Special

MmuINT0007039 @ mm9

Intron Retention

Gene
NA
Description
NA
Coordinates
chr6:47905816-47907601:+
Coord C1 exon
chr6:47905816-47906169
Coord A exon
chr6:47906170-47907474
Coord C2 exon
chr6:47907475-47907601
Length
1305 bp
Sequences
Splice sites
5' ss Seq
AAGGTATTC
5' ss Score
6.8
3' ss Seq
GGGGACTTGTATTCCTCCAGGTT
3' ss Score
6.57
Exon sequences
Seq C1 exon
GACTGGCATATGGGGACTGACCTCCAACAACAGACCCAGATCCAGTCTGCAGAGATCTCCCTTCTAGCTATCCTATCTGCTGTTCAGGCAGTGGAAAAGAAAACAGAGTCCCAGGCTGTCCACCTTCAAAACTTGGAAGTAAGAACAGGGTCAGCTGAGAAGAAGTTGGCTGACTTCGAGAAGACGGCCATGGAGCTCAGCAGCCAGCTGGAGGGCAAGTGGGCTGTTCTGGGGACCCTGCTGCAGGAGTACGGGCTGCTGCAACGGCGGCTGGAGAACCTGGAGAATCAGATGCAAAACCGGAACCCCTGGGTCCTGAGGCTCCCCCCCAGCAGCAGGGATGAAGCCCCCAAG
Seq A exon
GTATTCATAGAGTGAGGAAAGGCCTCCAATCTGAATTCTAGTGCTTAATACAGTCACTATGGACTTTAAGGAGCTTTTAAAATTGTCAGAAGTACAGTGTGACATTGGGAAGGTAACAGTAGAATGGGTTGTTGGGAAGGGTATGTTTGGGCAGCAACAGTTGTCTTCTTCCAAAATGAGCTTTTTTTTTCCTTATTGAAAAAGATTATTTTGCTAGCACACACCTTTAATCCCAGCACTTGGGAGGCCGAAGCAGTCATATATCTGAGTTTGAGGCTAGCCTGGTCTATAGAGTGAATTCCAGGACAGCCAGGGCTACACAGAGAAATTCTGCCTTGAAAAACCAAAAAAATGTTTTCACCAAGTGTGGGTGGTGCATGCCTTCAGAGGTAGGCAGATCTCTGTGAGTTGGTGGTCAGCCTAGTTTATATAGAGAGCTCTAGGACAGCCAGGACTAGAGAGAGAGACCCTGTCTCAAAAAAAGAAAAGAAAAGAAAAAGAAAAGAGAAAAAGAAGGGCTGGATAGATGGCTCAGTGGTTAAGAGCACTGACTGCTCTTTTGGAGGATGTAGGTTTAATTCCCAGCATCTAATGGCAGCTCACAACTGTCTGTAACTCCCAAGGTCTGAAACCCTCACATAGACGTACATGCAGGCAAAACAAGACAAAGTCTACAAAAATACCACTGAGTCTGTTTGATGATGGCCAATTACACCTGAAGCATGTTATTGATTGCAGATAGCTTTTTAGTTAGAGATAGGAGCCCATGACTACTTCACTTTCTCAGTACTGGGACTCCCATTTCCCTTTCTTCCTCCTTTCCCATAGATCCCTGAGCCTTCTGTGACGAAGACATTCCATTTAAGAATGAGTGCCCCAAAGTCTCTCACTCTCTCTACATTTTCCATTGTGGGTCTCTGTTAGTTCCCACATACTACAGGGAGAAGCCTCTCTGATGGCTGAGCGGGCACTGATCGGAGGCTCAGCCTGGTGTGGCCCTGGGGGTCCCCCGTGGAGAGTGCTTCTGAGGATGAGCAGCTGGCCTACAGGAATGGAGGTGGGCTAGAAGGGAAGGCCCAGGAAGACTGCTGAGAGTGAGAGCTGGTTTAAGTAGAGGAAGTCAACAGAAAGCATCTCCATTCAGGTCCCAAGGGAAGATACAAGTGTGCAGTGGAGCTAGAAGGACCCTGTGCACTTGTCTGTTTTTCTATAACAAATGTGGGCAGAAGCTAGCATTTAGTCAGAGGTGCCCTCAGTTTTGAAGGCTGGTTTCTGAAGGGGTGGTGGGGACTTGTATTCCTCCAG
Seq C2 exon
GTTTCTGTGACTACTGAAGAGGTGGCTGGGTGTTTCCCTGAGCAACAGGAAGGTAGCCCAGAAGACTGGCAGAAGGAACTCTGCAAGCGCGTAGCAAAGGAAAGGCGTGAGGTGCTAGGCTCTCTAG
VastDB Features
Vast-tools module Information
Secondary ID
-AI894139:NM_178898:2
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:
ENSMUSP00000098989





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000098989f4544A, ENSMUSP00000114227
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr8:144778165-144778438 
ALTERNATIVE
HsaINT0186958
(ZNF34)
Human
(hg19)
chr7:148984868-148985521 
ALTERNATIVE
HsaINT0093509
Rat
(rn6)
chr7:118517944-118517956 
Cow
(bosTau6)
chr4:113309374-113309497 
LOW PSI
BtaINT0166031
(ZNF746)
Chicken
(galGal4)
chr2:496826-498270 
ALTERNATIVE
GgaINT1002553
([1])
Chicken
(galGal3)
chrUn_random:9926744-9926903 
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CCAGGCTGTCCACCTTCAAAA

				
R: 
TCACGCCTTTCCTTTGCTACG

				
Band lengths: 
354-1659

			

		

	





	
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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