Special

MmuINT0077953 @ mm9

Intron Retention

Gene
ENSMUSG00000078582 | Hivep3
Description
human immunodeficiency virus type I enhancer binding protein 3 [Source:MGI Symbol;Acc:MGI:106589]
Coordinates
chr4:119804327-119808016:+
Coord C1 exon
chr4:119804327-119805234
Coord A exon
chr4:119805235-119806185
Coord C2 exon
chr4:119806186-119808016
Length
951 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
GTCTTGTTTTCTGACTCCAGCGG
3' ss Score
6.65
Exon sequences
Seq C1 exon
GAACCAGTGATGACCTGCACCAGGACTCAGAGGGGCAAGAGGGCGCCGAGGCTGTGGAGGAGCACCAGTTCTCAGACCTGGAGGACTCTGACTCAGACTCAGACCTGGATGAAGATGAGGAGGAGGAAGAGGAGGAGGAAGAGAGCCAGGATGAGCTGTCTGGGCCATGCTCGGAGGCAGCTCCGCCTTGCCTGCCCCCCACACTACAGGAGAACTCCTCACCCGTTGAGGGCCCTCAGGCTCCAGATAGCACTTCTGACGAGGTCCCGCAAGGCAGCTCCATCTCAGAAGCCACGCATTTGACCGCCAGCAGTTGTTCCACACCTAGCCGGGGTACCCAAGGCCTTCCCAGGCTGGGACTGGCCCCACTGGAGAAGGACATGAGCTCAGCCCCGAGTCCCAAGGCCACGTCCCCTAGGAGGCCGTGGTCCCCAAGCAAAGAAGCAGGCAGCCGCCCCTCACTCACTCGCAAACATTCACTCACCAAAAATGACTCGTCTCCCCAGCAATGTTCACCGGCCCGAGAAGCTCAGGCCTCAGTAACGAGCACACCTGGTCCCCAGATGGGCCCAGGAAGGGACCTGGGCCCTCACCTTTGTGGGTCTCCAAGACTGGAGCTGTCCTGTCTCACTCCCTACCCCATAGGAAGAGAAGCGCCCGCTGGACTCGAGCGTGCCACAGACACAGGCACCCCCAGATATTCACCCACCAGGAGATGGTCTCTGGGTCAGGCCGAGTCACCGCCACAGACAGTGCTGCCAGGGAAATGGGCCCTGGCTGGGCCCTGCAGCCCCTCAGCGGACAAGAGTGGCCTGGGCTTGGGGCCGGTTCCACGGGCCCTCCTCCAGCCCGTGCCTCTACCTCACACACTTCTCAGCAGAAGCCCTGAAACGTGCACCTCTGCATGG
Seq A exon
GTGAGTCCCTGCTGTGGCCCTCCCGGGGGTCAGAAGCTGCCCATTCACACCCTCTGCCCCTCACCCCAGAGCCAGGCCGGTATTCCTGGGCATGTGGCAAGCTTTTCTTAGGTCCCTGTGTCAGCTAGTTCATTGCACTTTGAGGCACCCTCAGAAGCCCCAGACATGGCTCTGGTGTTCACAGGCTCTGGGTTCAAGCCCTAGTGGGCAGTGTAGCCTTGGATATGGACGTAACACTTGTGTAATTCTTCGGCCATCACTTCCCTGTCCATGTATGTCCTTGGAGCAGTCGACAGCTTTACCAAAATCATCTGTCCCCATCTCCTCCCTGTGGAACTATGACAGCCTTGCCTCTGTCACCACCATGCCCCACCACACCCCGCTACTGCCCATCACCCTTCCTTGACAGTGCTTGCCTTACAGTATCTGTACCACTGCCTCACTGCCCCTCCCCCCACCCCCGAGGCTGACACTGTCCACGGCTGGCACTGTCCCTGTTGACATTTCTTACACTGTGCTGTCATGACCCCACAGCATCTCTCCTGGAAGAACACTAACTGAAGCATCTCTCTTGCCTCATTGAACTTCCTGTAGTGAAAGGTTGAGATCTTTGGGTGGGAATCCATATGCAAGGGTAAAGTTAGGCCAAGACCATCTTAAGAAGGGGAGAGGCAGAAGAGCCAAGGTAGACCAGGGTGAGCACAGAGCTCCCCCCACACCCCCCCACACCCCCACACACACACACAAGAGCTGCCTCCTACAGATGTGGGCCAACATGTACCTCTAAGTTGCCCAGTTGGAAGCTTGCCGAGAACTGCAGTAGGACTCCTGATTCTGGCCGTACTCACCAGCCGTACTGCAATCTCAGGCCTCCCCACCCTCTATACCGTTAGCCCTCAGTTCTGCAGGCACGTAACCCTTGCCTTCTCCCGTCTTGTTTTCTGACTCCAG
Seq C2 exon
