Special

MmuINT0078751 @ mm9

Intron Retention

Gene
ENSMUSG00000059723 | Hoxa3
Description
homeobox A3 [Source:MGI Symbol;Acc:MGI:96175]
Coordinates
chr6:52119061-52122768:-
Coord C1 exon
chr6:52122120-52122768
Coord A exon
chr6:52120742-52122119
Coord C2 exon
chr6:52119061-52120741
Length
1378 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAT
5' ss Score
8.76
3' ss Seq
TCCTCTCTGTGTCCTGGCAGGGG
3' ss Score
10.83
Exon sequences
Seq C1 exon
GTTTGCGCGCGGCGGCCATTGGCGGCGGAGTGTCACGTGACCGCGGGGGCGTGCCAATGTGCTCCCTTACGGGTGTCAAGCCCTTGTCAGAGAGTGTGATCACGATCGTGAAACATCGCGATGCAAAAAGCGACCTACTACGACAGCTCAGCGATCTACGGTGGCTACCCCTACCAAGCAGCCAATGGGTTCGCTTACAATGCCAGTCAGCAGCCATACGCGCCGTCCGCCGCTCTGGGCACCGATGGCGTTGAGTACCATCGACCTGCCTGCTCCCTCCAGTCTCCCGCCAGCGCTGGGGGCCACCCCAAAACTCATGAGCTGAGCGAAGCTTGTCTGCGCACCCTGAGCGGCCCTCCTAGTCAGCCCCCAGGCCTGGGTGAACCACCTTTGCCTCCACCTCCTCCCCAGGCAGCGCCCCCAGCGCCCCAGCCTCCACAGCCCCCACCACAGCCCCCTGCGCCCACCCCTGCAGCTCCTCCGCCTCCCTCGTCTGTCTCTCCCCCTCAAAGTGCCAACAGCAACCCTACCCCTGCCAGCACAGCCAAGAGCCCCCTGCTCAACTCTCCCACCGTGGGCAAACAAATCTTTCCCTGGATGAAAGAGTCAAGGCAGAACACTAAGCAGAAAACCAGCGGCTCCAGCTCAG
Seq A exon
GTAAATGAATGCCTTTAGGAGGTGGGGCCTCTGGCCTTGTACCAGCTCCACGCTCCAAGCCACTTCTAGCTATTACAGCCAGCCTAGGAGGAGAGAAACATCTCCAGAAATGTGCCCTCCCCGCCCCCCCCCCCCACACACACCAGGGAAAACAAATCTTTCCAGAATCTTTGCTACTTAGGAAGGTGATACGGTTACTGTGAGAGGATCCCTCAGACATAAATCTGACTGAAGTCCCTCTGGGCCTCTCTAAGGCGGTTTGAGCCTGGTGAAGTTGGAATCCCTCCTTGTTCCAGTGTTGGGAATTCTGACCTCTAGATAGAACCATCTTTAGGACCACTGTCTCTCTAAGCACACAACTCCTTTTTTCCTGGGCAAACAGTGGCATCCTCCCCATACTGAAACGTGGCAGAATAAAAGCAGGCCCACTCATCCCCCGGGTCAGAATCAATGCTTGGTCTATGATCAGAGCCAATGTTTTCTGCAGCAGATGGACTGGCTGCCTTACTTCTGGGAAGGCCTTGCTCAGTCTTAGTACAATGCAGGAGGCAGCCGGGCATCCCCTGGGGGAGGGGATTCGGCTTGTCATCCTAATGGGAACCACATGGGGCTTTGGGAACTGGACTCCAGTGGGGGAGCCTTAGCCTCAGGGACTTGGGTTTCCAAGCCTCTAGGTTACCTTGGCCCCTTCCTCTCTGGTTTCCTTTGCTCTCTCCTCCAGAACTGGTATTTGGGAAGCCAAGGAGGACAGGAGGCACAAATGCAATGGTCCAAATTGGGGCAGCCTTCATGGTGACATTGAGAACCAAATGACCAAGACTCTGTAAGGGTCTGGTAGCTAGAACTAGGTATCTCCAGTGAGGTCTAGTCTCCTTTGGTCAGAGAAGGCCTTCCAGTTTGACAATACCAATCTGTTACTCTTTTCTTGGGAGATACTGAAAAACTGGTTAGTAGAAGCTAATGGCTGGTCACACAGGCAGGATGCATGCATACACTAGGTCTCCTACATTTTCCAGCGACTGAAGGAATCAAGATAGTGGCACCCGCTCACAGGAAGCTTGTTGTCTGATGGGCCAGGAAATAAGCTGGCCGAGTAAAATAGAGAGGAAGTTCAGGCCAGCAAGGCAAGCAGGAGGCTCTGCAGCTCTGTCCTCTCCTTGAAGAAGCCCCTGATTCGCTCCTTAGAGGAAGGAAGGGCAGGCTAACCAGGCTGTTTCCGCAGACCAAGAGAGGACCACAGCACTGAAGTCCTGCTCCTCTCTGGCCTTGGACAGAGGCTTCTGTGGGGTGAAGAAAGGAGGGGCAGGCCTAGGACTGGGGAGCTAGGCGGGGTCGGTAGCAGCCCCTGACACCGCTCTTCCTCTCTGTGTCCTGGCAG
Seq C2 exon
