Special

MmuINT0077935 @ mm9

Intron Retention

Gene
ENSMUSG00000021366 | Hivep1
Description
human immunodeficiency virus type I enhancer binding protein 1 [Source:MGI Symbol;Acc:MGI:96100]
Coordinates
chr13:42259586-42263032:+
Coord C1 exon
chr13:42259586-42259761
Coord A exon
chr13:42259762-42262930
Coord C2 exon
chr13:42262931-42263032
Length
3169 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGA
5' ss Score
9.11
3' ss Seq
AGACACTCTTTCCCCTCAAGGAA
3' ss Score
5.72
Exon sequences
Seq C1 exon
ATACAAGTCAAATGAGGATTACGTGTATGTCCGAGGCAGGGGAAGAGGAAAGTACATTTGTGAAGAGTGTGGAATACGTTGTAAGAAGCCTAGTATGTTGAAGAAGCACATCCGAACCCACACAGATGTCCGCCCCTACCACTGCTCTTACTGTAACTTCTCCTTCAAGACGAAAG
Seq A exon
GTATGAGCTGCGCATCGCTGCGGTCCTCCTGTGTGCCTTTAAATGGGAGAGCCAGTGCTGTGTAGTCGGAGGATAAGCCGCTGCCACAGGCTAAGTTACATCTTTCAGCACTGGAGTATGCATGTATGTGTTCTTTATGTTTCTAGACCCTTTAAGGAAAGTACTTCTAATGACAGGGTTTTAGAAAATACAGAAGTAAGAGTAACATTTAAAAGGGATTAACTGTTTCTTTTTATATTTTACTTCCCAAATCATAGTTCCATAACAATAGCTAACATGTTTTCAAAATATGTACTTTGGAATTGAAGGAGAGAAAGAAATGTTTGTGATCACAAGTAAATTCATTAGAGTTCAAAAAGATTCGAGACAGATTTTAAATAATAATCAGAATGAATTTTATAGTCACTCATTTTACTATCTTATTTTAGCCACAGATAGCCATCTTTTATGATAAAGTTTAACCTAATTATATTAAATTATACTAAATTTTAAATTTAAATTCTTAAACATTTCTATTACTAAATGTTGTTAATGGGCTTTCAGAATTAGTAATATATATATTTAGCATGCTTCTGTTTTATGTTTATTTAAAGCCCAAGCCCTCATGATGAAACAATTTTACCTTTTATGGGTTTCCTGTTATGCATAATGGCTACAGTAGTATAAAGCATTTGCTTTTTGTTCACAGGTCATTATGTGACAAGTCATTAAAGATGGTGCTTTTGTATCCTATTCTTTATGAAGTAGGACTTCCTTTAGCCAAGCAATCTATTCCTGGGGATAGCTGACTTCAATGGCAGTGTCTATTTAAAAAATGGTCATTTTATGAAACTGTGCTCCTTTGAGTTCACATTTGTCTTTTTGGTAGTGCTGGTTATCTTTGTGGTTTTCTGGTAAAGACTAATCATTTCTTTAGCCAGTTTTGCTGCAGTTCTGGCTCAGATTTATTGGCATTTAAAGAAAGTTACAGCTGTCACAACTGAATGCTTTTCTGAGCGCTCAGACATCAGTAGTATCTGGGAAAGGATCACCAAAACAAAGTGTGCTTCAGAAAGCTCTGAGCTTCTAGAGAGTTCCAGGCAGGCCCTCGGGGCAGAGGAGCCTGCAGTTCTGGGCTCTCTGCTAGGTCTGTAGGCCCTTCTTCCCTTCAGGGTGGGCTAAGGGGAAAGTAGTCAGCCTGAGTCCTCAGGATTGCCTCAAAATGGAGTCTTGTAACCATGACTGCTGTGCCATTGCTGTGGCACTGTGATTTGGGAAGGATCTGTTACCTTGGGACGTGAGAACAGGACATGTTTAAAAAGCTAACGTAGGAAGAAAGCAAAGCCATGTATATCACCATCTTACAGAGGAGATTGCGGTGTGACATGGAATGAGTGTGTCCTACACATGTAGACGCATAGTTTCCTTTTAATTACTTAAGGAGTTGATTGATAGTAATAGGTTATGATGTAATATAGATATTAAAAACTTAAATTCCCAAGTTCACTCAGGCACAGTTGTAGAGTAGTTTCTTAGTACAGACCTTGCTCCGTCTAAGGAACCAAAGCTTGTGAAAGCGAACTCCTAGTGAGCCTTTAATTTACCTAAGCATGCTGGTACTTCTATGAAAGCGTATTGACTTACAAATGGAGGCCAAGGCCACTGCAAGAAGGCTTTTAACCAGCTATTTATTTATTTATTTATTTATTTATTTACATTTTAGTGTGAAAACTTTGAAGCTCTTACAGGAAGTAGAGATTTATATAACAAATTTCTGTGTGTCTTAATGACTCTTACCACTCTGCCTTAGTTTTCAGTGTGGTGTAAATGTCAGCCGCAGGCAGACCGGCTGAGGCCTGTGTTATCTGTCGGATCCACCTGGCTGCAGTCAGCAGTGATGCCTCTTAGCGAATCTGTGCTTCAGAAGCATCTTAGACTTCTTAAGCACTTGGCTTTGGGGTGCTGTGTGGTTGTTTGACAAGAATATACCGGATATTGCCAGAATTGGCATATACAGTTGTGACCAACTTCTCAAACTATGCATTTATCAAGGAATTGAAGCTGTGTGAATCCAACAGATTTGCATGGCTTTCTAGTACAAGCCCAACATTTGGAACAAAGAGTCCAACATTTTCAGCATTTCCGGTTTGTTCCTGTCCCCCAAATTGAATATTTAAATGTTGTGCTGTGTTTACTCTTGCTGACAGGGTTTTGAGGTATAGCATCATCCACTCAGGATGACTGGGGTTCTCAGGAGAGTCTGAGCAGCTCCGTGTCATCCTTGGTCACTCCAGGCAGTGTGCCCTGTGAACCTGTGATATTCACACAGGGGGCCATGCCAGCTGACATAGCAGATAGCCTACAGTTCTCCAGACACATTTGCTTAGCATGTGAAGGGAAAGTGCTGAGCTTGTCAGCTACTCTGTGCCATACACAGTGCAGTTTACAATGCTAAAAAGCAACCCAGAATAGTCATCAAACATTTAAACTTTAGAACCATAAGTGCCCAGGTGCCAGAAATGAAGGAGAAACTAAAAACTAGCAAGGTAGGGGATCATTCAAACATCATAGTGGAGCCAAGGCAATACTCATACCAATGGGTCTGGATGGCACTGCCTGCCAGGTGCTCCTGAAGTACGCCTGCCTGACCGTCCTTTCCAGTGACGTTGGGTCACATAGGAAATAAGCATTTGAAATTAATGAAATAGTTATGGTTTCAGGCAGAAAACTTATAAGAGATGCTTCTATAACTTGGAATCCTTAGAACACTTTACTGAAGATGGACTAAAAATTAAAATGAGAATATATACAGGAAAGTTATCTACTGTGAGAGCATGCCAGCAACACAACTAATGGATTGCTTACATGCCAGTAAGTGCAGGTCAGACGCACTCTGAAAGAGACACAGAGTGGGCATGTGCTTAGGAAATAAGAACTGGAGAATACGCCTCCAACGGGAAAAAGTAGCTACCATTAAAAGAGACAAGGCAGATTTGAAAACAGAATGCCAGTTAGTACAAAGGTCATTGCAAAGGTTATACCAGTGGTTTTTATATACAGTTTTAGTTGTTGAGATTGTCTAGCCATAGTCAGTGTAGCTGTTTCCTTGAAGAATAGAATTTTCCAGAGCTGATGAATGAAATAGCCGAGCACCACTCCATAAGTTTAATAGACACTCTTTCCCCTCAAG
Seq C2 exon
GAAACCTGACAAAACACATGAAGTCCAAGGCGCACAGTAAGAAGTGTGTGGATTTAGGCGTCTCGGTGGGCTTGATAGACGAGCAGGACACAGAAGAATCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000021366-Hivep1:NM_007772:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.129
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF134651=zf-H2C2_2=WD(100=43.3)

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000056147f982A





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000056147
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr6:12130943-12135790 
ALTERNATIVE
HsaINT0076318
(HIVEP1)
Human
(hg19)
chr6:12131176-12136023 
ALTERNATIVE
HsaINT0076318
(HIVEP1)
Rat
(rn6)
chr17:22299539-22303042 
ALTERNATIVE
RnoINT0070914
(Hivep1)
Cow
(bosTau6)
chr23:44161500-44166024 
LOW PSI
BtaINT0072260
(HIVEP1)
Chicken
(galGal4)
chr2:62807275-62809713 
ALTERNATIVE
GgaINT0091526
(HIVEP1)
Chicken
(galGal3)
chr2:63865945-63868383 
LOW PSI
GgaINT0091526
(HIVEP1)
Zebrafish
(danRer10)
chr19:3448638-3449240 
ALTERNATIVE
DreINT0078036
(hivep1)
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"