Special

MmuINT0131813 @ mm9

Intron Retention

Gene
ENSMUSG00000038020 | Rapgefl1
Description
Rap guanine nucleotide exchange factor (GEF)-like 1 [Source:MGI Symbol;Acc:MGI:3611446]
Coordinates
chr11:98698099-98701652:+
Coord C1 exon
chr11:98698099-98698987
Coord A exon
chr11:98698988-98701573
Coord C2 exon
chr11:98701574-98701652
Length
2586 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
ACGCCCATTGCTCTCCACAGATA
3' ss Score
8.55
Exon sequences
Seq C1 exon
CCCGGGGCCAGGAGCGCAGCCGCCGCCGCGTCCTCAGCCTTGCGCTCCGCCCGCTGCCTCTGTCGCCTCAGCCCGGCCCCGGAGCGCTGAGACGGGGACACCAGCCCCTCAGCCTGCCAACCCTTCGGCCGCAGCCGGCATGGGGGGCCGCTGAGAGCGAGCTCCTCTTCCCTCTGGCACCTCCCCCGGCCACTGGCCACTGGACTCTGGCCAGCGAGGCTCGGCCACCTCTCGCTCGCAGTCCGACGCCTGGCACGGCCCTCGGCTCTGCTCCCCCGGCTCTGAGCATCGTGTCCCCGCCTCCCCCCGCCCGCGCCTGGGACACCTGGGTCCCCCGGCGGCCCCTAAGAGAGGGGCGGGGGGGGGGGCATGAAGCCACTGGAGAAATTTTTGAAGAAGCAGACGTCTCAGCTGGCGGGGCGAGCGGTGACTGGAGGTCCCGGCGGGGGTCCGGGTTGCTGCGGAGGGCCTGGAGGGGGTGGGGGCCCTGGTGGGGGCGGCGGTCCGGCCGGGGGACTGCGGCCACTGCAGCGGCGTCAGAGCGTGTCTCGCCTGCTGCTCCCAGCTTTCCTCCGAGAGCCCCCAACCGAGCCCGGGCTGGAGCCGCCCGTTGAGGAGGAAGGGGGAGAGCCATTAGGGGTCTCTGAGGAGCCGGGCAGTGGGGGGCCCTGTTGGCTGCAGCTAGAGGAGGTTCCCGGGCCTGGGCCGATAGGATCTGGGGTGCCCCTGCGCTCTCCTTCCTCGTACTCCTCAGATGAGCTATCCCCCGGCGAACCCCTGGCTTCACCACCCTGGGCCCCCCTGGGCGCCCCCGAGCGGCCAGAGCATCTTCTGAACCGGGTTCTGGAGCGCCTGGCTGGAGGGACCACCAGGGACAGCAGCGCCTCAG
Seq A exon
GTAAGCCTGCTCATCCATCCCAGAGCAAGAGAGCACGGGGTTGGGGGTGGGAGGTGAGGGATTGGCCCGGGGGATGCTCCCTGATTGTTTTTTCTTGTCCTCAGTGTTGGTGTAGAGGATGAGGGGAAGCCCGAAGTAATGTAGGGGAAGGGGCATGGTAATGCGCACCCACCTTCCTCCCCACATTAGCTTCATTCTAGGGGAAGAAGGGAAACCATCTCTCTCCTTCAACTACCCTCCCTCTCTCTCGGCTATTTAAGCCAGTCTCCCACGAGCCCTTGATACTGCCTACCTCCTCCCACGCCCCTAAATTAGGGCCTGACACCCTAAGGTGGACGCTTTCCCGCTGAGGTTGTACGCTGCCCTCCAGACCATAGCTGAGGCCTGAAAACCGCTGACAGGAGTCCCTGGCTGTGTAGGAGCGCCTCACTTGGTGGGGCCATGTGGATAGTCACAGAACTCGGCTGCTTTTATTGGGGATGAATTCGAAGGTCTCTAAGGGAAGATACCAGGAGACTGCAGCATCCAGAAGGCTTTGGGCCTCCGTAGCACCCACCCTTCCCATGCCATGCCTCAGCAGAGGGCCTTTTTTAAAAAAATAATAACCACACCCTGAGAAGCCTGAGATGATGCCATTTCACCCACTATGAGAATGCCAGCACCCTATTAAAGGGCTTCTGAGGAACGTAGGCCCCCACATCGCTAGTTGGAATAGATGTAGAGATATCAGGGTCTTTAGATCTAACTAGGCACTCCACTAAACCCAGAAGGGGCTTAGGGTTGAGAGACCAAGCTTGAGACCCTAAAGAGGAGGGTGTTAGGAGTTACCCTTCCTTCTCTGCAAGGCATTCTGGCTCTAGGAGTGGAGTGTCACCCTCTACTCCATTTTTGTCCTGAAGGTCGGGGTCCCCTCTTTTGGCTCAGGCTGCAGTTGCCCTGGGGAGCTGACACCTTTTGGATTTAATTAGAAAAATATCAGACACACACAGCTCTCTTAACCATAACTTCCCGCCTACACCACACACCCTGTGTCTCTATGACACATTCCCCAGGGAGGCTGTGCGTTGGACCGGAGCCTACTTTGGAAGAAACAGATGCCAAACTGGAGCCCCCGTATCAGCATCTCTCCACTCTGCCCGCGTTCCTTGTCCTTTACTCCCATTTTAACATTCACACTCTAGTGAGAGAAAGATGCGAGGAAGGATGTCAGGCCTCTTTATGCCGAGGCCCCAAACCTGGAGCTGGGCGTGAGGGCTGGGGACCCTTCTGACTGACTCTCAGAACATAGCTGGGTAGCTGGGTAGAAAGGGAAAGAGAGGCTGTCCAGTTTGGACAGCGGATTGTCCAGTTTCCCCTGGGTTAAGACTCCCCATTTGTCACCCATATTATCTGGCCCGACAGGCTAAATCTCCAGAGTAACTAGTTTGGGAATCCTCCCCATTTAAACTGCCACTCCAATATTTTTAATATAAGCCACGTTATCAAGCCTCTTGATTTCTGCCCAGGCTGCATGGGAGGCGACAAATGCTTAGTGAGGGCTCTCCTCACCTAGCCAGAGCTCCTTCAAAGGTCTAGGCAGCCCCTTGTGGCCAGTAGGTACTAGGCCCCCCCCCCCACCCCCATACTCTGCTTGCCCCTGTATTGAGTTGAGAACACAGCATTCTAAGTTCATCTGGCTCCGGGCCTCAGTTTCTCCTCTGTGAAACAAAATGAATTCAAGTAGACAATCTTGTGTTGCTCCTCCACCTCCACCTTCGTGGCTGGCATTGGCAGCAGGGCATGACAACCATGGGTTGTCAGAAGCCATGGTTTTGTCCTGGAGCAGTGCCTGGGGACCTGGCCCTAACCTGTCCTGGTGAGGACACCTGGCTCCCTCCCTGTGCCCTGCCTGTCTGTGTGTGCCAAGCAAGCCCTGCCCCACCCCAAGGCTGGCGGCAAGTCAGGGCGACCGACCTTGTACCTGGCTGACTGGCTGAGCCAGGCCCAGACAGGGGTGTGGAGGGAAAAGGGTGGAGAGAGGAGCCCCTCCCCTGTCCTTCTCATCATTAACCCTTCCACCTCTGGGCACCCAGTGGACACAGGACTTCTATTTAAAGACTGAGATAAAGAGATGGCGGCCTGTCTCCGCTGTCAATTTTCATGGGGATGGTCCCCACCCTGCCCTGTGGAAATTCAAAACTGTGAGGTTGGGAGTGATCGAGGAGGATGGACACACATCCCACACATCCACATCCCTCTGACTGGAACCTCTGCTTGCCAATTCTCCGTCGATGGTCCCTTCTGTGGACCCCTTTTTCTCCTGAGCAGATCTCAGGCATGGTGGTATTATCTGACCAACTTCCCCCACACTGAAGAGAAGGGTGCATGGCCTTCAAAGGCACCCCCCCTCCCTCCAGCTGCCTTGGCAGCTGCCAGCCCCACCCCCGCAGCGGCTGCCCAGAACCTTCACACATGTGTGCACTCGCGTGCAGAGCATGACGGGACAGGTGGCCGGGGCTCCAGGCTTACCAAAGAGGAAAAAAAAAAAAGAGGGTTCAAGGTTTGCAGCCCCCTTCTGACCTCTGTGACGCCCATTGCTCTCCACAG
Seq C2 exon
ATATTCTTCTTGACGACATTGTTCTTACCCATTCCCTCTTCCTGCCAACAGAAAAGTTTCTACAAGAGCTACACCAGTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038020-Rapgefl1:NM_001080925:1
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=0.874 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0061815=RasGEF_N=PU(16.9=11.5)

							
A:
NA

							
C2:
PF0061815=RasGEF_N=FE(22.0=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000103103





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr17:40178382-40181615 
ALTERNATIVE
HsaINT0137473
(RAPGEFL1)
Human
(hg19)
chr17:38334634-38337867 
ALTERNATIVE
HsaINT0137473
(RAPGEFL1)
Rat
(rn6)
chr10:86750131-86752834 
Cow
(bosTau6)
chr19:41110390-41113228 
LOW PSI
BtaINT0122421
(RAPGEFL1)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
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"