GGGAGAGCTGCGCTGGTGACAAGAGCCCGCCTGGGCAGGCCTCGTCCAAGCGCGCGCGCACGGCGTACACGAGCGCGCAGCTGGTAGAGCTGGAGAAGGAGTTCCACTTCAACCGCTACCTATGCCGGCCGCGCCGGGTGGAGATGGCCAACCTGCTGAACCTCACCGAGCGCCAGATCAAGATCTGGTTCCAGAACCGCCGCATGAAGTACAAGAAAGACCAGAAGGGCAAAGGCATGCTGACCTCGTCTGGGGGCCAGTCCCCAAGTCGGAGCCCTGTGCCTCCCGGTGCAGGAGGCTATCTGAATTCTATGCATTCGCTGGTCAACAGTGTCCCATATGAGCCCCAGTCACCCCCTCCTTTCTCCAAGCCTCCCCAAGGCGCCTATGGGTTGCCTCCGGCCTCCTACCCTGCTCCCCTGCCCAGCTGCGCTCCCCCACCTCCCCCACAGAAACGCTACACAGCGGCGGGGTCAGGCGCAGGGGGCACCCCTGACTACGACCCGCATGCTCACGGCCTGCAGGGCAATGGCAGCTATGGGACCCCACACTTACAGGGAAGCCCCGTCTTCGTAGGGGGCAGCTATGTGGAGCCCATGAGCAACTCTGGGCCACTCTTTGGCCTAACTCACCTCCCCCACACCACCTCGGCTGCCATGGACTACGGGGGCACTGGGCCGCTGGGCAGCGGACACCACCATGGGCCGGGGCCTGGGGAGCCACACCCCACCTACACGGACCTTACTGCCCACCATCCTTCTCAGGGAAGAATTCAGGAAGCGCCCAAGCTCACCCACCTGTGATGATGGGCCCAGGGCTGTGAGCCAGGAGAGTTGCCCACCCGACCTTCTTTGGTTACTTTTTCCTTTTTTTGTTTTGTTCTATGTTCTTGCCTTTCCCTTTTCTCCTCTGCACCCCTCCCTCATTTTGTTTTCTTTGGTAATGCGTTTTTATAGTTTATGTGACGTAGCAATCTTGGTTGCTGGAAAGGCTGTCAGTATCAGTAGCAACATTTACCACCACCCCTCCTCGCCCTGGCCTCTGGCCCTGCATCCTTTTCCTTCTCTACTCTTTGATAAGAAACAGGGTATATGAACAAACTTTCTAGTCGAGTTTTCAATGTGAATTTGTTCATACTTTATGGCTCCCGAGAGGAAGCAACTGCGTTTTTTTTTTTTAAGTTTTAGTTTTTAAAATTGCACTTCTTGTACTGATCGAGAAAAAGAAATCAAAGGCGCTTTGAAACAGGGACTCCCTGTGCAAAGATGACTACGTGTACGTCTTTCCGTGTGTGTGTGCTTGTGAACAGTCAGATTTATTTATATTTTTTGCAAGCATTGAATAGTCTAAGTTTTAAATATTATTTATCCCCATCCGTTCGTATTTATATTAAAGAAATTCTGTACCCTGATTGTTCAGAAGGTTTCTTGAGCCTTTTGTTCAATGGTGTATTGGCATACATATAAAATTTATTTGAAAGGGAAATAAAATTCCTTTATTAAAAACCGTAGCAATGCAATAAGAACAGAGAGGACCCAGAGTTTGAAAATAGTGGTTTAGGTTTGTAACATCTGGCCAAACTGAACGCTAAAAATGCTAGATTTGTTTTGAGAGTTTTACATTCCTTGCTGCTCACATTCTGAGAAACAAAACAAAAAAAATAAAGTTTTTATTCTGATTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000059723-Hoxa3:NM_010452:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

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

				
Domain overlap (PFAM):

					





						

							
C1:
NA

							
A:
NA

							
C2:
NA

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000043008





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000110077, ENSMUSP00000114711
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr7:27108721-27110114 
ALTERNATIVE
HsaINT0077282
(HOXA3)
Human
(hg19)
chr7:27148340-27149733 
ALTERNATIVE
HsaINT0077282
(HOXA3)
Rat
(rn6)
chr4:82139489-82140856 
Cow
(bosTau6)
chr4:69386775-69388198 
ALTERNATIVE
BtaINT0073174
(HOXA3)
Chicken
(galGal4)
chr7:15764675-15764995 
ALTERNATIVE
GgaINT0047462
([1])
Chicken
(galGal3)
chr2:32525524-32526898 
ALTERNATIVE
GgaINT0091739
(HOXA3)
Zebrafish
(danRer10)
chr9:1937638-1937851 
LOW PSI
DreINT0078845
(hoxd3a)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CGTCTGTCTCTCCCCCTCAAA

				
R: 
CAGATCTTGATCTGGCGCTCG

				
Band lengths: 
346-1724

			

		

	





	
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"