Special

MmuINT0023082 @ mm9

Intron Retention

Gene
ENSMUSG00000033488 | BC026585
Description
cDNA sequence BC026585 [Source:MGI Symbol;Acc:MGI:2448516]
Coordinates
chr1:159395096-159395952:+
Coord C1 exon
chr1:159395096-159395161
Coord A exon
chr1:159395162-159395842
Coord C2 exon
chr1:159395843-159395952
Length
681 bp
Sequences
Splice sites
5' ss Seq
AAGGTATCT
5' ss Score
7.56
3' ss Seq
GATGTTATTTCTTTGTACAGACC
3' ss Score
7.02
Exon sequences
Seq C1 exon
GGAGATCGAGTTATTGGAGTAAGTAGCTTTCATGCTATGGCGGAGCAGTGCATCACGGACCAGAAG
Seq A exon
GTATCTCTGACTCTTGGCACTGATGGACACATGGGCGTTTCTTTTTCTCCACTGTTCTCTCTGGTTTCCTTGTCTCTCTTTCTCACACCGTTCTCTCCTCCTTTTGCGTTTGTTTCATTTTATCGTGTTTCCTGACCAAGCAGGTTTTTTTTTCCCTTTAAACGCTAACTTTCTTGACAGCCCTTGCACAGAGTTTTGTTTGTGTAGAGAGCCTTTTGTTCCTTCGTTGGCTATCCATTTGGACCATACTTAGTGAGTTATGGTTGAAAAACTGGTCTAGCACATGGAATTGGATATCATGGACATATTTTCCCATAAAGCTTGTGAAAATGGTCTGAGCTGGGTTGAGCAGGATGTGAATGGTGCCCCCTGGTGGGGCATGTTATATGGAACCCATCCAACTTTACTGGGATACATTTTACATAATAACCTAGAGCCGATTCTCCATCAATTGGCTCCTTTTTGAGCAGATGCCAGCCTTATGGGTTTGAAGTCTGACACACCCAGGTCCTAAACCCTACCTTGGCTTGCTTGGTCCGGACTTGTACTCCTTAGTAGGTGATGATAGACGTGTGCTTCCCATTGCAAATTACTCATCCAATCGAATCATAAGGTTAGCTAGGCAGCTTGTGTATCCAGCTACACATGTTTACTGCCAATCGATGTTATTTCTTTGTACAG
Seq C2 exon
ACCCTGTGGCGGATTCCAGAAAATGTCTCTTTGCAAGATGCTGCAGTGTTACCGGTATCTTATGGCACAGCTATTTTGGCTGTAGATCATCGGGCCCGCATCCAGCCCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000033488-BC026585:NM_001033284:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.018
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF082407=ADH_N=FE(17.1=100)

							
A:
NA

							
C2:
PF082407=ADH_N=PD(28.4=83.8)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000044945





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000044945f3144A, ENSMUSP00000113664
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr1:178000796-178001564 
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr16:60859872-60860631 
LOW PSI
BtaINT0008974
([1])
Chicken
(galGal4)
chr8:6588157-6588350 
ALTERNATIVE
GgaINT0036522
([2])
Chicken
(galGal3)
chr8:6916586-6916779 
ALTERNATIVE
GgaINT0036522
([3])
Zebrafish
(danRer10)
No conservation detected
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"