Special

MmuINT0078741 @ mm9

Intron Retention

Gene
ENSMUSG00000038210 | Hoxa11
Description
homeobox A11 [Source:MGI Symbol;Acc:MGI:96172]
Coordinates
chr6:52192105-52195766:-
Coord C1 exon
chr6:52195010-52195766
Coord A exon
chr6:52193592-52195009
Coord C2 exon
chr6:52192105-52193591
Length
1418 bp
Sequences
Splice sites
5' ss Seq
CCGGTGCGT
5' ss Score
9.74
3' ss Seq
TTGCCTCTCTCCTTCCTTAGGTG
3' ss Score
12.96
Exon sequences
Seq C1 exon
GGAGAATCATGTTAAGCTCGGCTACTGCGGAGAGCCCAAGGTAGCCCAATGATGGATTTTGATGAGCGTGGTCCCTGCTCCTCTAACATGTATTTGCCAAGTTGTACTTACTACGTCTCGGGTCCAGATTTCTCCAGCCTCCCTTCTTTTTTGCCCCAGACCCCGTCTTCGCGCCCAATGACATACTCCTACTCCTCCAACCTGCCCCAGGTCCAACCCGTGCGCGAAGTGACCTTCAGAGAGTACGCCATTGAGCCCGCCACTAAATGGCACCCCCGCGGCAATCTGGCCCACTGCTACTCCGCGGAGGAGCTCGTGCACAGAGACTGTCTGCAGGCGCCCAGCGCGGCCGGCGTGCCTGGCGACGTGCTGGCCAAGAGCTCGGCCAACGTCTACCACCACCCCACCCCCGCCGTCTCGTCCAATTTCTATAGCACGGTGGGCAGGAACGGCGTTCTGCCACAGGCTTTCGACCAGTTTTTCGAGACGGCTTACGGCACCCCGGAAAACCTCGCTTCCTCCGACTACCCCGGGGACAAGAACGCCGAGAAGGGGCCCCAAGCAGCAGCTGCGACCTCCGCTGCGGCGGTGGCGGCGGCGGCCACGGGCGCGCCGGCAACTTCAAGTTCGGACGGCGGCGGTGGCGGCGGCTGTCAGGAGGCGGCGGCGGAGGAGAAGGAGCGACGGCGGCGACCCGAGAGCAGCAGCAGCCCCGAGTCGTCTTCCGGCCACACTGAGGACAAGGCCGGTGGCTCCG
Seq A exon
GTGCGTATAAAGGCAGCGCCCAGCGCTTTATGAAAGGGGAGTTGGGAATCTAGCGCAGCACCGCTGTTAAATTTTTATATGCTGTTTTATAAGCATATAAGGTTTATGAAGGGCCTTTAGGTTTCCCCCAACAAAACTTTGTTATAAAAGGAGGGATCACGTGGCGAGTGCTGAAATTGGCCGTGAAATACCCACCGGCCAAAGCATGCCTGCAGAAAAAAAAAAAAATACAACTCCCCTTTTTCCTTTTTTCCCTTCTCAGCTCCCAAACTCAACAGCACGATCCCCGCTAGAGACCAGCTCCAGGCTGGGGAGCCGGAGGTGGGCGCCTGTAAATTCCCCCTACAAGGGCTTCAGGAGCCTTTGATAGCGGGGTAATCCGGAGATTTTTATAAAAGCCATGTGTTGCGGCGGGACTCCAGTCCCGGCTGGGATTCAAAGGCATCGGCTGTTTAATGATGGCGCTAAGAGCGCATTTAACAGATAAAGTAGCCCACTTAGCTCAAGCAATATATTAAAAGAAACAAATTAACTTAAATTTGGCCTTTTTGTCCAAAGGAAGCCATTTTCCTCTGGTCCGGTTGCAATTACATGCTGCCTTCTGTTATTCACAATTGTTTTTAAATCAGTCAAAAGTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTTCTTAAAGGTGAGGGTGAACAAATGGATCCTGCCTGAGGCTTAAGGTAGCCTCTCTTTCCTCTACCCTTCCTAAACTAGCATCCCTACCCTGCTGAGGGCCCTCTGGCAGTATGCTGACGGTGTGTACTGAGTGAAGGCCTGGGTAGGGGTTTCCTCTGCCACCTCCCACCTCGAGAGAGCTGGGAGGCTGGCGGAAGAGGCAAGAACTGATCAGAAGTCAGGCTGACAAAGACCCCTCAGCCGCCCCAGATGTTAAGGAGGGCTAAATCATGGCGGCAAGCAGGAAAGCCTGGGGCCAGGATGCATGCCTTTACTGCCTCGGGAACAGGCGGCCCAGGTGCTGAAGGTGAAATGTCCTCGGGCGGCTGTTTGTTTAGTCTGGCGGGGCAAGGAGCAGCCCGCAACCCCCACTTGCCTCCGTTCAAAGCAGTTCAACCAGCGCAAACTCGCCTGTTGCTGTGAGGAGCCTTCCTTTCAGCTCAAGGGGCAGCCTGAGTCCTTTCCCTGGGGGCCTATCTAGTGAGCTGGCTTTTATCTGAAGCCGGCTCCAGACTGCAACTTGTCCCTGACCAGCAATAGAAGCCTGAAGGCAGGGGCCTGGAAAGACTTTGAAAGGGCCTGGATTGGGCCTCCAGACCCTGTGGCCAGACCTTCTCCAATGGGGGTCCTGGGAGAGGGTTGCACCCCTATCGCCCTCTCACTCTTTGCCTCTCTCCTTCCTTAG
