Special

MmuINT0078440 @ mm9

Intron Retention

Gene
ENSMUSG00000004980 | Hnrnpa2b1
Description
heterogeneous nuclear ribonucleoprotein A2/B1 [Source:MGI Symbol;Acc:MGI:104819]
Coordinates
chr6:51417184-51419893:-
Coord C1 exon
chr6:51419670-51419893
Coord A exon
chr6:51417295-51419669
Coord C2 exon
chr6:51417184-51417294
Length
2375 bp
Sequences
Splice sites
5' ss Seq
GAGGTAACG
5' ss Score
9.65
3' ss Seq
AATGGTATTTCCCTTTGCAGAGA
3' ss Score
9.59
Exon sequences
Seq C1 exon
GTTAGTGGGGGGAAGGTTCTAGAAAAGCGGCGGTCTCGGCTCCAGCGGCAGTAGCAGCGGCGCCGGTCCCGTGTGCAGGAGCTCCTTTGCGGCCCAGTTTCTTGGCCATCGCCTGCTCTCCCCACAGCGCCAGGACGAGTCCCGTGCGCGTCCGTCCGCGGAGGTCTTTCTCATCTCGCTCGGCTGCGGGAAATCGGGCTGAAGCGACTGAGTCCGCGATGGAG
Seq A exon
GTAACGGGTTTGAAATCAATGAGTTATTAAAAATGGCATGGCGAGGCCGTAGGCACCGCAATGGAAACCGGCCACCCGCCTCCGTGGTCCGGCGGAGGGGATGCGGCCACTCGAGTGGCGGTTGGCCTTGGCGAGTTTCTGAGGGGTCGTTGGAGGAGGCCTCTGATTGTCCGACCGCCTTCCCCGCCCTCAGCCGCCCGGCGCCATTTCCCTCAGTTGGGGTGGGGGATGGGAAGTGCCCGCCGCGACCGGGCTGGACCGCTAAAGTAGCGCGTGAGCGGGCCATCGCTGGCCTTTCGATGTGCGCGGGCCTAGGGGCTCGGTTGTGTTCGCGGCGGAACGTTTCTGGGGCCCCCCCGGCTTCCCGGAGCGAGTCTGCGAAGCTTCCCCTCCCCCCTCTCCCGGGAACCGGATTTGGCGGCCGCCATTTTCCCGTCTCCTTCCTCGCCACGATTTTGCTTTCAACGCTTTAGGTTTACTAGTTTGGTTTTCTTTTTTCACCACTGCGTAGACGTGTTTAGCGATTTTCCTTTCTTTTGGAAGTCTTCATACCGTTTCGAGGTGGATTTAGCGTTTTGAGCTTGGGTCTTCAGCGTCCTGCGCACCTCGCTAAAGGCTCTCTGCCTTCCCCTCGACGAAATGGCGCCATTGCTTTCTGAAGCCACCGAGGCGCGGGGTGGGGGCGGGGTGGCGGCGCTCCACGAGCTTTACTGGAACAGGCAGAGAGAACGTAGTACAACCGAGGCCTGGGCGGGTGGCTGAAGGCAGCGTCGCTGCAAAGAGACCGTTTTATTTTTCATAATACGTAAGATTACGGGTGCTGTAGTAAAGCACTTGAGCATTAGTATAGTAGGAGGAAGTCAAAGTGGAAAAAATGGGAGCGCTCATCAGGAAGCTAGGGAGGCTATGTTGAGTGCAGGGTTACTTTCCTTTTATTGCAGAACTTTTATCTGCTTAAAGGATCCTCGGATCGAAATAATTCAAATTATAAGCATTTTTAAGGGAATCTTCGAATTTGTTGGTAAAGTCAACGGATCCTTAGCACGTGGTGTTCACTTTAAGGAAGTGAAATAGCTGACTTTTCATAGTTAGCCTTCGCTTAAAGCCTGGTTCAGTGGACGAAAATCCACGTCCTGGCTATATAAAAACTTAGTTTGGGGTCACAGTGTTTGAGCGTGGTCATTCGGTTTTTTTATTTTTTATTTGTTTGAAATTATGATGCATCATTACACTGATAAGCATTAGCTTTCGAATTGAAAGGGGTCTCCTTGGTTATTTTCTTTGACTCTAAGCACACTTATAAATAAAATAACCTTGTTTATAATCGATAGTGGACGTCTGGTAAGTTTGGAAAAAACCCGAGGTAAGTAAAGAGCTTTTGCTTTCGTTAGTGATATGAAAAAACAAGGTGTATTTAATACTTGCAACTTAGTTTAAGGAAAGCCAATTTACTGACATTTTAGTAGAGCTACCAGAAACACTATTTGGAGTCCTGATTAAGGCTTTTGTAACTATTTTGACTATTTAAAACAATTTTGGTCGTTTTTATTAAACATTTCAAAACCTAAAAATTGTAAACATTGGCTTTTTGAGCACATTTTGGAGAAACTTACAAATTTAGGCTATACAGTAAAATAACGGATTTGTTTTATAATTTTGCTTTTTCATTTCGTTGTGCAGTCATAGGTCCTGGATAGTATGACCTAATTTATGAACATCTTGATAAGTTTTTGTACTTAGCTATTGGAAAGCCAGTATTAAGTGCCTGACAAAACCAGATTTAAGGTGATATCTGGAGTTTCAGCATTCTTCATGGAGCTTGTTTCAGAGTTGCAGGATTTTTTTTTTTCATCTTGAGATACTTACAATTAACACCAGAGGGGGCAGCTCAGGGAAAAGCAAATATGCCACTTTTCAGAAACTGAATCTTGGAAGTGGTGAATTTGGAAACAGGTTTTTTAAATTTTTTTTAAATCTAAAAAGTAGTAAATTTTGGACTTGGGTTGTAGAATTTAATGAATTACAAAAGAATTCTTTAATACCCTTTAAATGACCTAAGAGCTGGGTATGGTTTTTCTGAATTTTTTTGAAGAAAATCTAAGAAAGTTTACGTGAATTAGAAGTTAGATCGAATATTAGTGACTTTGAAACTTGTATAGCTCAGGCAATTTTTGGTGTAACACAACTAATATGCAGTTTAACATATGGTTTAAATTTGATGTAAGTTTTTTTTCTCCCCCCCAGAAAACTTTAGAAACTGTTCCTTTGGAGAGGAAAAAGGTACTCTACCAGCAGGTCACCTCATATTTAAGAATTTAATTTCCTGCATACAAAGAAAGTGTAAATAAAAATTGAAATGGTATTTCCCTTTGCAG
Seq C2 exon
AGAGAAAAGGAACAGTTCCGAAAGCTCTTTATTGGTGGCTTAAGCTTTGAAACCACAGAAGAAAGTTTGAGAAACTACTATGAGCAATGGGGAAAGCTCACAGACTGTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000004980-Hnrnpa2b1:NM_016806:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion (1st CDS intron)





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.167 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
PF142591=RRM_6=PU(40.0=75.7)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000110103





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000067491
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr7:26197867-26200571 
ALTERNATIVE
HsaINT0076956
(HNRNPA2B1)
Human
(hg19)
chr7:26237353-26240191 
ALTERNATIVE
HsaINT0076956
(HNRNPA2B1)
Rat
(rn6)
chr4:81241280-81243489 
Cow
(bosTau6)
chr4:70198192-70200601 
ALTERNATIVE
BtaINT0072894
(HNRNPA2B1)
Chicken
(galGal4)
chr2:32323691-32327706 
LOW PSI
GgaINT0098560
(HNRNPA2B1)
Chicken
(galGal3)
chr2:32123645-32127660 
LOW PSI
GgaINT0098560
(Q5ZME1_CHICK)
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"