Special

MmuINT0023896 @ mm9

Intron Retention

Gene
ENSMUSG00000034384 | Barhl2
Description
BarH-like 2 (Drosophila) [Source:MGI Symbol;Acc:MGI:1859314]
Coordinates
chr5:106881542-106884694:-
Coord C1 exon
chr5:106884469-106884694
Coord A exon
chr5:106882689-106884468
Coord C2 exon
chr5:106881542-106882688
Length
1780 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
GCCCACCCGATTTCTTTCAGAAC
3' ss Score
7.68
Exon sequences
Seq C1 exon
GAACAAAGGAGGAAGGAGACCGGGAGATTACAAGTAGCCGAGAGAGTCCCCCCGTGAGAGCCAAGAAACCTCGAAAGGCCAGGACAGCTTTCTCAGACCACCAGCTCAACCAGCTGGAGCGTAGCTTTGAGCGGCAGAAGTACCTAAGTGTCCAGGACCGAATGGACCTGGCGGCCGCACTCAACCTCACTGACACCCAAGTCAAGACCTGGTACCAGAACCGAAG
Seq A exon
GTGAGGAGAGCCACTGGGTCCCTGCAGGCCAGGCCGGTACCATCTTCTCTCCTGGAGATGCGGGACAGAGAGTCACAGGGTCTGTAGTGGGTATTCTTGGGGCAGAGGTTAGGCACACATCCAAATGGGAGTGACTGAGGACACCGGGAGTTTGAACACTTTTGTGCTCTAAATGTCTTAACATTTGGTTCTCTCTCCCTGCCCCCCAGAAACTCGAGGCACCACAGTTTCCCTCATTTTGTCCTCAAGTCAAGCCGCACTCAGGTTGAAATATCTGTGTAACTGACACCCAGGAGGAATCTGTGTGCGCAGAGTACCCTTAGAACTGCCACAAGCTGGCTCCAAATATCTGTGTCAAGCAACATGGCCTAGCTATTGAGATCTTCACAGAGCTGTCCCACCAGCCTTGGCTTAAATGTTAGGCAGTTGGGAAAGCCAAAGTCCAAGCCTTGGTTGCCATAACATGGAAGATCAGGGAAACCCATCTGGATTAGAGCTGGACTGGAGGCCATGGGCTGGAGAATCAGGCAGCTGCTTGAGCATCTACTCAACAGTGTGCGTGGGGGAAGGGGAGGGAATTGTCTGTCCCCATGTCCTGGCTGTTTCTGCAGTCTCATAAAGAGGAAGGGTGGGGAGGGGACACAAACCCTGTCCCATGTGACTGATTAAAAAAAGACATTAAGAAAGTGTCTGGCCTCACCCTGGTGGCTAGGGACAGACTTGGGCAGTAGGAGTTGAGGTTATGTCCTGTTTCCACACCTGGTGCTAAACTCTCTAGGCTCAATTCTCTGCCCCCTCTGTCGTTTGTGTCCTAATCGTTCATAAGTGGGGTTGGAAATGCCCGTCCAGTTGTCATCTTACCATAATTTTCTGTCTCATTACATACGGTTTCAGCCACCCTAATTCTGTCGGAGAACATTAGTGTCATCTGTAGCCAATTTAAAACCGGCGACATGTTTATTAATTTGGCTAGAGCTGCTGGGTATGGATGCTCCACCAGGCTTGCCTTCCTAGGGCATTCGAGTAAAGTCCTCTCTCCCAGCTTGGTGCAGTGGGAAGAGAGGAGACCCCCTCCCCCCAAAAAAAATGGATCACAGGGTTTAAGCACTACTTTCTCTTTTAAGGAGAGAATATCTTGAGACCCATTTCCTTCCACCTAGAATGGTCGGAGGTACCGCTCCCTAGGGAGAGCTCACTCTCAAACGAATTCCAGTTTGAACCTCGTCGCCCTTCTTCCCTAAGCCTGTAATGCCTGGTCAGACTTAGGGAGGAACTGTCCCGGCAGCCATGGAGAGTGCAAACCCGGAGTGTCAGCCGCCCTTTGTTTCTGGTTTTGGTTTCCTTGGGTGTGATGGGGGGAGGGGCCGAGATCCAACCTTTCTGAGATTTCTGGTCAGAGAAGATTGGAGGAGAATTGGGGGACCAAGGGAAGAAGGCTGGTGAAAAGATGGGATTTCATTTGGCCTCCGGGAAAGTTGCAGGATATAGTTAAATCGTGGGGCAGACTGTAGGGCAGAGGGCCAGAGAAGGCAGTGAAGCTTGTACGACTCCATCTGCGAGTGTCCCCACGTAGAAGACGTAGTTTGAAGAACTGATTTTGGGCCTGGGCCGTCCTGAGAGCGCGTGGGTGAAGCAGAGTGGGGGTGGGGGCAGGAGAGGTGTATTTGAGGTTCCCCAGGCCTTCCTGAAGTAGGGAGGATAGGGGAGAGCGGGGAGCGGCGGGCGCGGTCCCGGGACCATCCTCCGCAGCCGCCACCCGCGCCCACCCGATTTCTTTCAG
