCTTTGTCCCACTTTATAGTTTATGGTAGAAGGAGAATGTTCTAGGCTGGAACCTCAGGTTTTGTCTCATTTCATTTTTTTCCTCTGTAGAAATACTTTGTACTTTGACTCATAGTATTTAGTTTCCATAGTATTTACTTGCAGGAACTTGTGATGTGCCGTGGATTAAATAAGGTTTTGTGGGCTTATCTATGATCTTGGCTACCCTGCTTCCATAGTCAGTTTATTTCTGAATTAACAAGATAGAGTTATAAACTAGTGTTAGAAGCTAAGTAACTGCATCTGTAAAAGCTAGCATCCTAAGAGTGAGGGATGGATGGATGGATGGATGGATGGATGGATGGATGGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGGACTGGGAATGAGGATCAAACCAGAGTGCTTGTCAGCAAGGATAAAGCCCTTACGTTCAATCCTTAGCAAAAGAAAGGAAAAAAAAATAGTGTGCTGTGTAACTCATAGCCCTGATGTATACATAGCACACACGGCACTCGCACTTCTTCCCACCCTCCCTCTCTTCCTTTACTTTTGCCATGTTGTGCTCAGGTTGTGCTGCAACTCTGTTGCCTCTCTGGCCTCAGCCTTTGCATGTACATGAGACTGCTGGTGTGCAGTGTTGAATCTGTGGAGACCAATTCTTACTTCCTAATTTAGATCAGAGTCTAATTAGTTAGTGTTTTACTCTTGTGAACAGATACTATGACCAAGACAATGCTTATAAGGACATTTAATTGGGGCTGGCATATAGGTTTGGAAGTTCAATCCATTATCATCAAGGCATGAGCTTGGCAGCTTCCAGGCAGATGTGGGGCTGGAGGAGCTAAGAGTTCTACATTTTCATCCAAAGGCGGACAGGAGAAGACTGGCTTCCAGGGAGCTCGGATGAGGGTCTTAAAGCCCATGTCCATATTGATAGACTTCCTCCAACAAGGCCACACCTTCTCTAATAGTGCCACTTCCTGGGCCAAGCATATTCAAACCAACCCAATCAGTTAGGAAATTTGTTTAGCTTATACTCACTGTGTTAGAACTAACAGTTTTACTTTTATTCTTGTCAGAGAAGATAATACTCCTTTGCCCTTGTGCAAGAAATTAAAGGCAGAACTATTTTAAATAAGTACCTCTGGTTTCATAGAGATTGAAACACTGTTGAGTTTTACAGTACCCAACGTTTTAGTCATTTACATCTATTATGATTTTAGTTTCATTTATTATTTTCTGTGTGAATTTTATAAGTAGACTATTTATATTATTGAATAGAGCAGAGCTCTCATAGGGACAGAGGGATTGTCATAAGGAGACTGTAAGATCTGGAAGCATTTTCATTAGCTGTTGGGTTATCTATAACACAATTTAGGTTTGGTATAATTTTCAGAAAAATGAATTACTTTATTTTTGGCAATCATTTGGACCATTTTTGCCTGTAG
Seq C2 exon
GCCAAACAGCAGTTGAACCTTCGTACGCATATGGCTGATGAGAATAAAAATGAATATGCTGCACAGCTGCAAAATTTTAATGGAGAACAGCACAAACATTTTTATGTGGTAATTCCTCAGATTTACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000039735-Fnbp1l:NM_153118:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.714 A=NA C2=0.444
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000096236





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000102046, ENSMUSP00000124439, ENSMUSP00000124947
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:93529757-93530754 
LOW PSI
HsaINT0065332
(FNBP1L)
Human
(hg19)
chr1:93995314-93996311 
LOW PSI
HsaINT0065332
(FNBP1L)
Rat
(rn6)
chr2:226710633-226713560 
LOW PSI
RnoINT0061842
(Fnbp1l)
Cow
(bosTau6)
chr3:50110978-50114950 
LOW PSI
BtaINT0063363
(FNBP1L)
Chicken
(galGal4)
chr8:12828242-12828754 
ALTERNATIVE
GgaINT0035268
(FNBP1L)
Chicken
(galGal3)
chr8:14578565-14579077 
LOW PSI
GgaINT0035268
(FNBP1L)
Zebrafish
(danRer10)
chr8:15024177-15024330 
LOW PSI
DreINT0069255
(fnbp1l)
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"