Special

MmuINT0131777 @ mm9

Intron Retention

Gene
ENSMUSG00000041992 | Rapgef5
Description
Rap guanine nucleotide exchange factor (GEF) 5 [Source:MGI Symbol;Acc:MGI:2444365]
Coordinates
chr12:118986859-118991949:+
Coord C1 exon
chr12:118986859-118986923
Coord A exon
chr12:118986924-118991894
Coord C2 exon
chr12:118991895-118991949
Length
4971 bp
Sequences
Splice sites
5' ss Seq
CTGGTATGT
5' ss Score
8.14
3' ss Seq
GCTCCCCCTCTGTCTTTCAGCAC
3' ss Score
9.64
Exon sequences
Seq C1 exon
ATGTAACGTTTATTCATGAAGGAAATAAAACATTCTTGGATAATCTCGTCAATTTTGAAAAGCTG
Seq A exon
GTATGTAAATTTCATTATGTTTCCCTTCTTCTCTCTGTAAAGGAAACACGCTTGTCTCTTCAGCTCTAGGAAGCAAACGGTCTGAGTATCTCTCTCTGTTGTACACAGAGTAACTCCCAGGGTCTCTTTGGGCATATGGAACAGTGCCATCACGATGCTTGCAAGATTCTGAGAATCTGATTCTTTTAAATAGCATTTCATTAGCTTAGCACCAGTGACTGTGTAAACACAGAACCGGGCATAAAAGCTGATGTCAGGAGTAGTCCCCACTTGTGAGAGTTCGGTTACTTCAAAAGCATCTCTTGATGCCCCAATGTAAACCACTTCGAGACAGTGAGCAACAAACTCCTCCCAGTGGACCTATTGTCTCCTAGTACACCAAGCTCAGATATGCACCTGAGATTTGTGGGTTCTACAAGTGAAGGGAAAGGCTGCCTCCTTATTGATCTCTGATCCTGGACCTCCCTGCTGATTATATGAATTCCTGAGCAGCTTCTCCCAAGTCTCCCTTCTAGGACAGTCGCAGTCCTCAGTGGGTTCCTCAGACCTTCTGCTCTGTCCTTGAGCCAAAAAGAAGCTGCCTACAGAACTGAGTGGGACCGAGTGGGTGCCCCACAGCAGTGCTCCAGAGAGACAGCTCAGGGACCAGATGAAGGCACCTGTCTGACAGATGACCTTTAGTGTCACAGATGAAATGTTACATCGTGGTCAGAGGTGACCCCAGCCAGCACTCCCCTCTAGGAACCTGACCTTTGAGTGACCTTTTCAATGATGATAATGGGCTATATGAACTCTTTCGGGAGCCATCCAAGCTCCCTGTGAGACTCAAGTCAGGCTTCAGAGAAGGTCATTTGAGGCTGAGGCCCCTGACCATATTCTGTATGGAATTATTTGAAGAATAGCTCAGACTGAAGTCTCCAAATGGTGTCTGGTGTCTGACACCTTAGCACTTACAACTCTGTTCTAGTCAGTCACAAGACCTCCAGGACACAAGGGCTTAGACCCACAGGAAGAGTAGACCTAGCTCCCCCACAACAACTCAGAGCCCAGCCCAAAACAGACATCCTCCAGCCGCTCTCTATAGCAGCCCTTAGCAACCCTGAAGATGTTGGCTTCATGACTGGTTATTCTAGGAAGTCAAGATGCAGAAGTGTTTTGTTCCTAAAACATTTCTCTCTGCCCTGGGTATCTCAGAATCAGAGCTCAGTTGTTTCCCATGCTATTGAGAAGCCAGCATGGTCAGAGGTGGGAATGTGAGCCACTGTCATCTTGCATTGCACTACTCTGTGATACCCCAAGGATCCCAGTATACCTGTTAGCAGCCAAAGGCCTCAATCACTAGAGTTGTCAGTCTGAGCAAGTTCATCTCCAGTGTGTGGCATCTATAAACAATCACAGGGAACCTTTTGGTCACTATTTACTCTGCCTCCTGTTGATGAGTCTGTTTCATATCGCCAGAAGACCTTTCAGGGCATGTGTGAGGATGTGAGATATTCTGTATCAGCTTGCATGGATCCCCTCTGACGCAGTGGGGACACAGGACAGAAACTGTACTCCTTATAAACGATCGCCTTTTACCAGCAGATGAGGAGTAGGCCTTTACCCTGAAGCAAACAGTGGCCTGGCTACTGTCTCTTCTCATCTAATGCCACACCAGTGAAAGAATGGAAAGAATTCTACCCAGGCTAAAATGGAGAGAGTCACAGGGAGCTTTAAGCACTCTCCACCCTCTTGTCCACATCGTTGCCTGTGGTCCTTAACTTTTTCCTCCAGCAATTCATCAGAGCCCAACAGAAGGGACTGACATAAGGTATAAATGCAGACTCTACTGTCTGTAAGAAAGTTTAAAAGCCCAGAAGCTGAGCATGAGTCTCTAATCCCAGCACTCAGATAGCTGAGGCAGGAGGATTGCCACAGGCTCAAGATCAGCCTGAGGTACATAGTGAGTTCCAGGACAGCCTAGGCTACAGTAGAAGATACTACCTTAAACAAAGTTAGCAGCTTTCTTGACCACCAGACAGCTACCAGTGGCACATCATTGTGTGCATGTGTGTGTATGTTTGTTCATGTGTGTGTATTCATCTGTGTGTTTGTGTACATGTGTGTATGTCTATGTGTGTGTGTGCATGTGTTTATGTGTGTGTGTGTACATGTGTGTATGTCTATGTGTCTGTGTGTGCATGTGTGTGTCTATGTGTGTGTATCTGTGTGTACATGTGTGTATGTCTATGTGTCTGTGTGTGCATGTGTGTGTATCTGTGTGTACGTGTGTGCCTATGTGTCCGTGTTCCTTGCTCTTTTGTTTTCCACATTATTCCCTTGAGAGAGGGTCTCTCACTGGACCTGGATCTAAGCTGACAGTCAGCCATCCCCAGCCATCCTCCTGTCCCTGCTCCCCAGTGCTGAGCTTACAGGGACACACAACCATGGCAAACTTTTTAGGCACCATACCATTCTCCCAGCCCTGGTATACCAATAAAGAGATGAAGGTGTGGTAATGGTGGCCTGGTCCTTACAGCAACCAGCATTCCAAGCGCAGCACGCCTTGAGTTGACCTATCTATGCGGAAAACACAGAAGCAGTTAGGTTTTTCAGAAAGACAAAAATCAATTTTATATCATACTTGGGCCAGTGTTCCACTCAGGCGTTGGAACGTCCTCACAGAGACGGTATTCTCAGAAAATGTCACTCAGCCGAGGACGGACGAACGAGGTTTCACTGAAGCTCTAGCAGGATCATCTTTCACAGTAATGAACCAATGGGACCTAAGTGAATTAGCTTATGAGGAGCCAATTCCTCATGGTGGATGTTAATTTAAGCCAGTCAGCAGATAACTCAGGGTGTTATCTTTATCTGGCTGACACAGGCCAGCGCATTAAATCAGGACCACATGCAGATCAAAGTGCTCATTGAATGCAATAAGATTCGCATTGTTCCCTGGGCTAAGTTCCTTGCTGCCTCAGCAACTCTAAATGTTTCCACCTCAAACTATGAAATGTTGAAGGAGCAAAGGGGTCTCTCCCTTTCTTTTCATCCCCCAATATTATGAGCAGGATCTTTTACCGAGTCCGCCTCCCTCCCTGTCAGAAAACCCGGAGATGAGAATCAGGACTCAGATTTCAGTGCTGCGCACAGCATTGAGCCTTACCTCAGCTCCAGCCTTTCAGGAGCTGTACAAATGGCACAGGATAGGAATCAGCGTGACGCCAGAGCCTGTAACAATGGAAAAATCTGTCCTGGGAATTGGGGTAGAATTTGGGGAAGGAAATGGAACAATCGTTCACACAGACGTGAGTCAGGTCCCATTTCCTTTGCAAATTCCGCCTGGAGTGCTGCCGTAATCATTACCCCTGCTGAGTCCTCTACTCTGGAGAAGCGTCGAATTAGCCCATCTGCAGGCAGGATAATTTAATCAGACTCTCGATTCACGTACTGCCTCTGTCTTTCCGCTGGACTGTAAGTGAGAAGATTTGAGCGTTAGCGTTATTCTTTTAGTGATAATTTACTGACCGTTTGTCATCTGCGGATGCTTCAGTGTCTGGCCTGTGCAGGCAGGCTATGATGATGGTGCTCGGAGGACCAGATAATGAATGTTAATCCTCGAATAATGGGATATCCGGGGTTTGATATGAAACAAAGTGAGGGGTTTCTGTCCTCCTCCAAGGGAATAGGACCAACTGTGACAAGGACATTTAGGGCGCCTTCTGGCAGATGTGTAGGAGGAGCTGTCCAGAGTGGAGGTTGGTTTCTTCCAAAACCATTATGGAGAAGTAAATGGAGCAGAGTGAGCTAAAGGCTGATTGTAGGGACACAGTGTGAGAGGTATGGACCCTGCTGCACCCACGTCTGAGCGTGTAGGTCTGTCACCCCAGCTACTCAGGAGGCTGAGGCAGGAAGAGCGCAAGTTCTAGGCCAACCTGGGCAAGCAGGTGGGACACTCGATAGAAATTTTAAAAATGAAAAGGGTCTGGGGCTGTAGTGGCTCGGTGGGTGGTAGAACACTTCCTTGTCTAATATGCATAAGACCTAAGCATGGTCTCCCCGCCCCCCACCCCAAAGATGCACATTTCAGATAACCTTTGTATGGAGATCAGGAGGAGCTAAAGGAAAGAAACTAAAGTTAGAAAACTAAAGCCAGTGAGGAAATGTGAGTTAGAAACAGAACAGTCCTTGGTCCTGTGAAGGCTCAGTGACCCAGTGTAGGGGAATGCCAGGGCAGGGAGGCAAGAGTGGGTGGGTGAGTGGTGGAACACCCTCATAGAAGCAGGGGGAGGGGGAGGACCAGGAAATGGGATAACATTTGAAATGTAAATAAAGAAAATATCTAACAATAACAATAATATTAATATTAAAAAGAAACAGAACAGCCTTTGTAAAATGCTGATGAATTCACTCTGCTTTCGCGAATACCTCACTTCCTGCTGTTGTTGGAGCCCTCGAGTCCACAGAACCATCCGGCCTCCACTCAGGACATGGAAGTGGCTCAGTTGGTAGAGTTGCCAGCTGAGCACTCCAGAGTCCCTGGGTTTGATCCCTGCCCTGTAGAAACTGGGGCAGTAGCACAAATGTGAGCCTGTGCCCTGAGTGTGCACAGCCCTCTCGTGGTGCCTGATTAGGAGGAAGGCAAAAGTCCCAGAAATGACAGTAACCCAGAGTGTGCTGTACTCTAGGAACACCTCACCTGCAGAGGAAACACAGGCAACATGTGGATGGGAAACTGGGGGCCCCAAAGATAGCATGCTCTCCTGTGGCTCAGAATACCTTGACTATTCGGGAGGCACTCTTCTTGCAGTCACAAAATCAATAGTCTTGAATAATTCACACTGCATACAATCAATTAAAGTCATGTCCAGCTCCAAGTTGAGCTCTTTGCTTTATACCCAGAGGGATTAGACTATTACCCATCCCAGGCAGGTTCTGTGGCATCAGTAAGTGACCCTTCTGTTTCTGTGCTCCCCCTCTGTCTTTCAG
Seq C2 exon
CACATGATTGCAGACACTGTCCGAACCCTGAGACACTGCAGGACTAACCAGTTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041992-Rapgef5:NM_175930:26
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=0.053
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0061714=RasGEF=FE(11.4=100)

							
A:
NA

							
C2:
PF0061714=RasGEF=PD(0.5=5.3)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000105313f4321A





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000105313
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr7:22125659-22131036 
ALTERNATIVE
HsaINT0137432
(RAPGEF5)
Human
(hg19)
chr7:22165277-22170654 
ALTERNATIVE
HsaINT0137432
(RAPGEF5)
Rat
(rn6)
chr6:145615177-145619029 
ALTERNATIVE
RnoINT0124286
(Rapgef5)
Cow
(bosTau6)
chr4:31020151-31025738 
LOW PSI
BtaINT0122412
(RAPGEF5)
Chicken
(galGal4)
chr2:30763279-30769225 
ALTERNATIVE
GgaINT0091868
(RAPGEF5)
Chicken
(galGal3)
chr2:30660413-30666359 
LOW PSI
GgaINT0091868
(RAPGEF5)
Zebrafish
(danRer10)
chr19:2857319-2857390 
LOW PSI
DreINT0124593
(rapgef5a)
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"