Special

MmuINT0003815 @ mm9

Intron Retention

Gene
NA
Description
NA
Coordinates
chr8:113639024-113640731:+
Coord C1 exon
chr8:113639024-113639141
Coord A exon
chr8:113639142-113640581
Coord C2 exon
chr8:113640582-113640731
Length
1440 bp
Sequences
Splice sites
5' ss Seq
CAAGTGAGG
5' ss Score
5.85
3' ss Seq
TTGTTGCTTCTCTTCTTCAGCCA
3' ss Score
7.81
Exon sequences
Seq C1 exon
TGGGCATATGAGCTGGGTCTGTCCAACGAGGAGCCGCTTAGTATCCCGCTACACGCCTGTGAACACTTCTACCTTCTGACTCGTCCCTGGGACACCCCTCTGCAGAGCAACACACCAA
Seq A exon
GTGAGGACTTGTATTTTTTTTTCTTTCTTTCATTCTTCTTTTAAAAAAATAATTTTATCTCCTCGCTAGCTAGTATCCTGTCCTTTGAAAGGAAAACTTCATTAAGGACATATTATGTCTAGAAGCCTTTCTTTCTTTTCTGGAGCATGTTACAGGGACGTGGATCCCATTCTAAATTTCCTTTGATTACTTCTTAGGAAAAGATAGCCAGAATGGAGATGCCACCAAGAATGTTCTTGCTTTTTGATTTTTGTTTGTTTTTGAGACAGGGTTTCTCTGTAATAACCCTAGCTGTCCTGGATTCTCTTTGTAGACCAGGCTGGCCTCAAGCTCACAGAGATCCACCTGCCTCTGCCTCCTGAGTGCTGAGATTTAAGGCGTGTGCCGCCCCACTTTCTTGGTTTGATTTTTTTTTCTGAAAGCTTATTTTAATCCCTAATATATATGGTTCATTGAGAATTTGGAATATACATTTTGTGCTTTCATCTTAAATGGTATCAGTTGTAGAAGTGTATAGGTAGTCCATGTACCTAGTGGTTTAATGGTTATAAGCCACGGAAGGAAGAAAAGGTGGGGCTATTTTACTCCTTCCTTGCTTGGCCGGTAAGTCTCTCTGTCTGCCTTCCTTTCTTTTCTTCTTCTTCCTCTTCCTACTCCTCTTCTCTCTCTCTCCTTCCTTCCTTCCTTTTGTTTTGGGGCAGACAGTAGCCTGCCTGTCCACCAATTCACTCTGTAAACCAGACTGGCCTTGAACTCAGAGGTTCACCTGCCTCTACCTCCCGAGTGTTAGGATTAAAGGTGTGTACCACTACTGCCTGGCTTATATTTTATTTTTTTGAGACAGAGTCTCATTGTGTAGTCCTGGCTGGCCTGAACTCACTGTTGTGGGCTTGGAGGCAGAGGCAGGCATGCTGAGCTTAGGAGGGTTTTGATATCATTTCAGGGAATGAACTCTGCACCTCCCCTTTCTGTTAGACTTTGGAAAGGCACAGTGCCACCATAGTTTAGTTTGATTGTGAGGTGTTGGCAAAGCGTTTAGGTTCCTGGTAATGTTTGGGATAATCAGAGAAACAATCTTTTCTGTAATCTTGAGTGGGAAGATCCTTCCCCCTGACTTCCAATGGTTTTCCTTTCCTTTTTTTTTCTTTTCTTTTTTTCGAGACAGGGTTTCTCTGTGTAGCCCTAGCTGTCCTGGAACTCACTCTGTAGACCAGGCTGGCCTCGAACTCTCAGAGATCCACCTGCCTCCTCCTCCAAAGTGCTGGGATTAAAGGCGTGCGCCACCGCTGCCTGGTCTTCAGTAGAAGTGTTTTAATGGATGCCTGTATTTATTGGCTGCTGCACTGTTGGTAAGGCAGTCTCTCCATCTAGGAATCTGGCTGGTCTCTAACCCCTTGTTTTTCTCCTTTGTCCCACTTCTTTGTTGCTTCTCTTCTTCAG
Seq C2 exon
CCATTGTGGATGCTGATGGAAGAATTTACATTAGGAACTGGCAGGGTGGCATCTTGTCTGGAGGCTTTGAGAAGAACCCCAAACCTATTTTCACTGAAGGCAAGAACCAGTTGGAAATTCAGAACCTTCGTGAAGACTGGGATCACTTTG
VastDB Features
Vast-tools module Information
Secondary ID
-4930402E16Rik:NM_198308:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

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

				
Domain overlap (PFAM):

					





						

							
C1:
NA

							
A:
NA

							
C2:
NA

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000046639





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000121325
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr16:70131420-70132150 
ALTERNATIVE
HsaINT1026590
(PDPR)
Human
(hg19)
chr16:70165323-70166053 
HsaINT0122647
(PDPR)
Rat
(rn6)
chr19:43128510-43129433 
ALTERNATIVE
RnoINT0109338
(Pdpr)
Cow
(bosTau6)
chr18:1932881-1933613 
LOW PSI
BtaINT0109635
(PDPR)
Chicken
(galGal4)
chr11:1785839-1787114 
ALTERNATIVE
GgaINT0025825
(PDPR)
Chicken
(galGal3)
chr11:1766899-1768174 
LOW PSI
GgaINT0025825
(F1NG59_CHICK)
Zebrafish
(danRer10)
chr18:50957966-50958194 
LOW PSI
DreINT0016272
(PDPR)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GGCATATGAGCTGGGTCTGTC

				
R: 
GTGATCCCAGTCTTCACGAAGG

				
Band lengths: 
262-1702

			

		

	





	
Functional annotations
(Submit an annotation)

	


There are 0 annotated functions for this event 


		










GENOMIC CONTEXT[edit]












INCLUSION PATTERN[edit]






SPECIAL DATASETS
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types






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