Special

MmuINT0077930 @ mm9

Intron Retention

Gene
ENSMUSG00000021366 | Hivep1
Description
human immunodeficiency virus type I enhancer binding protein 1 [Source:MGI Symbol;Acc:MGI:96100]
Coordinates
chr13:42147390-42150911:+
Coord C1 exon
chr13:42147390-42147459
Coord A exon
chr13:42147460-42150768
Coord C2 exon
chr13:42150769-42150911
Length
3309 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAG
5' ss Score
8.27
3' ss Seq
TTTTATCTTTTTCTTTGCAGCAT
3' ss Score
11.27
Exon sequences
Seq C1 exon
GGGGGAAGCCGCCGACCTTCGCCCTGGCCGCCCTCGCGCTGCCAGCCGTCCTCACGGACACCCGGGAGAG
Seq A exon
GTAAAGGCCGCTCTCCCGCCGGGTTCCACTCGGTCCCTCCCGCGCCCAGCTCGCGCCTCGGTGCCCGTCGGGAGGAGGCTCCGCTTGTGCTGATGTCCCGGTTGTCAAGTGCAGCGCAGTTCCCGACGGGTGCGGGGCCGGGCGCGGCGGTGGGGGCGCTGCACCCGGGAGAGCGCGGCGCGGGGGGCGGGGGCCGGGACCACCTCCCCCTGGCGGGCGGGCGCGCGGGTGTGCGTGTGAGTGAGTGTGTGCGCGTGTGCCGGCGCCGACCTTGCGGAGGGGATGCTGCGTGCGGGAGCCGCTTGCCACTTCGGCGGGTCCTGGCCGCACGGGCGGCGGGAGCTGCGGTCCTGCGAGCCCAGCAGGTACGGAGGGCCGGCCTCCTGGTCGCCGCGGCCGCTTCTCGCAGGAGGGCTCGGCGGGGCTGCGGGAGACCAGGCCGCGGCTTCCGCACCTCCCGGCTTTGTGGCTCGCTTTCCCTTTCGGTCTTTGCCCGGAGTGCCTGTTTACTCCGGGCCACCTGGGTAGTTTCCCTCCCCGTAGGGCGCGCGCCCGCCGCTGGTGGGTCGGGGCCGGTGGGTAGGGGCGCGGGGCGGCTTGGGCTCGCCGCGGGGTCGGGCTCCAGCCGGAGTTGCGGCTAGAGAGGGGAGGGGGCTGTGGCGAGGCTGGCGCGAGGAGGAGTCTCAAGGCTGCTGCTCTCGCCGACTCTGTCCTCCTCCTCCTCCTCCTCCTGCTCTCCGCATCCACTCTAGGCTCCTTCCGGAGCTGGCACTTCCATTCCCCCCTCCTTCTGGCATGCGAAGCGCTTTGTTCAGTGCAGCGTTGCAGAGGGGTTTTCCCAGGCTCCGCCCTCCACATTCATTCATGTTTTTTCTCCTTGTGACTGTCTTTACGCTTTTTTGATTGTGTCCTGTTTTTGCACCTTGTAGTATGTATTTCTTTCTCGAGAAAGAATGGTCGATCACTGGTCCTAGTCGCCACGGTGGTGCTGTCGTCTTTGAAAATAACCACTTCTCCACCGCGGATTTAAATGTGGGCTGGACAGCTAGGGACAGGGGGGCTGGAGGCTGCAAAACCGGGTCGCACAAAGCTGTTACAGGTTGGGAATTTGCATATTTTAACATTTAAGCTTGGGAGCTGTGGGAGGTCACGTGATCGGCTTACAATCCGAGTTCACGCTTTAAAAACTTCGTAATATCGTGACCGCTTAAAAGCTTTAGTTTTAATACGGAACGGAACACTTACAGCTTTATCTTTAAATTCTCTGTGCAGTCAAAACCTTTTTGGATGCTATAGCTGATGCCTCTGTGGTAGGGGGAGTTGAGGAGCTCTATCTTTCACCCATCATTGACCGTCCTGTTTCTTATTCTTCCCCTGGCGTTAGATTGGGGATAGTTTGTGTTATGCCGACTAATAGCCGTGTTAAGAGCCGTGTTGCTTACAGTCGCAAGCACGGTAATAGCCGCCTTTTCCTTATGCGTTTTAACTAAAGTGAAAACATACATCTAAAACCTTAGTCTGGGATACATGTTCTTTACCTTAGAGGCGTTCTTCCAGGGAATTAATATTTCAGCATTTTCATGTGGTAGGCAAAGCTTCTACATTGTGTAGCTTACTCCTCAGTCCTTAGCCCGTTTGGGGTGGATAATGTTTCCTGATTTTACAGCTTGGGAAATCTGATCTTCTTTTCTGAGAGCTTAAGTACCTTGAACAAGGCCACACAGAATGGGGTAAAGCCTGGCCTTGAACCTGGTCAGGTTTGATTCCAAAGTATGTCTTCATGATTTGCTGTGTCATTCATCCCTTTGGGAGGGGATTGTCCTTGGTAGGTAAATGTTATCTTCTCAGAGGAAATGGGCAAGGTGTCATGTGGGGCCACGTTCTGAGGAAGATTTCATAATCTCTCTCTAAACTTGTTTTTTTTTTGTTTTGTTTTGTTTTTTGTTTTGTTTTCTCTTTGTAAAATGGATGAATTGGAGTTGTTAATTTTTTTTTAATCTCTCCCAAAACTTTTTTCCCCTACCTCTGTAAAATGGCTGAGTTTGAGCAGTTGATTCGGTTGTTAGGATTAAATTAGGTGATAAGTAGAAACTCTACAGTAAACCCAATAAGTGTTCTCTTGTGTCGTGTACAGTAATAGATATGAGAGGTTTTAAACAAAAGCATCCTTAGTCTATTGTGTTTGCTTAGTGATTAAACTTGGTTTCACCCCATAGGGCCTGCTTAATGGGCTTTGCTTATCAGCACTGTTGCAGGAAGTTGAAGCTAAACTTTTAACTGATTATTGAGAAAGAATCTAGTGGAAGAGGAGAGAGGGAGGTTGCTGATTTGGACAGATGGGTGGTTAACTTTCAGGCACGTTCAACCTTTTGGCATTGCAACATAGGCTGGAGGACCTTGCAACAGAGTTACAAAAAAAAATCTCAAAAGAAATCTTGTAATGTTTTAAGTAAGTTTACTATTTTGTGTTAGGCAGCATTAGTAAAGGCAGCATGAGTAGAGATCTTCAGTCAGACTTAGTCCTTGGGCTGTAGGTTGGACATGCCTGTTGGGTCTTGGCATGATGCATTTCAGCTTGAAAAAGCAGAGTCAGGACAGACTAGGTTGTGCTGCAGTAACAAGTAATTCCCAAGCCTCAGATGCTTAAGTCAACAAAGGACTGCTTTTTGTTTAGGCAGCGTGATCATCTTGTGTCACTGGCAATGCAACTTTTTTAGTCACACATGCTGATTGGAACAGTGCCTGGCCTGTGCCAGAGGGGACAGAATGCTCTGGAATATCTTGCTTTGATAACTAAGTGCGCCAACATGGATTCGAGGCATGTCTGTGGTCTACTCAAAGGTCAACATGTAGCCGCTGATCACAGGCATGTGCAGTCCCGCCAAGGCATGTCAGCCATCACTGGGGAACAGCCACCATTGCAACTGTGCATGTTAACTGAGTCAACTGAAGTGACATGGCCAGGACATTGGGCTTCCCTTATAAATGACCATATGTATACAGCATAACTGTCACCTTACACTAACTTTCATTGTAACTAGCAGTGCTGTTCTAAAGTGAGCATTCTCATTCTCATCTAACTAATGTCTAGAGACTTTTTTTTCCACCTGTTTTCTCAACAAGGGGACCTAGAGAGTGGCCCGTCTTATGGCAAGATGACCTGGCTTATGTTTAGTTAAAAGCGAATGGTGCTTGCAGAGGTTACCTTCTATTGAGCTTAGGTCAGCACTGCTCTAAGCCCCTACCTTTTGAAGTGTCCTTCTCTTTTGACGGTGGTGAGATTTACTGCTTTTATCTTTTTCTTTGCAG
Seq C2 exon
CATGTGGATTAACTGATGGCCAACGAGTACATGGAGCCAGCCTTTTGTAACCTGCTCTTCCAACAGTTTCTAAGAAGAAAAGGGAGCTCTTAAATCTAAGAAAATGCCTCGCACGAAGCAGATTCATCCCAGAAATCTCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000021366-Hivep1:NM_007772:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
5' UTR





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=NA A=NA C2=1.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NA

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
NA





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000056147, ENSMUSP00000056147f982A, ENSMUSP00000056147f983A
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr6:12012567-12015525 
ALTERNATIVE
HsaINT0076313
(HIVEP1)
Human
(hg19)
chr6:12012800-12015758 
ALTERNATIVE
HsaINT0076313
(HIVEP1)
Rat
(rn6)
chr17:22400254-22403536 
Cow
(bosTau6)
chr23:44268541-44273068 
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
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"