Special

MmuINT0046882 @ mm9

Intron Retention

Gene
ENSMUSG00000041966 | Dcaf17
Description
DDB1 and CUL4 associated factor 17 [Source:MGI Symbol;Acc:MGI:1923013]
Coordinates
chr2:70898410-70901552:+
Coord C1 exon
chr2:70898410-70898500
Coord A exon
chr2:70898501-70901415
Coord C2 exon
chr2:70901416-70901552
Length
2915 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGA
5' ss Score
8.24
3' ss Seq
TTTGTTTGTTTGTTGTTTAGGGA
3' ss Score
8.31
Exon sequences
Seq C1 exon
TGTTGCATCAGAGCCAAGAAAACTTTATGAAATGCCAAAATGTTCCAAATCAGAAAAAATTGAGGATGCTTTATTATGGGAATGCCCAGTG
Seq A exon
GTAAGATTTCTTTCTAGAGCATTGGCTTTTAAAGCTTCCCCCATACCTAAATGTTTGTTCATTTATTTGTTTTTACACTTACTTCATTTTTTAAAAAGAATTCTATACATGAATACTGTATTTACATAATTTCTGCCTCACCCTCTTCCCATTTCAATTCCTTCCGTGTTTACCTATACACACTTTATCTCGAGTTCTTGGCTTCATCTTGATTATGGGACACACACACTATATATATACATAGAGCCTGCTGAATCCCTTTACTGTGCTCATGTGCATATGTGTTTAGGGCTGACTGTGGATTGGATAACCTAGCCCCTGGCAAGGGCCTATTTTCTCTCTCTTAGAAGCCATTAATTGCCTATAGCTCTTCACCTAGGGTTGGGGCTTTGTGAGATTTCCCCATCCACGTGCAGATGTCAGCTACTGTTACATTGTTCAGGTCTTGTTTAGGCAGCTGTATTGTTGAGATTTCATGGGTACGAGTCCCTGTCACCGGGACGCACAAAGGAGAAGTAAGAGCTGAGTTCTAAAAGTTGTCTGCTGACCTCCCCATGTGTGTGCGCGCACACACACACACACACACACACACACACGCACACAAACACAGACAGACAGACAGACAGACAGACAGACACATGTACACATACAGATACACACACACACATACACGTAATTTTTTTAAGTCAGTATTTGGAACTCATTTATTTATTTTGAACACGTTCATGTATGAGCCCAGGCTAGCTTAAAATTTCAGGTATAGCTGAGCGTGAGCTTGAACCTTGGAGTTCATCCACCCCTGACTACCTGGATGGAAGACATGTATCAGAAAAATTTTAAATTAGAGATGATTTGTAAATTTTGAAAAGGTAGAAACTGATTAAAGTTTATAACACTCTGAGGTAGTTTATAGTCGTTCTTCCTGTTCGAGATCATCCCACCCTTGTACTAAGACAAATTACTCTGAGGGCAACTATTATGTGGATTTTTGAAAGTAGGTAAATCCCACCTGTGGCTGTAGTTAGGAAAATAGTATAAAAGTTAAAGCTACATAGTGAAAGTCATGCCGTGAGGCCGGTGTTGCCCTGGCACGCGCCCTCCTGCACACTGTTTCCTTGGGATGTCAGCATCCAGAGACCCGAGAAGCTAGACTTGGTCTGGGGAAAAATAAATACGGAACATTGAAAGTTCCAAGGATGCTTGTCCGTCTCCTCCTCAGTCTTTAACATGGCTGTTTCTAATACTGCCTGCATGCACAGTGCTTGTGGGGCCCTCACAGCAAACTCTTTTAATCACAGCCCACTTTTGAGGGACAATTCATCTTTTTTAAGTTTTCCATAACATTGTTTCTAAGAAATCCTCCTAAGAAGACTGCAGCGAATTAATCAACGTCTGAAAGTCTAGTTGGTTGCTCTTCAAGAGAAGAGAACTTCTAGTCTGTAACCCAGAAGTACTGTTTAAGCCATGAGCAGCAATATTCAGAATTTAATGTTAATTTTTTTCTAGGTTGTTGTTTTTCCATAAAGCTATAATTTTTTTTAACTATCACTCCCCCCCCCCCATAATTACTCTTTTCATAGAAACCACCTTTTTAAAAATTAGAAAGTTAGAAGCCTGGTTTTTTTCCTCTTTAATTGAAAGCTGTAAATAATTGTGCCTTAAACCACTTAGAGCCTTTTAATCATTTTCTTGAGGGGAGATTAGAGAGATGATAGGTTTCTTAATTGAGAAAGATTGAATATACCAATTCAAACTCCCAAAATATAGAGCAGTCCTGAAAAAATAAAGTTAACCTACTCTTATTCCATAAACACTTAAGTGATTTTGTTTTTATTTGTGGTGACAACATTTTTTATGAAGAACTCAGAGGAGCACTGCATTATTATATGAATGCAAAACTACTTTAAAATGAATACTCTGTTTATTTTGTTTTGATTCTGAAGTAATGTATGAACTGCCACTTTTGGTTTAAGAAAAAAGTTCAAACCTGTAAGATACTTGTTTTAAATGTCTCTGTAATGGGCTAAATAGGAATAGTAGATATTTTAAAACTTTAAAATCTACATGAAATGACACATAAGTCATGTAGCATAGAAGCATTCATGTCATGGCCTTTGAGTTAAGTACAGGTGGCTAGTACATTTGAAAATCACAGCATCAGCATGAATGCAGGAGGACCAGTTCCCAGTCTGCACTGCACAGGGCCTGCCTGAGAAACAACAAAAATAAATGGAGCCAAGCAGACTAAAAGCAAATGGTTGTCTCCCTGGAATTTGAGAGGGAAGACAGGTTTTGCAGAGGCCAATAGCCACTTCTTTCCTGTTCAAATGCCGTATTAATTTCAACTTCTCAATTCAGAACTTTACTAATTGAAAGTCAGCACATTTGCTCCTCTTTCCCTTCTGCAGTCGAGCTGTACTAGTGGATGGCTCAGTGGTTAAAGCTCTTGCTTCCCAGTGGTGCAAGCCAGACAGCCTGAGTTTGAGCCTCAGAACCCACAGAAAGGCAGGAGAGCTGAGCATGCACACCTTCAGTCTCAGCACTAGGCGGGCAGAGGCAGGCAGACCTCTGAGTATGCGGCCAGCCTGCATCCAAGCAAACAAACCAGTGGAGGGAGAAAGCTGAGTCTACCCAGTTGTCCTCTGACCTCCACATGTGCACTGGGGCTTGTGCACCCTCAGGTACACAATGATAATGATGATAAAATGTAAACGCATTAAAACATAAAGACCAGTTAAAGTAACAGGCACAGCCTCGTCTGTCCCACTTTCTTCATTTGTGCAGTTGATATTTCTTTGGTTTACTTATTTGACAAGGTAACTAGCCATTTTCTTTGGACATAGAGTACTGCAGATTGTTCATAGCCAAGCAATTTGTTTTCACACCCTGGTTTAGTTTGTTTGTTTGTTGTTTAG
Seq C2 exon
GGAGACATACTTCCTGACCCATCAGACTATAAATCCTCACTCATAGCCCTGACTGCTCATAATTGGCTGCTTCGTATATCCGCAACTACAGGGGAAGTCCTGGAGAAAATATACCTTGCTTCCTACTGCAAATTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041966-Dcaf17:NM_001165982:3
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:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000065624





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000099762, ENSMUSP00000107785, ENSMUSP00000107791, ENSMUSP00000114459, ENSMUSP00000117830, ENSMUSP00000118011, ENSMUSP00000120016
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr2:171443614-171448680 
LOW PSI
HsaINT0045233
(DCAF17)
Human
(hg19)
chr2:172300124-172305190 
LOW PSI
HsaINT0045233
(DCAF17)
Rat
(rn6)
chr3:57651106-57654421 
ALTERNATIVE
RnoINT0045219
(Dcaf17)
Cow
(bosTau6)
chr2:25064798-25067123 
BtaINT0046896
(DCAF17)
Chicken
(galGal4)
chr7:17534080-17536012 
ALTERNATIVE
GgaINT0046073
(DCAF17)
Chicken
(galGal3)
chr7:19479309-19481240 
ALTERNATIVE
GgaINT0046073
(DCAF17)
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"