Special

MmuINT0133912 @ mm9

Intron Retention

Gene
ENSMUSG00000020696 | Rffl
Description
ring finger and FYVE like domain containing protein [Source:MGI Symbol;Acc:MGI:1914588]
Coordinates
chr11:82623510-82626312:-
Coord C1 exon
chr11:82625902-82626312
Coord A exon
chr11:82623721-82625901
Coord C2 exon
chr11:82623510-82623720
Length
2181 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGA
5' ss Score
9.79
3' ss Seq
TCTCATCTTTGCCATTGCAGTCC
3' ss Score
8.23
Exon sequences
Seq C1 exon
CAGACCTGCTTGGACTGTAAGAAAAACTTCTGCATGACTTGTTCGAGCCAAGAGGGGAATGGGCCACGCCTCTGCCTTCTCTGCCTACGGTTCCGAGCCACGGCCTTCCAGCGGGAGGAGCTCATGAAGATGAAGGTGAAGGACCTGAGGGACTATCTCAGCCTCCACGACATCTCTACGGAAATGTGCCGGGAGAAAGAGGAGCTGGTGTTCCTGGTGCTTGGCCAGCAGCCTGTAATTTCTGAGGCGGACAGGACTCGTGTTCCCCACTTGCCCCAGGCCTTCCCTGAGCAGCAGGCCTTCCTGACCCAGCCTCAAACCAGCACAGTGCCTCCTACCTCACCTGGCCTCCCTTCTTCACCTGCACAAGTCACCTCTGTCCCCTTAGCCCAGGATCAGGAAACTCAGCAG
Seq A exon
GTAGGAACCACCACGCAGCCTCTTCACCGCTGTGTCTGCTCTGGGACTCTTTTTATTCCCTCCGCTGCATTGTGGGAGTGGGGTGTCAGGTGTCATGTCTAGATGGTGTAAAACCTTTCTGCTTGTTGATTCTAGAAGTGGTGTTTTCTGATCATTAGGCTCAAGCTCTGACTTCAGGGAAGGTAGGCCTAGTAGTACTGTGTTTTTGTGCAGTTTGTTTGTGATACCTTCATCCCCTAATTAGACTTAAAAAAATCTTCTTTTCATTGCTTCAGAAATACTTTGAGGAAAATCATTCTCATCTCTAGTTTGCCCTTCAGTTTGCTGCCCTTTTGACTGATCTAAGTGGCAGGAGAGGAGAGCAATGGGGAGCATTGGGGAGGGCGGGCCTTGCCGCTGTCCTGCATACCATGTGCGAACAGAACAGCGGTGGCCAGCATGCTGTGGGGCTGTACCCTGCCTCCCTGTTACATAGTGTTGCCTGGAAACGGTAAGCCAGGAGCAGCCAGTTGGGTTGTGGGGAGTCCACAGTCAACACGTACCGTCTCCACCCTCGGGAAGCCCTGACAGAGAAAGGCTAAGCACGAGACCCGCTCTGAGGTTTGTCTGGGGTTTGTCAGGAGTGGTGGTGTCACAAAGATCTGCAGAAGTCTCTCACTCATTCTGCAAGTCACAGGGCTTGGGCACAGAAAGATTAGGACCTAGATCTCTATCCACTGTCATCGTCCCCCCTCCCTCCCCCCTTTGCACTGTCCTGAAACTCACTCTGTAGATCACACCAGGCTGACCTCAAACTCAGAGATCCACCTGCCTCTGCCTCCTGGGGCAGAGTGCTGGGCTTAAAGGCGTGTCCCCACCACGGGCATGAATGAGGTGTTTGAACAAACTAGTGGACACTGGTGCAGAGGCAGAACCGTGGGAGTGGGTGGAGGCTGTGGGGAGGGCATTGGGTTAAGACAGTCTGCTGGAGAGACACCTTTCACCTCAACTGTCCAGGCTGAGCACAGACTGGTGATGCGTGGCGGCTAATGCCACCCTCACTGCTGGGCAAAATTAGCACACTCTTGTACTTGATGCAGCTTTCCATCTGGTGAACTCTGTGTGTATCATCTCTGGCTGTGAGATTCGGCTGTTAGACAGCAGGCATTCGTGGTCCTCCTTCGGGAGCCTTGTTTCTGGAGGGAGACGGGAATACACTTTTGGACATTCGTGTGAACTGAGAGCGGCCCATGGTTTGTAAGTCACTGGGCATCTCTGTGGCTGTGATGGCACCTTTCTCTTCCCACAGGCCGTTGGCCATGTGTCTCAGGACCACGAGGAGCCCATCTTCCCGGAGAGCACAGCCAGAGTACCTACTGAGGATGAGACCCAGGTGGGGCCTCTGCTCGGGCTGTACTTGACCTTGTTTCTTTGCCTGGTCTTCTTGGGAAGTTCCGAGGAGCCTCAGCCGACTCGGGTGCAACAGGAGGGTCAGTCTGGAAGGACAGTCCTGAAGTCCTTGAGTCCAGTGGTACCACTCCAGATTAACCTTTGTTGCCGTCAGTGTGAGCAGGCAGATCTGAGGCTACAATAGAGGCTGGGGAACCTGCGGGCCCAGGCTGAGTTCCAGTCCTTTGGCTTTCTAAGAGCTGCCAGAGGCTACCCTATGGGTGCTGCTGTGACAGCCCTGTCACTGTCCTGTGGTCTGGGGTGCAGTAACCACTGTTGGGGAAGGAAGGAAGATGATGAGGCTTTCAGGCCTCAGCCACACAAGGGCGCCCAGTACAGAGCACGGTTCTGACGGGCCAGAGAGCTTCGGTGAGTCCATGCATGGAGTCCTGCCAGGGAGTCAGTACTGAGGAGAGGCAGTGCCACATCTGGGGTTTCCTCGGGAACCCTGAGTGGCAGGACAGTTGTCTTCTTTGAGGAAGGGTAACTGGTTCAGGATGGTAAACAACTTGAAAAATACTGTCCAGTATTTAGTGGAGGCAGCGGCATTGAGAATCGGGGCCCTCTGGCCAACTAGTGCGCCCTGTATGCATTTTATTGACATGTCAGTGTGTGGCTGTCTGCATAAAGTACATGACGGGGCAGGCAAAGACCAGCCTGTCAACAAAGTGCATTCTGATGAGTGCCCTGGGTTCCTTGAGAGCTTGCAGGACCCAAGAGCTGAACCACCTCATCTCATCTTTGCCATTGCAG
Seq C2 exon
TCCGTTGACTCAGAGGACAGCTTCGTCCCAGGCCGGAGGGCCTCGCTGTCTGACCTGACCCACCTGGAGGACATTGAAGGCCTGACCGTACGGCAGCTGAAGGAGATCCTGGCTCGTAACTTTGTCAACTATAAGGGCTGCTGCGAGAAGTGGGAGCTGATGGAGAGGGTGACTCGGCTGTACAAGGATCAGAAAGGACTCCAGCACCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000020696-Rffl:NM_026097:3
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.372 A=NA C2=0.191
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0136316=FYVE=PD(73.3=46.0),PF102084=Armet=WD(100=55.5),PF0203722=SAP=WD(100=15.3)

							
A:
NA

							
C2:
PF102084=Armet=PU(92.3=84.5)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000021036





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000071150, ENSMUSP00000074108, ENSMUSP00000091510, ENSMUSP00000103808
          









    
Other Skipping Isoforms:
ENSMUSP00000099507, ENSMUSP00000103804, ENSMUSP00000115846
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
chr17:35016581-35017522 
ALTERNATIVE
HsaINT0139633
(RFFL)
Human
(hg19)
chr17:33343600-33344541 
ALTERNATIVE
HsaINT0139633
(RFFL)
Rat
(rn6)
chr10:70164001-70164811 
ALTERNATIVE
RnoINT0126264
(Rffl)
Cow
(bosTau6)
chr19:15395191-15396081 
ALTERNATIVE
BtaINT0124257
(RFFL)
Chicken
(galGal4)
chr19:4498248-4498576 
ALTERNATIVE
GgaINT0132819
(RFFL)
Chicken
(galGal3)
chr19:4470529-4470857 
ALTERNATIVE
GgaINT0132819
(Q5ZI26_CHICK)
Zebrafish
(danRer10)
chr15:4562764-4564578 
ALTERNATIVE
DreINT0126239
(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"