Special

MmuINT0078756 @ mm9

Intron Retention

Gene
ENSMUSG00000038227 | Hoxa9
Description
homeobox A9 [Source:MGI Symbol;Acc:MGI:96180]
Coordinates
chr6:52174053-52177369:-
Coord C1 exon
chr6:52175527-52177369
Coord A exon
chr6:52174482-52175526
Coord C2 exon
chr6:52174053-52174481
Length
1045 bp
Sequences
Splice sites
5' ss Seq
CCAGTAAGT
5' ss Score
9.09
3' ss Seq
GTGTCTCTCTCCCTCCGCAGATA
3' ss Score
14.38
Exon sequences
Seq C1 exon
GAAAAAACAGAAGAGGGAAGGATACCAGAGCGGTTCATACAGGGCCCAGAAACTAGGCGAGGTGACCCCTCAGCAAGACAAACACCTCTTGATGTTGACTGGCGATTTTCCCCATCTCCAGTCTGGGGAGCGGGACTAGGCATACAGATGATGGAGCTTAGAACCCGCTGGCTAGGGAATAAAATTCGCTGGGCAGTTTGTGCTCAAAGAAGTGGGCCAGGGCGCTTGTGACACAATCAGGGCGTTTGTGACACAAACCCTTGAGGGTTGGCAGTTCTCTCCTTGGCGGTTGCTCTGGTTGCTCTGTGGGGCCTTCCCTGTGGAGCAAGGGTGATCTGGCCGATGTGCAAGCGCCTGGCTGGCTTTCCAGTCTGACTAGGGTCGGTAGCCCATTTTAGGTGGTTGTATCATCGACGGTGCGTCGCGACAGGGGCGGTGGTCACTCTGTTTGAGGTGGAGAGAGCCTTGTATTTGACTTTTCTAGGCCGGCCCTGGGGGCGCGCGCGGGCGGGGGGCTCACATCTCTGAGGACTGCAAGGATTATTTACAGGGTATTCACCAACCAAACACAACAGTCTAATTTAACCTTTCCAAGTCCTCATAAATTTTTACAGGGAGCCACAGCGAGGCAAACGAATCTGTTGGTCGCTCCTGACTTTCCACCAGCCTGTGTGGCTTCCGAAACAATAACTCCTTATGAAATATCATAAATATAGATTTAAATACAGTAGAGTGAGAATGCGATTTGGCTGCTTTTTTATGGCTTCAATTATTGTCTAATTTTATGTGAGGGGCTCTGCTGGCCGTGCTCACACGCGGGACCCGCGCCTTCCTGATGGCGTGATTAATTGTGATATAAAATAGTCCGCTTAAGAAGTGTGTGTGTCTGGTATGTGTGTGTGTTGGGGGGGTGGCAAGGGAGAGTACAGAGGCAAGGCCAGATTTGATCTTTTAATCTTCGTTGGCCACAATTAAAACAAACCAGATCGTGGAGCTGCGCGATCCCTTTGCATAAAAACATATGGCTTTTGCTATAAAAATTATGACTGCAAAACACCGGGCCATTAATAGCGTGCGGAGTGATTTACGCGTTATTGTTCTGCCGGGCGGACACGTGACGCGCGTGGCCAATGGGGGCGCGGGCGCCGGCAACTTATTAGGTGACTGTACTTCACCCCCCCCTGGTGCCACCAAGTTGTTACATGAAATCTGCAGTTTCATAATTTCGGCGGGTCGGGCTGGGCCGGCCAGGCGCGGGCTACTGCAATGGCCACCACCGGGGCCCTGGGCAACTACTATGTGGACTCCTTCCTGCTGGGCGCCGACGCTGCTGATGAGCTGGGTGCGGGACGCTACGCTCCAGGGACCCTGGGTCAACCCCCAAGGCAGGCGGCAGCTCTGGCCGAACACCCCGACTTCAGTCCTTGCAGCTTCCAGTCCAAGGCGGCGGTGTTTGGTGCCTCGTGGAACCCAGTGCACGCGGCGGGCGCCAATGCGGTGCCTGCTGCAGTGTATCATCACCACCACCACCCCTACGTGCATCCCCAGGCGCCCGTGGCGGCGGCGGCGCCGGACGGCAGGTATATGCGCTCCTGGCTGGAACCCACGCCCGGTGCGCTCTCCTTCGCGGGCTTACCCTCCAGCCGGCCTTATGGCATTAAACCTGAACCGCTCTCGGCCAGAAGGGGTGACTGTCCCACGCTTGACACTCACACTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAACAACCCAGCGAAGGCGCCTTCTCCGAAAACAATGCCGAGAATGAGAGCGGCGGAGACAAGCCCCCCATCGATCCCA
Seq A exon
