Special

MmuINT0133914 @ mm9

Intron Retention

Gene
ENSMUSG00000020696 | Rffl
Description
ring finger and FYVE like domain containing protein [Source:MGI Symbol;Acc:MGI:1914588]
Coordinates
chr11:82617321-82622038:-
Coord C1 exon
chr11:82622015-82622038
Coord A exon
chr11:82619692-82622014
Coord C2 exon
chr11:82617321-82619691
Length
2323 bp
Sequences
Splice sites
5' ss Seq
ACGGTATGT
5' ss Score
9.94
3' ss Seq
CTTTTCTTTTGTTTGTCCAGGGG
3' ss Score
9.33
Exon sequences
Seq C1 exon
TGTCTGGTAATGAAGACCAAAACG
Seq A exon
GTATGTAGTTGTTTCTGTTAAAGATAGGCTGAGGCTCTTAGCTGTTTTGTCCTTCTGATTTTAACTCTGATGATGGCTGTTCACAGTTTTAAGAATCCCAGGGAGGCTATAGGAAAGTAGAGTCAGGTATTGCCCTTGCCCCACCCTATGAAGGAAGCTGACAGCAGCCTAGGGGCTTGGCTGGACTGGATCTGACTCCCTGGGTAGGGAGTATCATGCTCAGTTTCTCTGAGCAGTCTGTCTGGAGAGAGTCTTAAACATCCAGAGATATCATTGAAGTTTTTATGTTTTTGTTTTTTTGAAGATAGGGTCTGTCTGTGTAGTCCTGGCTAACTGGGAACTCACGATATAGACCAAGCTGGCCTCAGGTATTTGTCAGCCAAACCAAAAAGCACAAGGATGGTGACCTGAGAGCCCTTTTTGAATGGTAGCTAAGGGGACAAAAGAGGTGGATGCCCTCTGAGCAAAAAATGCATATCCTACCTGGCTACCTTCACTCCCACCAGTGTGTTAAAGGCCACCACTGGGGGTATCCTCAGAGCACACTGTAGAACTTGGTTGCCTGTGGGATGTTTTCACATATATTGCACCCTTTTCGAAAGCCTTGAGGGGCATGGTTGTAAATTTCCCAAGAGAGAATATTCTCAGTAATGTTCTAGTCTGTAGAGCACTTTAAAACTTTTCTAAGTAAAATGGTCCACTGTGCAGAATAGGCAGACCTGAGCTTTCTACTTAGTCCCTGTAATCATCTGGGTTACCCCACCCCAATAATTCCAGGATGAAATTAATCTATGTGTCACCATCTTTCCTTCTCCCCATTCCTTGGAGAATGCTGACCACTGAGGGGATGTTTATTATAGTTTCTCCTCATTGATGACTGAATTTCTGTAGATGGCGCCATCTTGTTTTAGATATGTGTGCACCCTTCTAACCTCTGTATTAAGGCCACGGGTTTTTTTTTTTTTTTTTTCTCAGCCAGCCACCTGCTATGGGAAGTGTTCTTTGACTTGATGTTTCATAGTTATGTATGAGTAGCTACATGAAAAAGTTCCAGAACCAACAAACTAGCAATAAACAAATGTAAACGAGAGGACTTGTGCATTCAAGTGACTTTACTTTTTAGACTAGTCCAGAACAGAAAAAAGGACTTAGAAGCAACAGAGAAGTGGAGAGTTCCTTTGGAAAGTTACCAAGTCCTGTTGGGAGCAGCAGCAGTATGAGAACAATTTTGTTTTATGGCTGCTTAGTTTGACACACAGGAGATAGGTGGGCTTTTGACTACTGAGCTGAAGAAGGATAGTAGCTGTGTCTATCACTAGAATAAGCCTAAAGTTAGTATTTATTGAGAAGTCTGGGCAGTTAATAGTATCTTGATAGTCTCTGCTCTTGGAGCCCTTATCCAGACGGCCAGCATGCCTATGCCTCTCTGATTTGAATGTGGACAACCTCAGCAGCCCTATATCCTTGGGCAACCCACTTAGCTCTGGCCTACGTTGTCTCATCTGTAAAACCCACTTTAGTACCTCTGGGTTAACACAGAAAGCTCTTAGGACCCTGCCTGACACATGGTAGGCAGTTAGTCAATGTGAGCAGTTATCATTCCCTGGGCAGAATGTTCATTATCAGATGTTTAAAGAATACCTACCATGTGACTCATGTTTGGGGAATTCAAAGACAAGTATCTGACCTCAAAGCATAAAGCAAATGCTAAGCTTATGATTACTGTCTGAATAAGTTGAATTAGCAGCTCTTAGTCTACTGTGGGAGATAAGTGAATTATCATGCAGTACGATAAGCAGTCAGGGGTGTGAATAAAATTCAATGGCTGCAGCACAGAAAAGGGAGCCGTGTGTCTGCCCGTGTCCTTCTCTTAGGAAGTCTTTTCAGAAGCTTGGAGGTAGGTAGATTGCTGGATAGCACATGGGCTCCCCCGTGACTCTCAGCTTTATTAAATCAGGTCTATGTTTACAGATAAGCCTTAGGATTCTTAATGAACCATTTTAACAGCTCTGTTTATATCCAGACTTTTCTGAGCCAGTTTTTATCTTTTCTGCATATTCTTCCTCAAGGGATGTGGTACCTAAGCATTGTTCACTGACTGAATTACAGCCTCCTTGTCCTGGGATAGTTTTGATCTGAGAGTACCAGACTCAAACCTTTGTTATGTTAGCAGGCGTGGGTGCTTAACAAGCAGGTGGGGTGGTTTGGTTGCTGAGGTTTTGTTTTGGATGGTGCTGTATTTGAGGGGAAGTGTGGATTTGGGGGTTTCCTTAGTGCAGGCCCTTATATACAGAGACATCATCCTTTTCTTTTGTTTGTCCAG
Seq C2 exon
GGGGAGCAGTGCCTTCTGGCCTGGAGGAGAACCTGTGTAAGATTTGCATGGACTCACCCATTGACTGTGTTCTGCTGGAGTGTGGCCACATGGTGACCTGTACCAAGTGTGGCAAACGCATGAACGAATGTCCTATCTGCCGGCAGTATGTGATCAGAGCAGTGCACGTCTTCCGGTCCTGATGGCTAGCATTGGTTTCTTCAGTGCCTTACAGGACATAGCCCACGATGTCTGGGCTCAGGGTTGGTCCAATACACAAGGGCAGTCTACTGTGAGCAACTGGCAGTGTTCTTAAGACTAGGACAAGCAGAGTTGCCTGGCATGCTTGTTTTAGGTGGCAGAGCCCAAAACCAGTGGGAACTGGTTCACATCACATGGGTGAATGCCTGCATCTGTGATCATTGGATGGTGATGGTCATCAATGAAGAGGTCTTTCCAGAACGTGGACCAGTCTCTCCTGTCCTAAGATCCATTTCATACATCTGTACACCACTCCTCCTGTCAATCATAAGTTCTGCTAGAAATGGTCTTTCTCCCACCCCACCCCCAGCACATTTGGATTTAAATTTCTGGTCTCTCTGGCTTTCTGTGTGTTAATGTATCTTTTAAGTCTTCTCATTTGCCTAAAACCCATTTCTTTCTATGGACCAAAAAAATATGTTAATTGGGCCAATAGTATTCCTCAGGTCAGAGTTTGGATCAGTAAACTGACCTCTAGTGAGAAATTAAGTCTTAAGTGATATAGAAAAAAATTCTAGGTTGAGTCACTTCTGTTTAGTATTGGGGTTGGAAAGAACCAGTCTCTGACCTAACTGCTGGGAAGTCCTTCAGAGATGGTGCTGTTTCTCTTTGGGTTTGACTTTGTATCATCCTTAACTTTGGATTATGAGGAAAGAGAAATCAAGGCAGCGGCTTTGTCTTTGTCTTCTGGTCCTCATTTTCCAGCATGCTAAAATACTTTAAAATTTTTTCTCTTCCTTTGGTCTTAAATTTGCTTACTGAAAGCATAGGAACTTCAGCAAGGAGCTGTTCTCTAGCTTGGCTGTACATGGAGTTCTTGGAAAGCAGACACACAGGACAGTGCATGAGGCACTGGATGTGTTAGACTATGACTACGGCTGCTGAAAAGTCTTAACTGCACTCTGTTCTCAGCTGCTCGGGCAGGTCAAGACAAGCATTCTTTAAGTCATGATTGCAGCCCTCCCAGGGGCTTTACACCACTGACACAGCTGAGAACAGCTCAACAAAGCACAAAATATACTATCAGAAGAGCTGTGTGTTTCTCTGTGGGGTGTACGCTCAACTTGGCTAACACTACCCTTCACTGTGTAGCTATGTGAGACTGGAATAACCAACCACTCACTCATGACTGACTTGGAAAAGTGGAGGGACGCCTCTTAGGGGACTATTAGAAATGCTTAGGCTTCTCCACTGAATTCCTTCAGAGGATCAAGTAGTTCCATGAAGCTGTTGTCAGAGATGCCAGGCCCACTTACCTCTGCATTCGAAGTCCAGATGACCAGATTTTGGGTCAAAGCTTTTGTGGATGTCAGGGATTCAGATCCCTCCACAAAGACTCCCTTGCCCTCCCTCCCTGAACAGTGAATGCTGTCGTTTACAATGTTTCCAGATTAGCATGCCCACTGATTTTGCTGCTCCTGGACTCCACTGTGAAACAGGTCTGATCTTACAGCTCAGTAAGACCTAAGAATAACATTAAAGCCGGCTGGCTCTCCCTCATAACTGCTTTCTCTTCTGAGGCCTTATCTCCCTACCTCCTGTACAGGAACAGAAAATACACTGATGGCTGTGGTTAGCAACCCAAGTAACAACCAGAACCCATGCCATTTAATTTGGCGATCTTACCTTTAAATCTTTACCCTTGGTGTTCTCATTTGGGGGGGAAAAAAACCAAAACATGTCAAACAACTTTATTGTTAAACCAAATGAAAGTTGGAACCCATTCCAGTTAACATCTCAGGTAGAAAACCTTAATTTTTTTTTTTTTTTTTTTTGGTTAAATACCTGAGCCCCCTTTTTGTTCTTCACGGATCCTTGGTCTTAATGTTGAAACACCTAATCTTTCCAATTATTCTGTGGATTTTGCTGATTGCACCAAGATTTCAGTTGAGACTTAGTTTTCAAAGATGCTGTTTCATAGGTTGGAAATAGCCGGTTCTAAACTAATAAGCTGTAAAGGAATTAATAGTCTATGTTGTACAAATTTGTTGAGATCTCTCGGATGTAAATGTGTAGCTCCAAGTGGCTTACATTAAGATTTTCTCACCTGGGTGTTAAAAGCATACCCAAATGTGTATTTTTTTGTTACAGAGCTCTGCTTTATAATTTTGTAATAAAGTTTAAATACAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000020696-Rffl:NM_026097:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.619 A=NA C2=0.017
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF102084=Armet=PD(6.2=44.4)

							
A:
NA

							
C2:
PF139201=zf-C3HC4_3=WD(100=75.4)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000071150





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000021036, ENSMUSP00000074108, ENSMUSP00000091510, ENSMUSP00000103808
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr17:35012150-35014739 
ALTERNATIVE
HsaINT0139635
(RFFL)
Human
(hg19)
chr17:33339169-33341758 
ALTERNATIVE
HsaINT0139635
(RFFL)
Rat
(rn6)
chr10:70159988-70162253 
ALTERNATIVE
RnoINT0126266
(Rffl)
Cow
(bosTau6)
chr19:15397486-15399959 
LOW PSI
BtaINT0124259
(RFFL)
Chicken
(galGal4)
chr19:4499727-4499990 
ALTERNATIVE
GgaINT0132821
(RFFL)
Chicken
(galGal3)
chr19:4472008-4472271 
ALTERNATIVE
GgaINT0132821
(Q5ZI26_CHICK)
Zebrafish
(danRer10)
chr15:4558654-4560041 
LOW PSI
DreINT0126241
(rffl)
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"