Special

MmuINT0078443 @ mm9

Intron Retention

Gene
ENSMUSG00000004980 | Hnrnpa2b1
Description
heterogeneous nuclear ribonucleoprotein A2/B1 [Source:MGI Symbol;Acc:MGI:104819]
Coordinates
chr6:51416494-51417051:-
Coord C1 exon
chr6:51416905-51417051
Coord A exon
chr6:51416705-51416904
Coord C2 exon
chr6:51416494-51416704
Length
200 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGG
5' ss Score
10.28
3' ss Seq
TAACTTTGTAATTATTGCAGGAG
3' ss Score
6.79
Exon sequences
Seq C1 exon
GTTATGCGGGATCCTGCAAGCAAAAGATCAAGAGGATTTGGCTTTGTAACTTTCTCATCCATGGCCGAGGTTGACGCTGCCATGGCTGCAAGGCCCCATTCCATTGATGGCAGGGTAGTTGAGCCAAAACGTGCTGTAGCAAGAGAG
Seq A exon
GTAAGGAAAACCCAAACACATTGATCTCCTTTCTTGTACTGTTTTTTTTTTTTTTTGTTTTGTTTTTTTTTGGGTACATGTTATTCCAAGACCAACCTCTTAAAACCTATTATCTGGAGGAATTCGTCCTAAGATGTACAAATACAAGTTAGATGTAATCAAGGTTTTTTTCTGTCAGGATAACTTTGTAATTATTGCAG
Seq C2 exon
GAGTCTGGAAAACCAGGAGCCCATGTGACTGTGAAGAAGCTGTTTGTTGGTGGAATTAAGGAAGATACTGAGGAACACCACCTTAGAGATTACTTTGAAGAGTATGGAAAAATTGATACTATTGAAATAATTACCGATAGGCAGTCTGGAAAGAAAAGAGGCTTTGGCTTTGTTACTTTTGATGACCATGATCCTGTGGATAAAATTGTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000004980-Hnrnpa2b1:NM_016806:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.245 A=NA C2=0.155
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF142591=RRM_6=PD(57.1=81.6)

							
A:
NA

							
C2:
PF0007617=RRM_1=PU(81.4=80.3)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000087453





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000067491, ENSMUSP00000087453f5973A, ENSMUSP00000087453f5974A, ENSMUSP00000110103
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr7:26197018-26197314 
ALTERNATIVE
HsaINT0076959
(HNRNPA2B1)
Human
(hg19)
chr7:26236638-26236934 
ALTERNATIVE
HsaINT0076959
(HNRNPA2B1)
Rat
(rn6)
chr4:81240564-81240742 
LOW PSI
RnoINT0071390
(Hnrnpa2b1)
Cow
(bosTau6)
chr4:70201019-70201234 
LOW PSI
BtaINT0072898
(HNRNPA2B1)
Chicken
(galGal4)
chr2:32321077-32322634 
LOW PSI
GgaINT0098562
(HNRNPA2B1)
Chicken
(galGal3)
chr2:32121031-32122588 
LOW PSI
GgaINT0098562
(Q5ZME1_CHICK)
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CGGGATCCTGCAAGCAAAAGA

				
R: 
TCTTTCCAGACTGCCTATCGGT

				
Band lengths: 
295-495

			

		

	





	
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






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