GTAAGTGTCTCCTTCCTGCAAACCGGCCGCTGCCTCCACGCAGGCCACCAGGATCTACCAGCGCGTCAGCTTTCTCTGGAGCCTGCCTTCGTCCTCGATGGGTGCCTCTGGATCTAGGGTCCGAGAACCAGAAGTTGGTGTTTGGAACACCTCTGATAGGGGCCCCAAGTCCAGAGAACTGTGTGGAGCACCCGGGCCGGCTAGGGGAAAGGGAGGAGGCTGCTGCAGTGAGGGGGCGGGGCGGGCGGGCGAGTAGAGCGGAGACCCGCCGCCCCTCTCCTAAGCTGCCCTGGCCTAGGACAGACAGACTTTGGGCGGTTCTTCGAAAGCAGCGCAGAGAAGTCTTTTGTGCAGCTAGATTGTTCACAAACTGTGGCAGCAACGTCAGTCGGGCAATCTGACCCGGGAAGTTTGGGGAGACCTCAGATTCCCTCCATTTCTTGCTTTTGGAAGGTGGCGGCGGAAATCCTGCCCAAGATGAGGATGCGGGCTTTGGGTCCCTTTGCCAGATTTATTCAAATAAAGTGGAGATGTGATCAAAGGCCCTGGGGCATCCTGCCTTCCGTGGAGTTCCCACGGCCTTCCGGGAAGGTCAAATAAAGAGTGGGGACAGTTGCAAGGAAGCTGGGAAAGGAAGACAGTTGGAGAGAGAGGGGAAGAGAGGGAAAGAGAGAGGAAAAGAGAGGTGGGAGAGGTTAAGCTTGCCACAAGAACTCAGGGCAGCCTGCTCTTTTCTTTGCTGGCAAAAAAAAAAAAAAAAAAAATGGTTTCCAGATTTCATCCTTTCACAATATGCAGACTGTGGGAGGAAGAAGAAGAGGGGAGGACGGGAGAGAGGAGAAAGGAGGGTGGAGATGGGAGGGGGAGCTGAGACTTTCTTGGCTCTGTTGTAAGTGACCCTCCGTGGATCTGTCTGCCAGGGCTTCATTGTGTTTCCTCTAACCAATTCAGCGGCATCCTGCACTTCGGCCAGAGACCCCCAAGAGGCTCCTTCAGACCCTACCGGGATGCTCCTTCTAAACCCAGTGTCTCTCTCCCTCCGCAG
Seq C2 exon
ATAACCCGGCTGCCAACTGGCTACATGCTCGCTCCACTCGGAAGAAGCGATGCCCCTACACAAAACACCAGACGCTGGAACTGGAGAAGGAGTTTCTGTTTAACATGTACCTCACACGGGACCGCAGGTACGAGGTGGCCCGGCTGCTCAACCTCACCGAAAGGCAGGTCAAGATCTGGTTCCAGAACCGCAGGATGAAAATGAAGAAAATCAACAAGGACCGAGCAAAAGACGAGTGAGCCTTTTAGGGGCTCATTTAAAAAGAGAGCAAGCTAGAAAGAAAAAGAAAGGACTGTCCGTCTCCCTCTGTCTCCTCTCCCCCAAACCCAGCCTCCACCCGCACAAAGGGGCTCTAAATCCCAGGCCTCATCTCCCCACTGGCAGTCCGTGCTCAGGCTGGCTCTTAGGCCTGCGGCTTTGATGGAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038227-Hoxa9:NM_010456:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.509 A=NA C2=0.354
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF046178=Hox9_act=WD(100=99.5)

							
A:
NA

							
C2:
PF0004624=Homeobox=WD(100=71.2)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000046939





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000110068, ENSMUSP00000133409, ENSMUSP00000133896
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr7:27163842-27164877 
ALTERNATIVE
HsaINT0077287
(HOXA9)
Human
(hg19)
chr7:27203461-27204496 
ALTERNATIVE
HsaINT0077287
(HOXA9)
Rat
(rn6)
chr4:82193202-82194350 
Cow
(bosTau6)
chr4:69332448-69333528 
Chicken
(galGal4)
chr2:32971928-32972884 
Chicken
(galGal3)
chr2:32579955-32580911 
LOW PSI
GgaINT0103077
(F1NE14_CHICK)
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
TGCTTGTGGTTCTCCTCCAGT

				
R: 
TCGTCTTTTGCTCGGTCCTTG

				
Band lengths: 
345-1390

			

		

	





	
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"