Special

MmuINT0078755 @ mm9

Intron Retention

Gene
ENSMUSG00000038236 | Hoxa7
Description
homeobox A7 [Source:MGI Symbol;Acc:MGI:96179]
Coordinates
chr6:52165623-52168572:-
Coord C1 exon
chr6:52167029-52168572
Coord A exon
chr6:52166030-52167028
Coord C2 exon
chr6:52165623-52166029
Length
999 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGC
5' ss Score
9.88
3' ss Seq
GTCCAAATTTCTGTTCCTAGGAC
3' ss Score
8.56
Exon sequences
Seq C1 exon
AGTGCTTAGAAAGGTGAAGCCGCGGGATCTGGGTGGCCCCTAGAAAGGGCTCCCTTATTCGCTTTTATTGTCTCCTAAAGAACTGGGGTTCCACAATGAGCTACAGCACCCAGGTCCTGAGATTACCTCTCCTGTCTCTAATCCAGCTCTAAAACTGTTACCGGCCCACAGGGTGGAAGGCTTGCTTGCCTGAGAGCCGCCAGGAGTGTATGACGGATGTGTTTTAAAATTTGTGGAGCCGAGTTTCTCCCAAACTGAATGAGGATACCCCAGTTTTTTGTCATCTAGGGGGTAACTAGGGGTTGTGGCAAGGACAAAGCGGGTGTTGAGCTATCTCTGGAGTTGCTGCCAGCCAGCCAGGTGCCCAGGAGCAAATGCAGAGAAACTGCCAGGGCCGCAGTGTCCGGGAGGAGAAAAGGAATCCCATGTTAGTATATCTGTTGGCAAATGAGGCTCATTAATAGATAAATATTTCACTGCTTCCTTTAGGGCAGATAAACAGTGCGCCGCCGATTAAAGAAAGGAAGCTGAGAGACGTTGACTTTATTCGAACCACATGGTTCCAGTTTGTGGCAGCGGTCTCTCCGCTCGGCTAGAGGAGACACCGCGCCTGCGGTGTTGGCGCTGGAGCATCAAATCAGGTCTTAAAGGTTTCCCTGCTTATAGAGAGAGGTGGGCAAAGAGTGGATTTCCCTCTCTAGACCATCTTTGGGCGGACAGGTTACAGAGACCCTGGGTCTTGGACCCTCAGAGAGGGCCCGAACAGGGGGAATCCACACAGTGGATCTGGGGTTCAGGAATAGGTATGAGGTTGTCGGGGGAGGGGGCGAGATCCCTGCCTCCAGGCTTCGGCGGCTGGGACGGGGCTCTGGCGGAGCCTAGGGGTCTGATTGCGTCGGGCGCCCTGGCAGCCCGGTGCAGGCAGGCCGCGTCTGTGAGCCTCTTCCCCTTCCATTCTAGGAGGCAGGCGGCCCGTGGCGCGGGACCACCTGTGAGGGCTGCTGAGATTGGCGGAGGCGGTCATGTGGGCGGTCACGTGCCGCGGCGAGCTCCGTCCAAAAGAAAATGGGGTTTGGTGTAAATCTGGGGGTGTAATGTTATCATATATCACGCTACCTCGTAAAACCGACACTGAAAGCTGCCGGACAACAAATCACAGGTCAAAATTATGAGTTCTTCGTATTATGTGAACGCGCTTTTTAGCAAATATACGGCGGGGGCTTCTCTCTTCCAAAATGCCGAGCCGACTTCTTGCTCCTTTGCACCCAACTCGCAGAGAAGCGGCTACGGGCCGGGCGCCGGCGCCTTCGCCTCCACTGTGCCGGGCTTATACAATGTCAACAGCCCCCTCTATCAGAGCCCCTTCGCGTCCGGCTATGGCCTGGGAGCCGACGCCTACAACCTGCCCTGCGCCTCCTACGACCAAAACATCCCCGGGCTCTGCAGTGACCTCGCCAAAGGCGCCTGCGACAAGGCGGACGAGGGCGTGCTTCACGGCCCGGCCGAAGCCAGTTTCCGCATCTACCCCTGGATGCGCAGTTCAG
Seq A exon