Seq C2 exon
GTGGCCAACGCACCCGCAAAAAGCGCTGCCCTTATACCAAATACCAGATCCGAGAGCTGGAGCGAGAGTTCTTCTTCAGCGTCTACATCAACAAAGAGAAGCGTCTGCAACTGTCCCGCATGCTCAACCTCACCGACCGTCAAGTCAAAATCTGGTTTCAGAACAGAAGAATGAAGGAAAAAAAGATTAACAGAGACCGGTTACAGTACTACTCAGCTAATCCACTTCTCTAAGGCTCCAGCCTACTGGAATTGGGAGGGGGGCTTCATACATGTGAAATAATATGCAGATTTTGCCCTTGACAAGGTCAAGCCACATTGCGACTTGGAAAAGGGGGGTGATATAGGAGAGAGGAGAGGTTTCCTTATCAGAGATTCGTCCAATAGGAAGGGGGCCTGAAACTCTCTTGGTTCAGATCTCCGTGGTTAAGCTTCCTATTAGTAATTGAATTCTAAGGGTTGTGAATCAACAGAATGAATGGTTTGGGACCCCTGGTGGTTCACTCTTAGAGCCTGCAAAAGCTTTGAGCTGGGTGTGGTCACTGGAGATTGGGCCCCCTGCCAAACCCTAAGGAGGCCACCCGCTCAAGACCCTCTGCACAGAGCCTGCCCACCCCCAGGTCTCCCAAGTCAAGAAACTGTGTGCCCCAAGCCTAGTTCAGCTTGGGGATAGGAGCAGGAGGAAAGGGGATGACTCCTAGAGATTCAGGCTGGGGTTGCTTTCCAAAAGTAATGTGAAAGACAGTTAACCAAAAGGTGGCTGTGAAAAGGGAGAGAGAGTGGGAGGGGGGTGTCCTGGAGGAAGGAGAAACCTATCCAGATGTCATTAATATCATCCCACCACTGATCTGCACCCAAACCTGAGCTCCTAGCAGCCACCTTCTGCAGCCTACCTGGGTTTTCTACCTCCCAATGGTGGTGATGGGTCTTCCATCTCAGAGCTGACTATTCCTAGGGTAGAAGACATTGAAAACTCCAGAGGCTGTGCTGGTTCCTGGCCCCTCAATCTCTACAGGAAATGCCTGCGGAGGGCTACAGTTTGGCAAACTCTTCACCACATTAAGGAAACTTGGATTTGGTGTCTGTCAGGCAGCAGAGCAGCAGGCCTGGCCAGTGGGTCCTTGGCCTTTGGCTGTGAGGGGCTGAAGTTCCCCCCCCCCTCCCAAATCCCTCATTCCTACCCTGCACTCTGTGCTCATCAACTCAGAACTGAGCTTGGAAGCTTCTGGCAATCTTCTAAGAGCCGGAGAGTGATTTGGAGCTATTTTAAAAGATAAATATTATATTATATATATATATTTCCCCGAAGGAACCAAAGCGAATTTTAAGAAGCAATGTAGAGGGGGGGGTGGGGATAATAAAAATATTTAAAGGCTCTATCTGTTTACAGTGTTCCAAGGTTAAACTCGCTCACTGCTAAAATATTTGAATGTATGCTTCATACAGGGATGGTGTTCAAAAGACTGTAAATAAAGAAACCATAACCTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038210-Hoxa11:NM_010450:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.447 A=NA C2=0.234
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF120453=DUF3528=WD(100=62.9),PF146721=LCE=PU(91.6=32.1),PF105004=SR-25=PU(56.5=35.0)

							
A:
NA

							
C2:
PF146721=LCE=PD(7.2=7.7),PF105004=SR-25=PD(42.9=80.8),PF0004624=Homeobox=WD(100=73.1)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000040920





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Conservation


Human
(hg38)
chr7:27183029-27184435 
LOW PSI
HsaINT0077275
(HOXA11)
Human
(hg19)
chr7:27222648-27224054 
LOW PSI
HsaINT0077275
(HOXA11)
Rat
(rn6)
chr4:82212861-82214270 
Cow
(bosTau6)
chr4:69312702-69314117 
LOW PSI
BtaINT0073170
(HOXA11)
Chicken
(galGal4)
chr2:32991615-33173721 
Chicken
(galGal3)
chr2:32600880-32603212 
ALTERNATIVE
GgaINT0095063
(HXA11_CHICK)
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GACCAGTTTTTCGAGACGGCT

				
R: 
AGAACTCTCGCTCCAGCTCTC

				
Band lengths: 
358-1776

			

		

	





	
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"