Special

MmuINT0005651 @ mm9

Intron Retention

Gene
NA
Description
NA
Coordinates
chr17:22474956-22478060:-
Coord C1 exon
chr17:22477934-22478060
Coord A exon
chr17:22477075-22477933
Coord C2 exon
chr17:22474956-22477074
Length
859 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGA
5' ss Score
8.91
3' ss Seq
TTGCACCTTTTTTTTTCCAGAGA
3' ss Score
9.27
Exon sequences
Seq C1 exon
GGTCAGTTAACATTCAAGGACGTGGCTGTGGACTTCTCACAGGAGGAATGGGAATGTCTTGACTGTGCTCAGAGGGCATTGTACATGGATGTTATGTTGGAGAATTACAACAATCTGTTTTTTGTGG
Seq A exon
GTAAGAATACTCTTCTTGTAGAATTTCTGATACATTTTTTGAATTTACCTATTGTGTGTTTGTTATCTCTCTGAAAAATCTAAAAACTCCCAGAATGAAGGAAATTCTAGTTACAAACTTTTCATTGTTTTTCTTTTACATTTCTCTACATTCTTTTGAAGAGGAATCAGTGTTATATGCTCGGTAGTCTCTCCAAACTTATTGTCTACTTTTAATCAAAACTTCCGATTTCCAAAAAAAAATTGAATATTCACAGTAAGAAAATATATTGCTACACACATAATAATTGGAATATTTTAATTTTACTACTGAATTAAAGTCTTCACTTATTTATGAATTTTAAAAATGGAGATTGTTTTAAATGGAAAAGAGCTGTTGGTTTGAGAATTTTGTTGTTATCTCAACATTTTTACATGTAATCTATGTTTAGTCCTGATACAGGATGGTCTTTGTATTGTGAATTCCATGCCAATGTGAATTACATAATGAATTTGTAGCTGACCAAACTTACACAGTGTCACGATCATAAAACTTCAACAAGAAAATAGAGAAATAGTTGATGACATGATATTTTAGTGGGCTCCTTTCTCAAAGTTATTTCCTGTCAGGCTTTTTTCTACCTTCTGCAAAATATACTGTGTATATAAGGGTTTTGAGGCTGTTATCATGTCCTTTCATTTGTTAATAGATGAGCTTTAAGGTTGTTCTAAGCATCCATGAAATAATTGTGAAAAAGACTACTTTTGAGCCCTATCCTTGAGAATCACCAAATTATATTAGAAAATGTCAGGAAACATGTGCTATTGTCTTACTTATCCATCAATCCCTATCATCTCTAATTGCACCTTTTTTTTTCCAG
Seq C2 exon
AGAATCATTGTGTGTGTCCTAAATATGAGAATGTCTTGGATCAAGACACACAGCATATTTTCCACAAGCATGTAAATATCCAAAAGAAGTCTTGTAAATGTAATGATCGTGGCAAAGATATTTATGAATACACCCAAAGTGTACTTTACCAAGATAACTTCAGGGATACACATGTTAAGTCATCAGATGTAAACAGACATGAAACTGGAAACACCAGAGAACCTTGCAAATATAAAAACTGTGTAAACTGTTTAAATTTGTGTTCTATCATTGGTCTAAATCAAGGAATCCACATAGGAAAGAAAGAACACAATGGGACAGTGCTTGATAAGGTTTTTGACTCTAAACAAATACTCGGGCTGAAACAAACCAATAGTGGAAAGAAACCTTACAGATGTAGTGAATGTTCCAGATGCTTCACCAAGAAATGCAAGCTTAGACAACATCAGATAATTCATACAGGAGAGAAACCTTACAGATGTAGTCAATGTGACAAATGCTTTTCCCAAAAATGCAGTCATAGTACTCATAAGAAAATTCATACAGGAGAGAAACCTTACAAATGTACTGAATGTGACAAATGCTTTACCTTTAAAACTGACCTAAGAATTCATCAGAGAATTCATACAGGAGAGAAACCATACAAATGTATCGAATGTGACAAATCTTTTACCCAGAAAGGCCATCTTATAATTCATCAGAGAATTCATACAGGAGAGAAGCCTTATAAATGCAGTGAATGTGACAAATGCTTTACCCAAAAATGTAGTCTTACTATTCATCAGAGAATTCATACAGGGGAAAAACCGTATAAATGTGGCAAATGTGAAAAATGCTTCACTCACAAAGGTGATCTTAGAAGTCATCAGAGAATTCATACAGGAGAGAAACCTTATAAATGTAGTGAATGTGACAAATGCTTTACCCACAAACGCAGTCTTAGAAGTCATCAAAGAATTCATACAGGAGAGAAGCCTTACAAATGTAGTGAATGTGACAAATGCTTTACCCACAAACGCAGTCTTAGTATTCATCAAATAATTCATACAGAAGAGAAGCCTTATAGATGTAGTGGATGTGACAAAATCTTTAATCACAAAGGTGATCTTAGAAATCATCAGAGAATTCATACAGGACAGAAACCTTATAAATGTAGTGAATGTGACAAGTGCTTTGTTCATAAATACAGTCTTAGTATTCATCAGAGAATTCATACAGGAGAGAAACCTTATAAATGTAATGAATGTAATGAATTCTTTAGATATAAATGTAGTCTTAGGACTCATCAGAAAATGCACACATTAGAGCATATTTACAAATGAAACAAATGACACAAACCCTTCAAAAAAGATCATGTTAAAACTCATCAAACAATATATACAGGAGAGTGTCCTTTCAAATATAAATGTTTAAATCCTTTACTGTTAGCTCATCTCTGACAGTACATCAGAGAATTCATACGGGAGAGAAACCTCACAAATGTAACATGAGGAAAGAGCTTTACCTGAAAAGTAGTTTCTGCTGGAAAACATGTGGCATGTATTTTACCCAAGTGGAATTCTTTGCAACACTTTAGGCTCCACACTAGAGTTAATTATGAATATTAAGATCTTGTGAAAGCACCTAAGTAGTGTTCAAATCATAGAAACTATAAAGCATTTATGCTGGAGAATGACTGAAAATGTGACAATGAAGAAAAATTTTCAAAATGTTTACTATCAAATGTTCCATAATGAAGACAAAGAAGAGAAGCCACAAGAATCTGTAACACTTTTGTGGAGACGGAAATAATCCATTACAGAGGAAATCTGATTATGGTGGATAATACACTTCTCAAAATAGATAGTGACACCAATAGCATTCTGTATGTTTAACTCAAATGAAGAAACTCAGAAAAATCATATTTGTTAAAAGAGGGTTTGATAAACTGAGCCACCAAAATGGAATGCTCTTCATGCCAGTATTCCTACAGATACAGTTTGCCCTCAGTGTATTCAAAATCTGTATCATGCTGGTTTCAAGTTTCAGGATAGCAAGTGTCTTTGAGTCCCTTGGGCTCTGATCACCAACTCCTTCCCCATAGTCCTGTATATAACTGTAATAAATATTGATTGAACAA
VastDB Features
Vast-tools module Information
Secondary ID
-6330416L07Rik:NM_176962:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





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:
ENSMUSP00000111197





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000073907
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr17:52030439-52030802 
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr7:14062501-14063110 
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
chrUn_random:54166231-54166232 
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
ACATTCAAGGACGTGGCTGTG

				
R: 
GCAAGGTTCTCTGGTGTTTCCA

				
Band lengths: 
345-1204

			

		

	





	
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






Retrieved from "https://vastdb.crg.eu/wiki/Special:VastDB"