Special

MmuINT0075625 @ mm9

Intron Retention

Gene
NA
Description
NA
Coordinates
chr17:35460412-35460757:+
Coord C1 exon
chr17:35460412-35460546
Coord A exon
chr17:35460547-35460724
Coord C2 exon
chr17:35460725-35460757
Length
178 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGA
5' ss Score
9.45
3' ss Seq
CACAGCTTTTCTTCTCACAGGTG
3' ss Score
9.69
Exon sequences
Seq C1 exon
AGCCTCCTCCATACACTGTTTCCAACATGGTAATCATAGCTGTTCTGGTTGTCCTTGGAGCTGTGATAGTCATTGGAGCTGTGGTCATCATTGGAGTTATGGTGTCTTTTGTGATGAAGAGGAGGAGAAACAAAG
Seq A exon
GTAGGAAAGGCCAGGGTCTGAGTTTTCTCATAGCCTTCTTTAGAGTGTCCTCTGCTCATTAAATGGAAACACAGCCACACCCCTCATTGCTACTGTCTCTAACTGGGTCAGCTGTCAGTTCCGGGAACTTCCTAGAGTCAAGATCTTCCTTGAACTCTCACAGCTTTTCTTCTCACAG
Seq C2 exon
GTGGACAAGGAGAGGACTGTGCTCTGGCTCCAA
VastDB Features
Vast-tools module Information
Secondary ID
-H2-Q1:NM_010390:5
Average complexity
IR-C
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:
ENSMUSP00000072942





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr6:29896351-29896795 
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr23:28355389-28355809 
ALTERNATIVE
BtaINT0026389
(BOLA-NC)
Chicken
(galGal4)
chr16:61153-61269 
LOW PSI
GgaINT1007334
(BFIV21)
Chicken
(galGal3)
chr16:258858-258906 
GgaINT0123611
(F1NKE5_CHICK)
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
AGCCTCCTCCATACACTGTTTC

				
R: 
CCAGAGCACAGTCCTCTCCTT

				
Band lengths: 
162-340

			

		

	





	
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"