CGGAAGACTGAGTCCCGAAGTCCATCAGCTGGCCCTGCTCCTCTCTTCCCCCGACCATTCTCCGCCCCTCATGACTTCCATGGCCACCTCCCTAGCCGAAGTGAGGAGAACCTCTTCAGCCACCTGCCTCTGCATTCCCAGCTCCTGAGCCGCGCCCCCTGCCCCCTCATTCCCATCGGTGGGATCCAGATGGTACAGGCCCGGCCAGGAGCCCAGCCCACCGTGCTTCCTGGACCCTGCGCGGCCTGGGTCAGTGGCTTCTCAGGGGGCGGCAGTGACCTAACTGGGGCCCGAGAGGCCCAGGAGCGCAGCCGCTGGAGTCCCACAGAGAGCCCTTCAGCATCGGTGTCCCCTGTGGCCAAGGTCTCCAAGTTTACACTCTCGTCAGAGCTGGAAGAGGAAAGGACCGGCAGAGGCCCAGGAAGACCTCCTGACTGGGAACCTCACAGGGCTGAAGCCCCTCCAGGACCCATGGGCACACACAGCCCCTGCTCCCCACAGCTGCCCCAAGGCCACCAGGTGGCACCTTCCTGGAGGGGCCTCTTGGGGTCACCACACACACTGGCCAACCTAAAGGCCTCAAGCTTCCCACCACTGGATCGCAGCAGCTCCATGGACTGCCTGGCAGAGACCTCCACTTACTCTCCACCCCGGAGCAGGAACCTCTCTGGAGAACCCAGGACCCGTCAAGGCTCCCCTGAGCTCTTAGGTAGAGGGGAGCTCAGGACACCTCTATTCCTGCCCAAGGGTAGTGGCCCCCCAAGCATCTAGCCTCTACAGCTACTTCAGCGCCTGGCCTCCAGTGTCGGCAGCAGACATGCCCAGACAACCGCCTGGAGTCATCTTGCTCCCTTGGGCATCCTCTCCCATCTGTCCATCTGTCCATCTATCCATGCAGCTTCTGCTCAGCCCCATCTGTTCTATTTCTCCACATATGCAGTTACCTGTGCCTTTTTCTAGACCTTTTGTTGCTTGAGAAAAAAAAAAAGAAACAAAACAAATCACACACATCCATAAACAAAACAAAACAAAACAAAACGCATCCCTGAGGAGCTGAAGGCTGTGAGTGTGCTCTGGGGACAAGGCTGGAGGAGGGAATCTCACCTCCACCACCACCATGTGCCACATGGGCAGCTGTCCCCACCTCAAGGTCCAGGAGAGGGTCTGTGGCACTGAGAGAGAAGAAGAAAAGGGGAGAAAAACTGTAATTAAATTCAAAGGCAAGCACTCCTACAGTCAGATGCCCACCATCCCCACTGAAAGACGCACAGCTCGTAGCCGCCCTTCTCTGCCATCAGAGGGACACAAATACAGGCAGGAACCAATCTACCACTCCCCACCCTACCCGACCAAGGACATTATCTTTTATCCTTTTTTTTTTTTTCAAGAGTAGGAACCAAAAAGAAAAACTACTTTCTAGCATCTCAGCAGCACAGACTAGCAGCAGGAAAGAGAAGAATTCTGTAGTATGAACTGTGGCTCTCACTTCTCCCTTCCACACCCCACCTCCCCTCCCCTCACCCCACCCCATCCCCCAGGCTCATAAAGGAGCCCGGGTTGCCCATCTCCTTTCTCCTATACACTATAGGTCTCTGCCTCCCAGGCCTGGCCAAAGGCTGGCTCCTCTATGATTAGAAATACCTGCAGGATGAAGGGACCAAGGCCGGACTAGGGATGGTCCTAGTCTGGGCCTGTTTTGAGCCTGGGGTTTGGATTGGTTCACCTCTGTCCCTGAGGAACAACATGTCACATTTCCTTCATGGCTGGATTAACGTATGTGTGTGTGTATATAGATACACAGAGAGAAACCAAAGATGGTGTTTGGTACTTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000078582-Hivep3:NM_010657:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

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

				
Domain overlap (PFAM):

					





						

							
C1:
NA

							
A:
NA

							
C2:
NA

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000101914





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000130249
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:41511264-41512815 
ALTERNATIVE
HsaINT0076338
(HIVEP3)
Human
(hg19)
chr1:41976938-41978486 
ALTERNATIVE
HsaINT0076338
(HIVEP3)
Rat
(rn6)
chr5:139071999-139072987 
LOW PSI
RnoINT0070928
(Hivep3)
Cow
(bosTau6)
chr3:105266226-105267760 
BtaINT0072272
(HIVEP3)
Chicken
(galGal4)
chr23:912965-915254 
HIGH PSI
GgaINT1014831
(HIVEP3)
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
chr16:34368978-34371145 
LOW PSI
DreINT0078051
(hivep3b)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GTCCTGTCTCACTCCCTACCC

				
R: 
AGAATGGTCGGGGGAAGAGAG

				
Band lengths: 
350-1301

			

		

	





	
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"