GTAGGCTCAGTGGTCGGCGGGGTCGGCGAGCGGGAGGAGCGGAGGGGCGGGAGCAGGGCGCGGGGGGCTGAGAGAGCCCAGCCCGGCGGCTTCCAGCCGGCGGCCCCGCAAGTCCCCGTGGCGCTGCCTTTCTGGTTTTAATTAGAGCTGAGGCGCCATAGCGTGGAGAGACCCGTAGCATTGTATGTAAATGAGGCTCATAAAACTTTTTATGGCCCAATTAATGGGTTCGATCCTCGTAAATTTATTTAACTCCATTTGCCTTGGAATTTTTACAATAAGTTTCTCCGCTATTCTCATTCTCATATTCTCTCTCTTTCTCCCCCCCCTCTCCCCCTTCTTCCCTTCCCTCTCTTTTTCTCTCCCTCAGTCTTTCTTTCTATCCCCCTCTTTTCTGTCCTCTATCTCTTTCTTGACTCCAGCTCTCTCTCCCCTCCTTCCCTTCTTTCGGCCTGGCTTTCTTTCTCAAAGGCAAGGAGAATTGAGACCTCCGGGATCCCTCACTCATCACTGTACCAGAGGCCATTTCCAGAACGGGGCTGAAGCCAATGGGACAGAGGGTGGGAAAGTCACAGGAAGGTCTTGTGGATGGGGCTGCTGATGAGGGTCGCCCACTAGCAAGGCTGGGGAGCAGCCAGGCTCGCCTTTGAATGGCAAAAGCGCAGAGTCCCCCACTTGCCACACTCTATATTGACAATTTCCCTTTGTCAGGGGGAAGCAGGACATTGTGGAAACGTAGCCGGCTGGAAAGGCCAGTTGTAAAGTTGGAATTCTGCCCTAAGGCTTCTCACAGATGTTCTTGCTTGTCTGGCCCTGGGGCCTTCCGCTCACAATTTCCCTCCCCCAGCTCAATTGAGGGTGATGAGGGTTGCACCTGGATTTGGGCAAGGTGGAAGGTGCAGGTTCTTGGGCTGCTGGCCTGACTAAAGCACTCTTCTGTCCACATCCTAGTCTGCTTGTCTGTTTTGTCTATCTATATGTCCAAATTTCTGTTCCTAG
Seq C2 exon
GACCCGACAGGAAGCGGGGACGCCAGACCTACACGCGCTACCAGACGCTGGAACTGGAGAAGGAATTCCATTTCAACCGCTACCTGACGCGGCGCCGCCGCATCGAGATCGCTCACGCGCTCTGCCTCACTGAGCGCCAGATCAAGATCTGGTTCCAGAATCGGCGCATGAAGTGGAAGAAAGAGCATAAAGATGAGAGCCAGGCTCCCACTGCAGCCCCGGAAGACGCGGTGCCCTCCGTTTCCACAGCTGCTGACAAGGCGGACGAGGAGGAAGAGGAGGAAGAGGAGGAAGAAGAGGAGGAAGAGGAGTAAAGGGCCAGGCACAGGACCCTGGCTGCACAGGACAGTTGGAAAAGCGTCTTTAAGAGACTCATTGATTTTAGTTACAAAAATGGGGGGAAATAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038236-Hoxa7:NM_010455:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.008 A=NA C2=0.500
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NO

							
C2:
PF0004624=Homeobox=WD(100=54.3),PF085535=VID27=WD(100=64.8),PF0042814=Ribosomal_60s=WD(100=60.0)

						

					

				








    
Main Inclusion Isoform:
ENSMUSP00000134514





     
                   









    
Main Skipping Isoform:
ENSMUSP00000048648





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000134610, ENSMUSP00000134641
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr7:27155223-27156166 
LOW PSI
HsaINT0077286
(HOXA7)
Human
(hg19)
chr7:27194842-27195785 
LOW PSI
HsaINT0077286
(HOXA7)
Rat
(rn6)
chr4:82184733-82185722 
Cow
(bosTau6)
chr4:69341117-69342084 
LOW PSI
BtaINT0073176
(HOXA7)
Chicken
(galGal4)
chr7:15793477-15793853 
Chicken
(galGal3)
chr2:32570607-32571708 
ALTERNATIVE
GgaINT0097591
(HOXA7)
Zebrafish
(danRer10)
chr3:23561723-23564953 
LOW PSI
DreINT0078833
(hoxb7a)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CCCCTCTATCAGAGCCCCTTC

				
R: 
CTTGATCTGGCGCTCAGTGAG

				
Band lengths: 
345-1344

			

		

	





	
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"