Special

MmuINT0131751 @ mm9

Intron Retention

Gene
ENSMUSG00000049044 | Rapgef4
Description
Rap guanine nucleotide exchange factor (GEF) 4 [Source:MGI Symbol;Acc:MGI:1917723]
Coordinates
chr2:72090997-72094433:+
Coord C1 exon
chr2:72090997-72091051
Coord A exon
chr2:72091052-72094305
Coord C2 exon
chr2:72094306-72094433
Length
3254 bp
Sequences
Splice sites
5' ss Seq
TCAGTAAGT
5' ss Score
9.14
3' ss Seq
TGCTATTATTCTTTTAACAGATC
3' ss Score
9.48
Exon sequences
Seq C1 exon
CGCATGATTGCAAACACTGCCAGAACAGTACGGTACTACAGGAGCCAGCCCTTCA
Seq A exon
GTAAGTTCTGAGTTACTGCATGCCGTCATGGACATGGTGGTGATTAAGTCCTTTTTAATGAGACTTCCAAGGCACTCTGGGAGTCTGGATGGCATGTGACACAGCGTGAACCGTGAAACCCACGTGTGCCTTGGGTTTAAGAACTTTGTTTTGCTGTTGTAAGGCTCAACTATATTTGCATTGTAACCCTAGAAAATAGGGTCAGGCTATTATTTTAATAAGTGAATTTGAAGGAAATTCATTTGCTCATCTCGGTGTAGCTAGAACAGGTAGGCTGCAAAGGCCCACATAAGCCTGCCTCCAAGCTGTTCTCGGGTGTGACTCATGCTCGATGCTGAGAAGCCCAGCAGCCCTCAGTGAGTCAGTACTATCGTTTATAAACTGGGAAAGGTAATAGTTACTGTCTTCTGAGTATGCGTGAGTGTTTATAGCACATTTGCAGAGAGTCCTATGGCAGGATTCTACACAACATTGCCAGTATTTCAGGTGCTCTTTTGAATGTTGGGTGTATGTCCTGAACACCCATGCTATTTTTTCATATGTTTGAAATATTACTATTGACAAATGGCCATTTTAACCTGTAGGGAGTTAGGTTTCCTCGTAACACCAGCAGGGCAAGTTAGATCAGTGAAGCCGTCTCCCCAGGCCTAGAACTTGGGATAAGAACCAGAGCTTTGGGGGCTGGTGAGCTGCCTCAGCGGGCAGGAGCACTGACTGCTCTTCTAAAGGTTCTGAGTTCAAATCCCAGCAACCACATGGTGGCTCACAACCATCCGTAATGAGGTCTGATGCCCTCTTCTGCTGTGTCTGAAGACAGCTACAGTGTACTTACATATAATAAATAAATCTTTAAAAAAAATGTTAAAAAAAAAAAGAAAGAAAAAAAGAAAAGAGCTTTGCACCTCCAGTCTGGTTTGGGAGAGAGCAGGCGAACCCTTGGAAGTTTTGTGCTAATGTCATTATGTGAGTCATTTTGGAGAACTGACATCGGTAAGAAGACACAGATGTGACAGCAGCCTACCTGAATATCCTCTCCAGTAGAGACTGACAGGTTCTCGTTTTAATAATCACAGTGGTATGCTCTTTGTAGTGTAGCTCTGGCCCAAAGCCAGAGCTTGCTAACAGAATGCCAGAACTACTCCCTCCTCCTTGTCCTCCTCCTCCTCCTCCTCTTCTTCTTTTTAATGTTCAAGAGAAAAGAACAATTAGAGAAAGTAGTCTTGGCTTACGGAGTGAGAAGAGCTCTAAAAGTTAATTCAACCAACCATGCCCTTGTGCTTCTAAAAGTGAGAATGGTCTTACACGTCGCCAAGCCTTTCTCCGTGGATTCTTCCTGAATTCAAGTGTCTCATATCTTTTCCTATAATAATGTGCTCTGTGTGTAAAAGACAGCCATAGATTAGCTGAAAACGAGGAGAGAAAGTACCAGTTACAACAAGCTCTGTAACCAAAATCCACAGCCCTTCTGGGGATTTGGAGCTGTTTTCGAAATTCCACGCAAACAATCCTGTGTGCTGAATGAGAGCTCAGAGCCTCAAGAAGGGTTCTCAGGGGGCTTCCAGAGCCAAACAGGAGCAGTAATAGGCTCGGCTTTGTTCCGCAGCCTCTTCGGCAGTAAATTCTACATTCTTCCACATCTTTGAGACAAGTGAGGGGATTTTTTTTTTAAATTTCCACTGCATTTGTTGAACTTATCAGCAAGTGCTCGTAAACAGCAGCTGCCAGGCTCTGAAGTCAACAATCTATAGATAAAACTATAGGAATAGATTCATAAACATCGTGGGGCTATGTACAATGTAATTACAGTATATTGTACATGCAGAGTACGCTGCCAGTGGGAAGCAGAGGAAATTAAGCACAATGTGTTCTGTGGTTCACTGTGGTATTATTTATATGTGATAATTATACTGATGAGTTTCTTCTTACAGCGAGCAGGGGCCTTTGTAGCTTGTCTTTGCTTTCTGTGCTCAGACCTGCTTCACACCCCACACCCCCCCCCCCCACAACCCTTTACGCAGATGGCAGTCTAATTGTCTTGTGGAGTAGTGGGTGGAGCTAACAGGAGCAACCGGACTTCTGAAGGCAGCGCAGGGGTGGGAGGGAAGAACTTTGGTTCAGAGTCCAGATTCCAGCTTGGCTACTCCCCGTTTACTGCTAGAGAAGAGAGTGAGCCCTGGGAGAGGGACCCGCGAACTGCAGCCGAGGTCTGGGTTATGTTTAAACATTTCCTTCTCTGTATGGAAAGTCTTGATTTAAAACTTGGAGAAATTTACACGGGAGAAATTTAGAGTCCCTGTTTCAAAAGGAAAGGAAAGAAAAAGGAAGGAAGAGAAGTGAAGGGAAGGTCCTGCTGGCCACTCTGGGCAGATCCCTACAAGGTGATGACAGTCAGGAGCTCCGTAGCCACTTCCCAAGGTAGTTTGCTTCCAGTTTCCCCGCTCTGCTATTAAATCTGGCCTTCCTCCTTCTTATATATATATGGTATGTAGGAAGTATGCACATTAGATTTTCTTAGAGTCCTGGTTTGGATAAATCCACTTACCTCTTTGATAGCCCGGGTACTCGCATCCATAGATAAAACAGTCAGTGGACTTTCGGAGCAAGTCATGTCAGAGAAGAAAAGTTTGCTAGAAGTCACCAATTAGCCAGAAGGTATCCTTACCCAGTTCAAGCTGTGCCTAGGGGCATACAGCTGGAGTGGTGCTGTATACATATACAGGCAAAGGGGACCTATGAGGCCCAGTGCCCACTGGCTGGCTTCAGATCAGTCATGATGTTAAGTGCTTTTCTGAGTTGCTAATGAAACTCCATCTTTGACATTAGTCCTCATCTGGATCAAAGGAGGTGGAGTCAGAGTGTGAGACATAGAGATGAGCCGGGAAGGAAAAACAATTTTCATCTATCACCAGGGCCATCAGACAGATGCTTTCCTTTTTATTTGGTGCCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTGTGTGTGTGTGTGCAATGCAAAGGAAAATGATCAAAAGAGATGATTCCAGGGGGAGGGGGAAAGAAAATTGGAGAGTAGAAGGAAGTAGATGGACCAACCAAGTAAAAATATTCCAGTGAATGTGTGTGGAAAGGTCTTGACAGAACCCAGGGAATGTATTATGATAAATGCAATACGTCATTGGGAGGAATAAAGCCACATCTCACATGCAGATATTACCCAATGCCAACTCGCCTGCTATTATTCTTTTAACAG
Seq C2 exon
ATCCGGATGCCGCTCAAGCTAATAAGAACCATCAGGATGTCCGGAGTTATGTACGGCAATTAAATGTGATTGACAACCAGAGAACTTTATCACAGATGTCACACAGATTAGAGCCTCGAAGGCCATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000049044-Rapgef4:NM_019688:29
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.105 A=NA C2=0.690
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0061714=RasGEF=PD(0.5=5.3)

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000088336





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000028525, ENSMUSP00000099759, ENSMUSP00000126095
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr2:173048655-173051639 
ALTERNATIVE
HsaINT0137409
(RAPGEF4)
Human
(hg19)
chr2:173913383-173916367 
ALTERNATIVE
HsaINT0137409
(RAPGEF4)
Rat
(rn6)
chr3:58920540-58923913 
LOW PSI
RnoINT0124273
(Rapgef4)
Cow
(bosTau6)
chr2:23646257-23649118 
LOW PSI
BtaINT0122390
(RAPGEF4)
Chicken
(galGal4)
chr7:16923319-16940592 
GgaINT0049912
([1])
Chicken
(galGal3)
chr7:18753817-18755316 
LOW PSI
GgaINT0049912
(RAPGEF4)
Zebrafish
(danRer10)
chr9:2943712-2947434 
LOW PSI
DreINT0124579
(rapgef4)
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"