Special

MmuINT0078740 @ mm9

Intron Retention

Gene
ENSMUSG00000000938 | Hoxa10
Description
homeobox A10 [Source:MGI Symbol;Acc:MGI:96171]
Coordinates
chr6:52181196-52184938:-
Coord C1 exon
chr6:52183958-52184938
Coord A exon
chr6:52182780-52183957
Coord C2 exon
chr6:52181196-52182779
Length
1178 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGC
5' ss Score
8.84
3' ss Seq
TGTATTCTCTTAAACTCCAGGCA
3' ss Score
7.28
Exon sequences
Seq C1 exon
AAGAAATGTCAGCCAGAAAGGGCTATCTGCTCCCTTCGCCAAATTATCCCACAACAATGTCATGCTCGGAGAGCCCTGCCGCGAACTCCTTTTTGGTCGACTCGCTCATCAGCTCAGGCAGAGGCGAGGCTGGTGTTGGTGGCGGTAGCGCGGGGGGCGGTGGAGGTGGCTACTACGCCCACGGTGGGGTCTACCTGCCGCCTGCCAGCGACCTGCCCTACGGGCTGCAAAGCTGCGGGCTCTTCCCCGCGCTGGGCAGCAAGCGTAATGAAGCGCCGTCGCCCGGAGGCGGTGGCGGTGGTGGCAGCGGGGGCCTGGGTCCTGGGACGCATGGCTACGCGCCCGCGCCCCTAGACCTGTGGCTGGACGCGCCCCGCTCCTGCCGGATGGAGCCGCCCGACGGGCCGCCGCCACCGCAGCCACAACCCCAGCAGCAGCAGCAGCAGCCGCCGCCGCCCCCGCCGCAGCCACCTCAACCCCAGCCACAGGCCACTTCGTGTTCTTTTGCGCAGAACATCAAAGAAGAGAGCTCCTACTGCCTCTACGATGCTGCGGACAAATGCCCCAAGGGCTCGGCCGCCGCTGATCTGGCCCCTTTCCCGCGGGGCCCGCCGCCCGACGGCTGCGCCCTGGGCGCCTCCAGCGGAGTGCCAGTACCCGGCTACTTCCGCCTGTCGCAGGCCTACGGCACGGCCAAGGGCTTCGGCAGTGGCGGCGGCGGCACGCAGCAGCTCGCTAGTCCCTTTCCTGCGCAGCCCCCGGGGCGCGGTTTCGACCCGCCGCCCGCACTGGCCTCTGGCTCGACCGAGGCAGCCGGGAAGGAGCGAGTCCTAGACTCCACGCCACCACCCACTCTGGTTTGCACCGGTGGCGGCGGCTCGCAGGGCGACGAGGAGGCACACGCGTCATCCTCGGCGGCTGAGGAGCTGTCTCCAGCCCCTTCAGAAAACAGTAAAGCTTCGCCGGAGAAGGACTCCCTGG
Seq A exon
GTAAGCAGAGCTCAACCGAGGGCTCAAGTCAGACGGGCAGACAGACAGACAGACAGACCCACAAGGAAGGAGCAGAGGACCAGAAGCCCGCGCGGCAGCCGTAGGCCTTGGCCCAAACTGACGGCAGGCTGACCTTCTGAACTTGTTTTTAATATTTGGGCGTGGGGATGCTGTAAAAATCCACGTCCGGCTTAGGGCCCCACACCAAGACGTCCTCAGCTCTGGCCCCTGCTCACCCAGACTTGGGGGATGAGAACACCAGCGAGCAGCCCTCCTCCCGTGCTTGCACTTTCTCGTGGCCCTGAGTACCCCCAAGCCCTGGTCCTTAGCCCAGCCTGCTCAGCGCGGCCCACGCGGGGGGGAGGGGCAGGGAGGAAAAGTGGCTCGCTTGCAGATAGCACGGATGTTTGTAAGGCATCCAAAATAAGCAGCCGCCAGAGCCAATAAATAAGCCCATTAACCGGCGAAGTTCGAGTTTACGATCCCCCATGCGTTTTTCAAAGTTTCTGGAGGGGCGGGAGTCCTGGTTGTAAGAAAAAAGAAAAGACAAATTCGGCCGGAACGCTTGGGCCCAGAGCTGAAAACCTAGGAATGGCCATTCCCCTTCTCCTGGAATCTGGTGCTGCCCAGCTTCACACTCCGGTTACTTGGAGGGACAGGAGCCAAACCCAAGCCCTTGACCCCAGAATCGGGTTTTTGGAACTTCCCCATTGGCCCAACTATGCCCTTCTCCTCTAGCCTGGGGCGATCTAGGAGGCTAGGGTAAGCCAGTGGAGCTGCCAGCCTCTCGTCCAAAGAAGCATTCCCTTACCCCAGCTTGGGGGCCGGCAGGAAATGCTTCCCTGCCCCTGGGTGAGAGGCAGAGAAAGGCGTTAAGTTCAAGATGTACGGCCTCGCCTCCTCCGGCCTTTCATTCTCTCAGCGCCCCGCGGCGTGGTGCTAAAACAGGTGCCTGGAAAAAAGTAGAGGAAAATGTAAATTGGGAGGACCGGGTGTGGATTTGAGGCCGATTTTGTCATGCCTTTTTGGAGGGATTTCTTGCAAAAGGAGGGAGGGCATAACCCTCTCTCTATGACTTCGGGCATCCCACTAAATGGGAAAGACCCGGAATTCACCCCCCTCATACAGCCCGAGTGGCCTCGACTTAACCTTCCCCTCTGTATTCTCTTAAACTCCAG
