Special

MmuINT0168750 @ mm9

Intron Retention

Gene
ENSMUSG00000026670 | Uap1
Description
UDP-N-acetylglucosamine pyrophosphorylase 1 [Source:MGI Symbol;Acc:MGI:1334459]
Coordinates
chr1:172088882-172091702:-
Coord C1 exon
chr1:172091498-172091702
Coord A exon
chr1:172089058-172091497
Coord C2 exon
chr1:172088882-172089057
Length
2440 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGC
5' ss Score
9.26
3' ss Seq
AAATGGACTCTCTTTTGCAGGTA
3' ss Score
9.08
Exon sequences
Seq C1 exon
GACTTTCTCAGATTTCTCAGAACAAAGTAGCAGTTCTTCTTCTAGCTGGTGGGCAGGGGACAAGACTTGGAGTCTCATATCCCAAGGGCATGTATGATGTTGGCTTGCCATCCCACAAGACGCTTTTTCAGATTCAAGCAGAACGTATTCTGAAACTCCAGCAGTTAGCTGAAAAACACCATGGCAACAAGTGCACCATCCCATG
Seq A exon
GTAAGCTGCGGCTCGCGCTGGAGCATCTGCTCTGCAGCATTCAAATGTATATAAACTTGCTGACAAGAGGGCACACTTCCTGTGCTCGGCGATCTGTGGAGAGATAATTCTATATATGCTGGAAGTAGTATATGTTATAGCTATCTAGCTGGCTTTACTGGGAGTATCTACGCACTTTTCTACCCTTAACCGAGCACCTTAAGAATACCTTTCAGTATCCAACAAACCCTCGGTGCAGAAATTTCTTCCTGACTGATGGATAGTGTCTAAAATAGGCCTTCTGGTTGAAACTTAATTTCCTCCTGAAATCTGAAGGTGTTGCTTTATTGTTCCCAATGTTGCTGCCAGGTGTCCAGTGTCATTTTGACCCCTAACCATTTTGTTTCCTCTCTCACGCATTTGGGTCTCTTCCTTATAGTGTCTGAAACTTCATGATAAGATGGAATGGCCCATTAGGCCTTTTCAGTCTAGCAGTGCAGGTCCTAAGCACCAGGTTAGGTAGTTCTTACTTCCTGCCCCACCTCTTCCATACATTCCCCCAGATGAAAGCCACTTTGACCTCTCTGCTATGGGTCACATTTGTTTTCTCAGCGCCTACTGGAGTGCTGCATAGGGCACTGTCTTGGCCACTGCCTCCTAAGCACTGAGAGTGACACTCAGCTGGATGGCTGCCTTTCACTTTTGTTTTCCTTTTCTCTTTAGCTCTCTGATTAGTTTCCCAGAGCAGGTTTTAAGGGGGGAGCCAGCTGTGTATTTGACATCCCTCAGGGCCTTGATCTTATCACTTCAGTCCCATAGGACCAATCAAAACTGCTGGTTTTCTGTCTCCCAGCAACAGCCTCTGGTCCTCGTGCAGGTTCCCTAGCCTGTACCAGCATCAGAAAAGACTGTGAAGAAGTAGCAGCTGCTTTTCTTAATGCCCTTTGGAAGATGCTCCCCCTCTGGGGCTCCCGGGCTCAACCATGCTGCTCTGGGGCTCTCTGGTTCCTTTGAAGACGTGGTTTTTGGAATAAGTTTTCAAGATGTTCAAGTTCTGTTTCAATACAAAAGTATTGGGATGCTGCCAACTTTTCTTTCTTCCATTTCTTTCTTTTCTTGATTCCTGTGGGGGTTTGGAGGGACATCTGTGTTCTCTGTGGTCAGCGGGTTATTTACAGCCCTGCTCTGTTGTCATGTTGGACTTCCTTCTCTCTTCCCTCTACTTTTTAGTGCTCTGCGTCTGTATGCAGAACAGTTTCCCACCTCTTTTTTATTTCTATAAAACAAAGAGTTGTGGCTCACCTTATTACAAAGGTTCAAATGCCCCAAATAATTTCATTGGCATACATATTTACTGTGGCAGGAGATCATGCCATTTTCTAAATCAATTTAAATAATTATTTTTGTTTTATGTTCTGCCTTGTATGTCTGCACTACATGCTTGCAGTATCTGCAGAGATCAGAAGAGGGCATCAGACCCTCTAGAAATGGGCCTACAGTGGTCATTAACTACCAAATGGGAGCCAACCTGAGTCCTCTGTAAGAGCAGTGCTCTTAACTGCGAGCCCTCTCTCCAGCTCTGTGCTTCATCAGTTGATTTATGTAATGATTATTAGTTGAGTTACTGTTTCTAAGTCCTAAGTATTGATCACTAACGAGAACAAGAATTCCAACTTTTATGTAGCTTAAATTCTGGTAAGGCCCTGAACCACTTCAGTTTCTAATTATAGTCTTAGGCAGGATCTTTGTAATCTTTTGCTATTCTGTCATGAATTCAATTTTTTTTTGAAAATGAAAGATTTGTTTTAATTTTTCATGTGTATACATGCTTACGTCTGAACACCCTTATGTGTGCCTGATACCCAGGGAGACCAGAAGCGGTACTGGTTTCCTAGGACTGGAGTTAGAGGCAGTTGGGAGCCACATGCTGATGTTGGGGATGGAATGGTGACCTCTGGAAGAGCACACAGTGGTCTTAACTGCCGAGCCATCCCTCGAGATCCTGAGTTAAGGCTCTGTGGCAACAGAACGTACACTTTCACTTCTGTGGTTCTCACTGGGTGGCGAGCAGAGTCTGGGCTTCGTTTCAGATTTTAATAAGAAGCACAAGATGATATTAGCCTGCATTACTGTTATCTTTTTTCCTCTATTTACAACAAGAGACTTAATGTTAGTGTACACAGAGTTTACAGGCTTGCTTATGCCTCTAGGCATGGGTTCTCTGCTGCTGGAATCAGGTTTGATATTTTCATAGGCTTATTTTAGACATAAGGACCAGTAAAATCGTGGAAGAAATACAACTGCTAATTAGTGTGTCTGAGCCAGAAAAAAAGATGAAGTAAGTCAAATATAAAGCAAGCGCTCTTTAGAGTCTCTGCAGCTTGGGAGATATATTGAGTGTACTTTCTTTTGCCTTAATTCTTGCAATATCATTGCTTATAAAATGGACTCTCTTTTGCAG
Seq C2 exon
GTATATAATGACCAGCGGCAGAACAATGGAATCAACGAAGGAGTTCTTCACAAAGCACAAGTTCTTTGGTTTAAAAAAGGAGAATGTGGTGTTTTTCCAGCAGGGAATGCTGCCTGCTATGAGTTTTGATGGGAAAATTATCTTGGAAGAGAAAAACAAAGTGTCTATGGCTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026670-Uap1:NM_133806:3
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=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0170413=UDPGP=FE(15.9=100)

							
A:
NA

							
C2:
PF0170413=UDPGP=FE(13.8=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000106983





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000027981, ENSMUSP00000106982
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:162576982-162579427 
LOW PSI
HsaINT0175978
(UAP1)
Human
(hg19)
chr1:162546772-162549217 
LOW PSI
HsaINT0175978
(UAP1)
Rat
(rn6)
chr13:88480701-88483000 
LOW PSI
RnoINT0158903
(Uap1)
Cow
(bosTau6)
chr3:6916017-6918212 
LOW PSI
BtaINT0155861
(UAP1)
Chicken
(galGal4)
chr8:3807136-3807300 
LOW PSI
GgaINT0036342
(UAP1)
Chicken
(galGal3)
chr8:3844248-3844412 
LOW PSI
GgaINT0036342
(UAP1)
Zebrafish
(danRer10)
chr6:35063917-35065576 
LOW PSI
DreINT0170277
(uap1)
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"