Special

MmuINT0175908 @ mm9

Intron Retention

Gene
ENSMUSG00000026988 | Wdsub1
Description
WD repeat, SAM and U-box domain containing 1 [Source:MGI Symbol;Acc:MGI:1919387]
Coordinates
chr2:59696667-59699794:-
Coord C1 exon
chr2:59699618-59699794
Coord A exon
chr2:59696808-59699617
Coord C2 exon
chr2:59696667-59696807
Length
2810 bp
Sequences
Splice sites
5' ss Seq
TCGGTAAGG
5' ss Score
10.48
3' ss Seq
TGTAACGGATCTTCTTTCAGAAT
3' ss Score
9.19
Exon sequences
Seq C1 exon
GAAGCATGAACGACCCGCTGAAACATTTCACTGAAGAATGGTCAGAGGAGGATGTCTCCGTGTGGCTTCGTGCTCAAGGCTTGGAAGACCTCGTCGGTATTTTCAGGGCAAACAACATCGATGGGAAAGAACTATTGCATCTCACAAAGGAAAGTCTGGCTGGTGATTTGAAAATCG
Seq A exon
GTAAGGATAGTGGAGCTAGGCAGTCTCTAGAGTCTTAGTGAGGTCCCCTGCTGATGGGCTTAGCTGCTTGCACTTCCCTCTTCCTCTTCTAATCCAGGTTAGTCCTTCATTGGAGAGGGAAGAAGAACGCATTTCTTCATGTAACCAAACCTCGCTTGGAATTACAATTTTAGAAAGTTACGCATTTTAAAACTTGATTACAGTTCAGATCCTTAAAATTTACTTTTCAAAACAAAACCCTTTGTGTTTGTGTGTCTAAGTCCGTGTAACAGGCGTGTCTGCATGTGGGGGTGGGGCACAGGGCAAACTCTGCTGTTGCTCAGGAGCCAGCCACACTGTTTTTGCAACCTGCTGTGTATCCTCAGGGCTAAGATTATAAACATGGGCCACCACACCTGGCTTGTCACATGGGTTCTGGCTGTTGAACTCAGACCCTCATGCTTGTGTGACAGCTGAGATACCTCACCAGTCAAAATGACTCTCTGAAGAGAGGTGTACACCACGCAGTGGTGTGTATGTGTGTGTGTGTGTGTGTGTGTGTGTGCACGCGCGCATGTAGTACAGTCATTACCACTATTTAATTTTGGAATATGTTTATCAGTGGTAAAAGAAACCTCATCTCTTATTTCTTTCCCTTTCTAGCTTTTGGAACCCGTATTTTGTGTGCAAACCCACCCGTTATTGACATTTTATATTAGTACTTGCCACAAGTGACCTTTTCTTTCCATCCTGTCTCCTTTTGCTTGTCATCAGCTGATAGAATTCAGGACAGTGCCGTGTTTTTAAATGTAATGAATAATACTTCTATGAACATGAAGTTTTTGTATGAATGTCTTTTTTCAGGTTTCTTGTGCATCTGTTCAGAGTAGAATTGGTGAATCATAGATGACTCTGTGTGTGACACTGGAGACGTTGTCAGGCGTTGTACAGTCCCACCAGCACTGGGGGCGGGCCTGGTTTCTCCCCACGCCTGTCTCCTCTTGTTATTAGCATCGTCCAGCAGTTATGGTTTCTCCTTTAGGTTTTGGTTTTCATTTCCTTGTTGACTGATTAGGTTTTTGTCTCATTGCATCTGAGTTGCTATGGCAAAACCTATAAACTAGGTACGACCAGAAATTGATTTCTTCATTCTGCCAAGTCCAAGCTGAAGGGACCGGCAGGTTTGGTGTCTCGTCAGGAGTGATTTCTGGTTTCTGGACAGTGCTTTTCCCACTGTGCCACCTTCACCCAGTGGGATGGGTGAGCTCACTCTCTGGGGCCTCTGATCCTGTTTGTCCCCAAAGCCTCACCCTTTAACACCACTGTGTGATTTGCTTGTTTTCATACTTGGTCCTGGCCTAAGGCTGGAAAGCAATGGTGACAGATTTCAACATGTCAACATTCTGATTTACAGTTTGGAAAACTGGCAATTTCAGTAATTTAGAAGCAGAACTAGAAAATATGTTCACTGGAACATCTGGTCCTTCATATCACTCTGAAATATCTGATATCTTAGTATTATATATCAAGATCTATGTGGCTATGATGCTGTGATCCTCCTGCCTCAGCCTCTCGCAGGCTATGATTATAGGCATGCACGCCACATACCCAGCCATTCTGAAGGGCGTTGAAACGTTGTTTTATTTCTCTTCAGGATAGAAGTTAACTTTTAATCTTCAAATCCTATTTTAAACTACAAAGAACCTTCTTTAGCTTTGAGATTTAGGAAAAGCATATTTTTCCTTAAGACAGTAAATAGGACTGAGACAGAATTAATGGTGGGATTGAAAATAAGTAGAAGAGGCAAACTGGTGGCATACATGCTGATGCCTGCATTTTGCACGCAGAAATGTTTGCCTACATTCGTCATTGTAGCTTGATCTCCCAGTTTCTAATGCCAGTTAAAATCCAGATCTGTTAACCATTTGGGGTATGGGAGTAGCCATGTGCTCGCTATAAAGCATGGTGGGGTGGGGTGGTCCCAAGCTAGAGTATCCATTCTTGGTGGACACAGGAACTGTTGCTAAGAGACTGAGCACTGTCACGCCCCTTGTCAAGAGGCCTTTTGTAAATGTAGGAAAAGGGGCTTTTAACATGCTTGAGTTTCTCAATAGAGTGCTTTAACCAAAGGTAAGCCAATTTCTGCGTTGCCAGTGAAACCCTCATAGTGAGGTCTTGTCTCATCAGAACCAGGTTCCCAAGAAGGGTGAATAAGGTGTGCCACTGTGGATGTGTCCTCCGCTCATCTTCTACCTTCCAACGCTTCCCCTTCAGAGTCCTTGTTTCCCCTAAGGGCTAACTCCTTATGTCATACATACATTTGTACAAGGAGCATCCGTCCACGATGTTAAGACTGAAGAGCAAGAAAATCAATTCTGGACAGGATTAGTGAAGCCCTCAGTCCAGTCACTAGACCCGTGTGTGCACACTGGCCCGAGTTCACAGCCAGGCCCTCAGAATACTGCGAGGTGCCGTGGAGCTTGGAACTTGCAGTCGATAACTGGCATTAGGAACTGAGAGATCGCATTGCCTGTATTTTCCCTCTCCCTCTCTTACTTGCTGGACACCAGGAGGCATCCAGCTTCATTACTGAGTATTCCCTTGCAGTCCTCTGCCTCTAGACAGGCCAGCTCTCCTTCCACTTTTTGTTGGTCTGAGTGTTGTGCCGTTAAGTGAAAGCGAATCACTAACTCCGTCAGTGAGGTAACACCGATGGCTCCAGGCCTTACCCATCTTCACAGCCTCAAGTTCTGAAAGTCCATTTCCCTTCCCAGGAACGTTTCACTTCACAGACCTTCCCTTGCTGCCTAATGTAACGGATCTTCTTTCAG
Seq C2 exon
AATCTCTAGGGCTGCGCAGCAAAGTCCTGAGGAGTATTGAAGAGCTCAGGGCCAAGATGGATTCCCTCTCTTCCGGAATCCCTGACGAGTTCATCTGCCCAATAACCAGAGAACTCATGAAGGACCCCGTCATCGCATCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026988-Wdsub1:NM_001159636:9
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.029 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0764712=SAM_2=PU(74.2=81.7)

							
A:
NA

							
C2:
PF0764712=SAM_2=PD(24.2=33.3),PF0456410=U-box=PU(28.8=43.8)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000028368





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000099812, ENSMUSP00000121438
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr2:159248513-159256195 
ALTERNATIVE
HsaINT0182800
(WDSUB1)
Human
(hg19)
chr2:160105024-160112706 
ALTERNATIVE
HsaINT0182800
(WDSUB1)
Rat
(rn6)
chr3:45930782-45934081 
ALTERNATIVE
RnoINT0165483
(Wdsub1)
Cow
(bosTau6)
chr2:37199336-37208562 
LOW PSI
BtaINT0162048
(WDSUB1)
Chicken
(galGal4)
chr7:36033041-36036395 
ALTERNATIVE
GgaINT0048540
(WDSUB1)
Chicken
(galGal3)
chr7:38169377-38172731 
ALTERNATIVE
GgaINT0048540
(WSDU1_CHICK)
Zebrafish
(danRer10)
chr6:11788807-11794569 
LOW PSI
DreINT0175632
(wdsub1)
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"