Seq C2 exon
GCAGTTCCAAAGGCGAAAATGCAGCCAACTGGCTCACAGCAAAGAGCGGCCGGAAGAAACGCTGCCCTTACACGAAGCACCAGACGCTGGAGCTGGAGAAGGAGTTTCTATTCAACATGTACCTTACTCGAGAGCGGCGCCTAGAGATCAGCCGTAGCGTCCACCTCACGGACAGACAAGTGAAAATCTGGTTTCAGAATCGCAGGATGAAACTGAAGAAAATGAACCGAGAAAACCGAATCCGGGAGCTCACAGCCAACTTTAATTTTTCCTGATGAAACTTCCAGACAACGTCTTTTCGCTTCCTGAGCGCCTGGACCCATCCTCTGCCTCCAGCCTCTGCCCCAGAACTCACACCTGTGCCGGAGCCCCTTTCTCCCTCCCACACTCGCCATCTCCCAGGCCGTTTCGTCTGTGCAGGGCTGGTTTGTTCTGGCTTTTTTTGTTTGTTTGTTTCTTTGTCTGTTTGCTTGGTGTTTGTTTGCTTGTTTTCTGGGGGAAAAAGCCATATCGCTAAAATTCTATAGAGGTTGAGATCTTTCTCAGTGTCAAGTCCTGAATGGGCTGGGTTTGCTGCCTCTGGGACCCACTGCTAGGAAAGGGCCCCAGTACTCCTCCACGGATCTGGTTTCCTGCCCAGCCCTGGGTAAACTTAGCCGGAAGCCTTAGGTCCCATTGTCGGCGCTGAGGTGTCTGGCCTGAGGTCAATGGTGCAAGGAGCCGCCACCGGGTTCGCCAGCCTGGAGTGCTGGGCTGTGTTTAATCAGGGAGTCCAGGCCTGGTTTCTCTTTTCTTTCTTCTTTTCTTCCTTGGCCAAGAGCAGAGTATGGAAGCATGGACATTCAGGTTAGCTAAAGGGCTTGACCTGGCTGGTTGAAAAAGTGAAAAAGAAATAATCAGTAAGATTAATTTTTCCTTCTTTTGTAAGATCTCCCAGCTTTAAATGAAAATTAAAATGGGCAAGAGAAGGAAACCTCTCTTCCCGTTTGCCTAAGGTCTTGCTTGCCTGGCTAAAATCCTTCATTCACCTTTGAGTTTCCATATCCCTGCTGTTAACAAATAATGCAGGTTTGTTTATACATGTGGAACTGGTGGATTTTCGTCATTAAAACTGTTACCAATTGGTAACACAAGAAAAGCACACCACAATTCTCCCTATTTAATGGAGGTTGTTTTTTTTTTTTTGCTTTAATTCACTTTTTGTTTTTGTTTTTGTTTTTTATTTTGTAGGCTTTCTGAAATTCATGGAAGCCTAGGTGGGCTGGGGCAAGCAGAAATAAAAATGAGAGAAGGGAGATATTGTTTGGATTTCCTTTATACTGTGAAGTTACATGCATAAAAGGGTCAAACCTGTAGGTGCAGAAAAGAAAAAAAAAACCTATAAATACAAATCTGTATAAATGTCTATTATTATGAAAAATTGCCAATCTTGTTTAAGCAAATGCATTCTATCGTTATTATAAATGTTAGTTCTAGCTTTATTTACTTCAAAATCTTAAATCAGAATAAATTAATATTGTATTGCTGCTGTGCGTGGAAAAAGATGATGTTTATGTTCTTATAGAATAAAAGCTGTGGAATGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000000938-Hoxa10:NM_008263:1
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.776 A=NA C2=0.325
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
PF0004624=Homeobox=WD(100=62.0)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000120276





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000000962
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
chr7:27172174-27173348 
ALTERNATIVE
HsaINT1015836
(HOXA10)
Human
(hg19)
chr7:27211793-27212967 
HsaINT0077273
(HOXA10)
Rat
(rn6)
chr4:82201735-82202905 
Cow
(bosTau6)
chr4:69323998-69325208 
ALTERNATIVE
BtaINT0073169
(HOXA10)
Chicken
(galGal4)
chr2:32980098-32981445 
Chicken
(galGal3)
chr2:32588821-32590168 
Zebrafish
(danRer10)
chr3:23539142-23540321 
ALTERNATIVE
DreINT0078828
(hoxb10a)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
AACAGTAAAGCTTCGCCGGAG

				
R: 
GCTCAGGAAGCGAAAAGACGT

				
Band lengths: 
345-1523

			

		

	





	
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"