Special

MmuINT0131821 @ mm9

Intron Retention

Gene
ENSMUSG00000038020 | Rapgefl1
Description
Rap guanine nucleotide exchange factor (GEF)-like 1 [Source:MGI Symbol;Acc:MGI:3611446]
Coordinates
chr11:98703872-98707301:+
Coord C1 exon
chr11:98703872-98703969
Coord A exon
chr11:98703970-98707188
Coord C2 exon
chr11:98707189-98707301
Length
3219 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGG
5' ss Score
4.44
3' ss Seq
CCCAGCAATGCTCATGCCAGGAT
3' ss Score
1.71
Exon sequences
Seq C1 exon
GAACTGTATCTACTAATTATGAAGGATGAGTCTCTTTACCAGGACCTCCGAGAGGACACACTGAGGCTACACCAGCTGGTGGAGACAGTGGAGCTAAA
Seq A exon
GTGAGGAGAAAGGGGACCCCTGAGTTCCTCTAATACAGGGGCTGCCTCTGGTCTTGTGGCTTCAACATATCAGTTATTTGTTTCTTTGCTTGCTTGCTTTCTAAGCTATTTATTTATTTATATTGCTTTATCTGCATGTATATCTGTGTACTACCTCCATGCTTGGGTATGCCAAGGTCAGAAGAGGGTTCCCAGGAACTTAAGTCATAGATGGCTATAAGCTACAAAGTGGGTGTTGGGAACAAAATGGGGTCCTCTCTGCAAGAACAGCCAGTACTCTAAATCACGAAGCCATTTCTCCGGCACCTTTAATATTTCAATATGATTTTCTTTCAGCTCTTTTCCCTTATTGGAGAGTAACATAGAATCACACAGAATGATGTCTCTAAATCAATGTATTTTTAGAGGGGCAAGGAAGGAGCTGGGCAATGTCTCTTACTTACTCTATAGCTCAAGCTAACCTCCAGCTCAATTTGTAGCCCAAGACGGCTTCTGCCAGCAGCAATCCTCCTGTCTCAGGGTTCCGAGTGGGCCTGTGCCACCAGGTCCAGCTCCATTCTTTTAGTTTTTGGTCTGCTTTTCCTATTAGTTGGGTAGTGTTCCAGCAGGTATTTAACAGCCCCTGCTTTCTGGGAAAGAGCCCAGTTTTCTAGTTTATAGCTCTGATTCCCATGGCGTAAATTTTCTCACCATGGTTTGTCTCAAGCTATCAACATGGTATCCTTGACTGTGGAGTTGAGAAGAGATCTGCAGTAGTTACATAGTATTTCCACTACCTCCACAGCAGGCCTGAATAAGCTGGAGCAGAGGCAGTACAAAACTTAGTAAAAAGAACTTAGAAAAACTACCTTTTGGGTTTTTTCCCCCTCTTCTTTCTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTGGTTTTTTGAGACAGGGTTTCTCTGTGTAGCCTTGGCTGTCCTGGAACTCACTTTGTAGACCAGGCTGGCCTTGAACTCAGAAAATCGCCTGCCTCTGCCTCCCAAGTGCTGGGATTGAAGTCGTGCGCTACCATACCTAGCTTTTCTTATTTATTTATTTACTTACTTTTCAGATGGAGTCCTTGAAACTTGCCCCAGTTTTTTTTTTTTTTTTTTTCACATTTGCCTCCTAAAGTCAAATTATAGGCTTTTCCATGGTGCCTGGCACAGGTTTTGCTATGTTTTGTTTTGTTTGTTTTCTGAGACAGGGTTTCTCTGTGTTCTTAGAACTCATTCTGTAGATCAGGCTGGCCTCAAACGCACAGAGATCCACCTGTCTTCTGCCTTCCCAGTGCTGGGATTAAAGGCATGTGCCACCACTGCCTGGTGAAGCTGTCTTTTCAACAATGATTTATTTGACCTTAAGTTTATAACAGGTGCCAGGCGGTGGTAGCGCATGCCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGGTAGATTTCTGAGTTTGAGGACAGTCAGGGCTACACAGAGAAACCCTGTCTCGAAAAACCAAAAAAAAAAAAAAAAAAAAAAAGTTTATAACAGGTGTATGTATGAATGAATACGCATCCAATGGCTGTCCTTAAATTTTAGCTAACATGAGTGACAGAGATGGTTCAGTGGTTAAGAGCACTTACTGCTCTTCAAGAGGACCCAGGTTGCATTCCCAGCACATGGGCTCACAACCATCTGTAAGTTTAGTTCCAGAGGCTCTGATGCTCTCTTATACACTCTAAGTGTAGGGCTTGCCATGGTACACAGGGCACATGCAGGCAAAAATACCCATACGCATTAAAAACGTATTGGTCGATAGCTGAGCGTGGTGGCGTATCCCTGTGATCCCAGGTATTTGGGAGGCTAAAGTGGTAGAAGAATCATCAGTTCAAGGCCAGCTTGGACAACTTAATGAGATCACATCTCAAGATTCGAAAAAAAATAGTAAGGGCTTGAGACACAGCAGTGGTGCAATGCTTGTCTAGTATGTGTGGTGTCCTAGGTTTAATCCCCACTTTTACCAAAACAAACAAACAAACAAACAAACAAACAAACAAACAACAGTTGGCAAAAATCCCCAGAATTGACCTCCCTAGCATCAGGACACGAGTGCATCAAGTCATCCCTTGGTTTTCTCTGCTCCATTCCTGCTGCTACACGGTTCATTAACTCCCCTAGGCTGTTGCCACAGCCTGTTCGGGACTTCAGCCTCTGGCCTTGCCTCTTTCTCCCTTCTGACACCAAAGGTATCTTGCAGACTTTCCTAAAGGAGTCTTTCACCTCCCTGTTCCCAAAGCATCCGTTTTCTAATGTCTCCAAGCCAGCACCAGCATCCTTCCCTTCCCACCACCCGATCATCTAAATATCCTAAGCCACCATCAGCATCCTTCCCTTCTCACCACCTCCTGATCTTCTCTGACTCCTCTCATGTTTCCTTTTCACCTATTTTTTAAATTTATTTTTATTTTATGTACATTGGTGTTTTGCTTGTCTGTATGTTGGATCCCCTGAGGGTGGAGTTGCAGGCAGTTGTAAGGTGCCATGTGGGTGATGGGAATTGAACCCCGGTCCTCTGGAAAAGCAGCTGGTGCTCTTAACCACTGAGCCATCACTCCAGCACCCCCTCTTCATCTATTTTTCTGGCAACTTTGGTGCCTTCCTACTTTTTCTTCCCATGATCCTTCAGGGCTCTGGTCAAAGGCCGTCTCTTTTATGGAAACACCTCAGATTTCTCCCTTTCAGGAACTTTCCTTCCCCCACCCACAAGTCTCCCCCTCCTGCACCTTTGTCACCTCACCAACACTTCCTGGCTGGTGTAAGAAGTAGCTGCAATGTCTGTCTCCTTCACAGACTGTGAAACCCTTGTCAGCAAAATTCAGGCATCTGATGTCCTACTACCTACCCTGTGCTGAGTGTGGCAGGACATGAAGGGTGAAGGACTGTAAAAAATAATCCCGTTCCCCAAGAGCTGTCAATCTGGTAGAAAAGACGACACGAACCCAAACAATATTGTTCCATCATTTTATGGCTTTTGAGACGAGTCATCTTTCCTCATGGGTGGGTGGACCAGAGAAGAGCCCCTGAAAGAGGTGGCATTTGATCTGGGCCACTTGGACAGTTGTCCTGTGCTGGTCATTGTCCTACCCCTGCTTAATGTTCCTGCCTGGTGCTCCATATGCCTGGCAGGGCTTGCTGATGCCCAGCAATGCTCATGCCAG
Seq C2 exon
GATTCCAGAAGAGAGCCAGCCGCCCAGCAAGCAGGTTAAGCCGCTCTTCCGACACTTCCGCCGGATAGATTCCTGTCTGCAGACCCGAGTGGCATTCAGGGGCTCCGATGAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038020-Rapgefl1:NM_001080925:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.077
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0061815=RasGEF_N=PD(21.2=75.8)

							
A:
NA

							
C2:
PF0078818=RA=PU(2.5=5.1)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000103103





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr17:40184679-40188865 
ALTERNATIVE
HsaINT0137481
(RAPGEFL1)
Human
(hg19)
chr17:38340931-38345117 
HsaINT0137481
(RAPGEFL1)
Rat
(rn6)
chr10:86754653-86757758 
Cow
(bosTau6)
chr19:41114690-41116610 
LOW PSI
BtaINT0122431
(RAPGEFL1)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
chr3:23229227-23232570 
LOW PSI
DreINT0124630
(rapgefl1)
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"