Special

MmuINT0078765 @ mm9

Intron Retention

Gene
ENSMUSG00000038721 | Hoxb7
Description
homeobox B7 [Source:MGI Symbol;Acc:MGI:96188]
Coordinates
chr11:96147960-96151477:+
Coord C1 exon
chr11:96147960-96148441
Coord A exon
chr11:96148442-96150690
Coord C2 exon
chr11:96150691-96151477
Length
2249 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAG
5' ss Score
9.65
3' ss Seq
CTCTCTAATCCTGTGTGTAGGGC
3' ss Score
7.64
Exon sequences
Seq C1 exon
GGACTCTAATTCTGTAATATATCAAGGAATCTCGTAAAACCGACACTAAAACGTCCCCGACTACAAATCATCCGGCCAAATTATGAGTTCATTGTATTATGCGAATGCTTTATTTTCTAAATATCCAGCCGCAAGTTCGGTTTTCGCTCCAGGAGCCTTCCCCGAACAAACTTCTTGCGCCTTTGCTTCCAACCCCCAGCGCCCGGGCTATGGAGCAGGTCCGGGCGCTCCTTTCTCCGCCTCGGTGCAGGGTCTGTACTCCGGCGGGGGGGCCATGGCGGGCCAGAGCGCGGCTGGCGTCTATGCGGCCGGCTACGGGCTCGAACCGAGTTCCTTCAACATGCACTGCGCGCCCTTTGAGCAGAACCTCTCCGGGGTGTGTCCGGGCGACCCCGCCAAGGCGGCTGGCGCCAAGGAGCAGAGGGACTCGGACTTGGCGGCCGAGAGTAACTTCCGGATCTACCCCTGGATGCGAAGCTCAG
Seq A exon
GTAAAGCCGCGCTCTGAGCGGTCCCGAGCCGCAGTGTCCGGGCCACGGTCCCCAGAAGGGCTCCCTTCCGGCCAGGGCACCCTTCTCTGTGTCCAGGTTATTCCCGGCTGCAGATCGGCCATTGCCACGCCGTTTAAGTCTGGGCTGGGACCACGCGCGCCACCCCCACTCCCAGTTTTGCTCAGTGCTCTCAGGCCCTAGCGGATCTCTTTTTGCCGACGCCACAGAGCTCAAAGCCCCCAGCCCGCCCCCAACCCTTCCTCCCGGCCTTTTAGCTTTAAATATTTATCAGCAGCGCCGGCACGGGCTGGAGACGAGGCCGTTTGTCTTGCCTAGAAAGGCTGGGGTTTGCAGAGAATAGCCATTAGGGTCTTTCTCTTCTCTCTCCCCCCTTCCCTGCCTGAGAGCTCAGTTCTGGGTGTGTCCCCCCAGCCCTAGCTTGGGCAAGATATGGAGGAGGGGGCCATGGCGCTAAGCGATTCTCCCCTCCCCCTTCCTTTCTAGCCAACCCCGCTCCCCCATTATTCCCATCAGGACAATTAGAGGTGGGCTCTAGAGGCCTGGTGGGATGGGGGAGAGGAAACAGAAGAGATGAGGACCCAGACAGGGACACAGAGTCAAAGAGTGGTGAAGGAGTTAGTCTGAGACCCAGAGCGATGAGTCTACTGACCCCCACCTCCTGATGGACTTAGAAGGCCCGTCAGCTCCCCAGGAGAGCATAGGTTGTTTGTTATTTTTTTTTTCCAGGTGTCTTTCCAAGGGCTCTGTGGGCCCCTGAGGAACAGCCAAGTTTGGTGGTATCACTCCAGAAAGATGACTCTCCTCTTGGGGAGGGCTAGGACTCTTCAGAACCAAATCAAGATTTAGGGAGTGCACGATGCTTTAAGAACCATAGGTTTTCTTCCCTCAGGTCTCCTTCACAGCTTCCTCGCACACCTTTTACATTTCCCCGAGGCAGGTGGGCTTGGGAGCCAACTCCAAGGCTCAGAAGACCCAACCGGGCCAGAGACTCCTATACTCATGGGCTTGGGGGCCACGAGGAAACCATTTCTTGACTATTGTTCTTCACGGTTCCTGTTACCTACCCTGTAATTGAACTGACCTTCCAGTTGGTTTATCAAAGTCCCTCCCCCCCCCCACCTCGTAAATATTTCAGCTTGGCTTATAGCTGACTTGAAATTAAGGTCCTTAGCCTCTCTCCCCTCTCCTGTCTCCTTCCCAAGAGGGCGGATACCAGCATCTCCCCAGTCTCCTTGGGGTTCTGAGCCTATGCTGGGAGTTCTCAGATACCCTTTTGCCCCACCATAGGAATCTTCACCTTGCTCTCTCTCGTAGACTCTGGTCATTCTTTTCTTCCTTGCAGTCCTGGAGGCCCAAATATTGCTTCAGACAAGTAGGTTTCATGTGCAGGAAGGCAGGCAGTAGTCAGACCTTGCTTGATACTTACTGGGAAGGAATCATCAGAGCCAAGTTCTGTCAGTCTACTAATGCCAAGGTCCAAGGAAATAATGTCCTTGTCTCTTCCCCATTCCACAACAAGTTTGGGTGGGGACTGGGCCTATGGCTCCTTTTATTTCTGTTCTTCTCAGACTAGGCCTGGAGCCCCACTCTAGGGACACTAATATGGTTTCCAGAGCCCTGTACCTCAAAGGCCACCTGAATGGGGAAAGGGTAGACTTGGTGCCCCTGACCTTAGAGAGTGACTGATGACAGAATTTGCTCTCTTTCTGTGTTAGCCCCTTTGGAATAGAGTCTCAGGGAGCCAGCAGCTGAGAACTACCTGGTTTTCAGAAGCTCCTGGCAGAGCAAAACCACCCTTCATGGATGACAGGACTACCTGGTGTGCTGGGGCTGGCCTGGGAACCCAGCACTTAGTACTTGGGGCTGAATCAGGAGGATGGCTGCTAGTGTGAAACCAGCCAGAGGCTCCATAGCATGACCCAGCTTGAAAAACAGAACAACTCTTATGGACACACACACACTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCACACACACACACACACACACACACACACACAAAGAAAAGAAAATGTTTTCTGCACCTAGTAGTGAAAGGGGATTAATGTAGTTCCAGCAAGGTAACCACCTAGGAAGGGGGTCAGAATTCTGTTGGTGTTTTTCACACAGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTAATCCTGTGTGTAG
Seq C2 exon
GGCCTGACCGAAAGCGAGGCCGCCAGACCTACACGCGCTACCAGACCCTGGAGCTGGAGAAAGAATTTCACTACAATCGCTACCTGACTCGGCGGAGGCGCATCGAGATCGCGCACACGCTCTGCCTCACCGAAAGACAGATCAAGATCTGGTTTCAGAACCGGCGCATGAAGTGGAAAAAGGAGAACAAAACCTCAGGACCGGGAACCACCGGCCAGGACAAGGCGGAAGCGGAGGAGGAGGAGGAAGAGTGAGGGACAGAGAAAGCCAAGAGGAGGAAAGCGAAGAGAGGGAGAACCCAATTATGGGAACTGAAGCATGAAACTCAAATAAAGGGGCAAACTATTTAAATGAAGAGGTCTAAAAATAATAAGGAAAGAGAAGGGTGAAATTTGGGTTTCTTAACACTGTAAAAAAATATACTACCTATGGGAAAGTGTGTTGTCTGTTTTTGTACAGTATCGGAAGGACATTATCTACCTGTTCTGTGGCTTTCTGGAATGTGCCTCCCCTTTTCTATGTTGCTAGTAAGGTCTTTGTAAAATCTTGCTGTTTTGTAAGCCCTCTTTGAAGCTGTCTTTGTGAACTGTGGTTCCAGATGAACAGATTAGTGCGGTTCCTTACCTACCCCATACTTCCCAGTAGCAGTACTAGAGGGGTTGTATGGAGCCCTGAGGATCCACTAGCTTCTGCGTCTGGTGCATTTTGGCTGCTGTTTCTAGGTCCTATTCACGAGCCTCTTTCTGTATATCTGAAGGATGGAAAATAAAACAGGATTAAATATCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038721-Hoxb7:NM_010460:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.194 A=NA C2=0.417
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
PF0004624=Homeobox=WD(100=67.1)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000040121





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr17:48608096-48610518 
LOW PSI
HsaINT0077299
(HOXB7)
Human
(hg19)
chr17:46685458-46687880 
LOW PSI
HsaINT0077299
(HOXB7)
Rat
(rn6)
chr10:84135643-84137848 
LOW PSI
RnoINT0071651
(Hoxb7)
Cow
(bosTau6)
chr19:38519056-38520804 
ALTERNATIVE
BtaINT0073183
(HOXB7)
Chicken
(galGal4)
chr27:3586581-3589198 
ALTERNATIVE
GgaINT1015125
(Hoxb-7)
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: 
No suggested primer sequences

				
R: 
No suggested primer sequences

				
Band lengths: 

			

		

	





	
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"