Seq C2 exon
AACCAAGTGGAAGCGGCAGACTGCAGTGGGCCTGGAGCTGCTAGCCGAGGCCGGGAACTACTCCGCGCTGCAGAGGATGTTTCCGTCGCCTTATTTCTATCACCCAAGCCTGCTGGGGAGCATGGACAGCACCACGGCGGCGGCGGCGGCCGCGGCCATGTACAGCAGCATGTACCGAACTCCTCCAGCACCTCATCCGCAGCTGCAGCGGCCGCTGGTACCCCGCGTGCTCATCCACGGCCTGGGGCCTGGGGGACAGCCGGCCCTCAACCCTTTGTCCAACCCCATCCCAGGCACCCCGCATCCCCGGTGAGGAAGGAGGGACAGGAGGGACAGTGCCACAGCCCTCCAGGTTCCCACCTCACCCCGGACGGCTGCCCCGCCTCTTCCCGCACCAAACCAACTGGAATAGAGGCAGAGGAGTAAAAGGGGGAGCTCACCGGTGGGCTGGGGTCCCCAAGGACCAGCCAGCTCTCAGATCTCCATCTGCCCACTCAGAGGCAGGGCTGCAAAGCTCCCCGAGTGTGACTGGAGAAAATACTGAAAAGTGCAACCAGTAAGTGAAAACACCCATCCACCCACACATACACACACACACACACACACACACACACACACACACACACACACACACACACACACAAAACGAACCCTCGAGTTCTTTCTTTCTTTCTTTTTTTTTTCTTTTAAACAAAATGACTTTAGGGACATGCAGCAGGGAGGGAGGGGGGAGGGCAAAGAGGGGAGAGACTGGATGGAGAGGAGCCTTCGGGCAGAGAGAATTGTTACTGGACAGAAGCCTGAAGTTCACCCCCAGGCAGAAGGTGGTACCCTGGACATCCAGTCTGCCTCAGAGCAGAGGAGGGTGATGGAGAACTTTGCACTGATTTTTCATGAGCTTTTTTTTTTTCTTTTGGAAAAGTGGCATGCTACATAATATGAAAAAAATGTACATTTGAAAGACTGAGCGATGAGTGATATATCATATTTATTATATGTTGTCCAAAAAAGAGTCACTTATATACGTCAGTAATAACATGACTTTTCTTTTCATGTCTTTTTGATTCAGTAAAATAAATGCTTAGACAAAAGTATAGATTTTTTGTGATTGAAAATTACAAAAATAAAGTTTATCTTTTTTTAACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034384-Barhl2:NM_001005477:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.618 A=NA C2=0.375
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0004624=Homeobox=PU(89.5=67.1)

							
A:
NA

							
C2:
PF0004624=Homeobox=PD(8.8=4.8)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000084005





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000042420
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:90712625-90714530 
ALTERNATIVE
HsaINT0016648
(BARHL2)
Human
(hg19)
chr1:91178182-91180087 
ALTERNATIVE
HsaINT0016648
(BARHL2)
Rat
(rn6)
chr14:4365208-4366951 
LOW PSI
RnoINT0024729
(Barhl2)
Cow
(bosTau6)
chr3:52694429-52696179 
LOW PSI
BtaINT0024956
(BARHL2)
Chicken
(galGal4)
chr17:6589457-6589460 
Chicken
(galGal3)
chr17:7221248-7221347 
Zebrafish
(danRer10)
chr6:24720506-24721339 
LOW PSI
DreINT0036773
(barhl2)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GCACTCAACCTCACTGACACC

				
R: 
CTGGGATGGGGTTGGACAAAG

				
Band lengths: 
343-2123

			

		

	





	
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"