Special

MmuINT0078441 @ mm9

Intron Retention

Gene
ENSMUSG00000004980 | Hnrnpa2b1
Description
heterogeneous nuclear ribonucleoprotein A2/B1 [Source:MGI Symbol;Acc:MGI:104819]
Coordinates
chr6:51410434-51413492:-
Coord C1 exon
chr6:51413410-51413492
Coord A exon
chr6:51413254-51413409
Coord C2 exon
chr6:51410434-51413253
Length
156 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGT
5' ss Score
10.24
3' ss Seq
CTTTACTTCTGTTGAAACAGGCT
3' ss Score
6.57
Exon sequences
Seq C1 exon
GGAACTATGGTCCTGGAGGAAGTGGAGGAAGTGGTGGCTATGGTGGAAGGAGCAGATATTAAGCTTCTTCCTACTTACCATGG
Seq A exon
GTAAGTAGTTTTTAAGTTTTACAATTATTATTATCTTGGGAGAACTAGCTGCAGGAGTTAAAAGCATTTTAGGATCATGTTATCTTTCCTTAAAATCTGGTTAGATGGATAATTTCATAACCTATTTTTTTTTACTCTTTACTTCTGTTGAAACAG
Seq C2 exon
GCTTCACTGTATAAATAGGAGAGGATGAGAGCCCAGAGGTAACAGAACAGCTTCAGGTTATGGAAATAACAATGTTAAGGAAACTCTTATCTCAGTCATGCATAAATATGCAGTGGTATGGCAGAAGACACCAGAGCAGATGCAGACAGCCATTTTGTGAATGGATTGGATTATTTAATAACATTACCTTACTGTGGAGGAAGGATTGTAAAAAAAAATGCCTTTGAGACAGTTTCTTAGCTTTTTAATTGTTGTTTCTTTCTAGTGGTCTTTGTAAGAGTGTAGAAGCATTCCTTCTTTGATAATGTTAAATTTGTAAGTTTCAGGTGACATGTGAAACCTTTTTTAAGATTTTTCTCAAAAGTTTTGAAAAGCTATTAGCCAGGATCATGGTGTAATAAGACATAACGTTTTTCCTTTAAAAATTTTAAGTGCGTGTGTAGAGTTAAGAAGCTGTTGTACATTTATGATTTAATAAAATAATTCTAAAGGAAATTGTGTAATTATAGACTTTTTATTTTAAATAAGTTAAGGAGTGGGTAGTATAATTAAGGTCCATTGCAAAGCTGTTGTTGTATTTGTGTAAGATAAAAATGCTGGTCAGATTTAAGTGTGTTGTCTGAAATTCATCAGGAATAAATTACCTAGTTAACTTAAGGGATATCTCTGCAAAGAGAAACACCTTTTTAGATCTTTTAGATGCTGCTTCTTCAATGCAAGGAAAGGAAATAACCCCAGCGAGGTACTCTTCAGGGACACAGGTCTAGTACAAGAGAACTCTTGACGACTAATCGCAGCCAGTCTTAAAAAACTGTGCTGTATCTACAAAGCTTTAACTACAGTAGTTGATAAGGATGCCAACGAAAGCTGAGGGTGTAGAGCAAAGTAGTTCTAAGCTTCAGTTAAACTTCTTTAGGTAAGAACTTATTTACTTTTTCTTTCTTAATTTTCCTCCCTTAAAAGATAAACTAATAAACTCTTCAATGGTCTTTTCAGTATAGTTCTTATGTAGTTTAACATAGCTTATAAATTGAGTTTAACAATAAACTCAAGATAATTTTATAAACCCTGTTTTCCAATCTGTCATTTACTTAAATTATTTTGGTTGTTTTCCCTTTTTTTCCTTCTTTCTCACCCCCTCCCTTTCCATGAAGATTCAGGTGCTTAACATATCATTTTTTTCCCTGCTGGAATTTTAGCATTGATATGAACCATGGACAAGTATATTCTGCTGCCACAAAGACTGTAAAGTGCTTCATTTCAACAGCTGAGGCAAGCCAAGTGATCATTAATAAAGCTTTTCTTGCTTCCTTCAGTGGTGTTGGTAGTAAAATGGTAGGTAAAAGTTAGGCTGCAAGTTCAATAAATGAGATTTACCTATCATTCCACCCTTGTGTATTCATTCACCTATCCTGGTTCAAGCAGTTTGAGTCAACTAGGCATTTAAAGGCATTGTGTTTATTGTGGTAACAACTATACATGCTTATCAGGGATGAGTCTGACAGTGTTTTCTTACAGTAGAAGTTTCTGTGCAACAGCAGCAGCAAAACCCTCTATGTACCCTGTACTAAATAGTTGGGGTAAAATGTGGTAATTTTTTGCCCATTGTCCTGCCCTAAAATGTTGTAGGTTGGCTATTGAAATTTCCTGAAACAGCCCTCTTGATTTCTAGGCTTTATTGCCTTTTCAGAAATGTGATATTGAGCGCTTATTATACACATCAGTGAGTCTGCTTTAATCCTAAACCCACCACTGAAGTTACTTAGGTTCTGTGGACAAACATGATAAACTTCTTCAGATACTTTTTTTTTCCTTTGGCAGGAAGGTGTCTTGCTGCAGGTAACTAATGAAGAAGTGGTCAACCACAGAGTCTTCAAGAAATAAGAAATTCTGTACCATCTGAAAGTAGTTCTTGTTGGTGCCTTCATTTAAGAAGCACTTTTAAGAAAAGGGAATGTTTTCTGATTTAAAACTTCATTTAGTACAGGTTCTTAATAAAATTACAAAAATGCTGATTGTAAAGGGTAACATCAAATTAGCAAAGGATAATGTATTGTTTTAGGATTTGTGAGTAGACAGATAAGAGCTCTATTTTAAATACAAGTTTTATAAAATAAATACTTTTGTATCCAAATTACTTGGTGTAATGCTTACACATAAGTGTGAATCTTGTTCTATCAACATCAGTTGTCTACAAGATCGACACTATAAATGCTAGACTAGTTTTGCACAGAACTATACATTTAGTTCTCATTCAATACTAATAGGAGAAAAAAGCATTAATAGGCATTATTTACTGTCTAATAAAATATACCTTACTATGAATTGTGCACTGCTACAACTTGATGCTGAACACTAATGGTGGCATTTTGAAACCATGGATTTTAACCAGATAGTGTTTTGAGTTACCACTTTTGCAGAACACCAAAACACTGATTTTTATTCCAATTGTGAATGGGTAGCAGTGGTTAAGGTACTGTGGTTTAAGAGTAATGGGAAATTGATTTAAAACAACCAGAGTTAACTTCATTTGCTTACGCCAATAAAGCAATATATACAGGTAAGTCAATGGCTAAAAAATGTGAGCTCTTAACATCTTGTAAAGTGTATCAACAGTCATTCTAAATACTTGGCTTTTGGCTAGAAAAGCTAGCAAACCCATTAGGTAGTGTTGTGCATGCCCTCAGTCCCAGCACTTGGGAAGTTAAAGGCTATGTTCCAGACAAGGCTGCATGTGAGTCTCATACACATACCCGTCGCCATTAAGAGTTTGTTTTTGGACTTCAAAGCAAAATAAAGTCTCACACAATTGTTTTTTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000004980-Hnrnpa2b1:NM_016806:10
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact





	

	
No protein impact description available





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.958 A=NA C2=NA
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF116273=HnRNPA1=PD(0.1=0.0)

							
A:
NA

							
C2:
NA

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000087453f5973A





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000067491, ENSMUSP00000087453, ENSMUSP00000087453f5974A, ENSMUSP00000110103
  



Associated events






Conservation


Human
(hg38)
chr7:26192339-26192494 
ALTERNATIVE
HsaINT0076957
(HNRNPA2B1)
Human
(hg19)
chr7:26231959-26232114 
ALTERNATIVE
HsaINT0076957
(HNRNPA2B1)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr4:70204688-70206062 
ALTERNATIVE
BtaINT0072895
(HNRNPA2B1)
Chicken
(galGal4)
chr2:32317827-32317978 
ALTERNATIVE
GgaINT0098569
(HNRNPA2B1)
Chicken
(galGal3)
chr2:32117781-32117932 
LOW PSI
GgaINT0098569
(Q5ZME1_CHICK)
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
TGGTGGCTATGGTGGAAGGAG

				
R: 
ATCCTTCCTCCACAGTAAGGT

				
Band lengths: 
258-414

			

		

	





	
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"