Special

MmuINT0180350 @ mm9

Intron Retention

Gene
ENSMUSG00000030757 | Zkscan2
Description
zinc finger with KRAB and SCAN domains 2 [Source:MGI Symbol;Acc:MGI:2444060]
Coordinates
chr7:130638807-130642286:-
Coord C1 exon
chr7:130642100-130642286
Coord A exon
chr7:130638878-130642099
Coord C2 exon
chr7:130638807-130638877
Length
3222 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGG
5' ss Score
9.33
3' ss Seq
TGTTTCTTCTCTTTTTCTAGCTC
3' ss Score
10.67
Exon sequences
Seq C1 exon
GTCAGTAGCCCTCTGCCTTCAGAGAAGCAAGCCCCACCTAGAACTGTGTGGGAAGTAGCTGACTTTGAGCCAGAGCAACTGGAGACCCAGCACAGGGTTGTTTCTCTGGAGGAAGCTGGAAGCCTCCACTCAGGACACCAAGAACAGCTGAACCAAAAAAGGGAACATAGGCCATTACCTAAGAATG
Seq A exon
GTAAGGACTCAGAGTACACCAGGTCAGAGACCGTGTAGTTTATACTGTATCCCTAACACTATGGCTCACTCAGTAGAGGTCCCTTCAATATCCATTTGACAAGTAAATTGAATATTTGAAGTAAATTTTTCATCTATTTCAAGAATCAGAATTATTTACTACCAAAATAAAATGGGATCATAAAGATGGAAATTATGCAAACTTAGATTGTCCAGGGAAACCTTGAATCTTATTGTTATTTTAAAATGCCCATTCAATGTTCAGTTTGTGTCTTTAGTTATGCTATATGTATGTGTGCTCTTGAAAAACTATTAAGAAATGGAAACGGGGCATTTTTATTCCAAAACTTGACTCATAAGAACAGGCATCCCAGCATGATGTATGAGAGGGATAAAAGGTGAGACTCCCAAACAAGGGACAGTGTGCTGTTGTGAATAGGTGTGGTGCCCACAGACTCATGTGTTTGAATGCTTGGCCCATAGGGAGTGGCACTGTTAGGAGGTGTGGTCTTGCTGGAGGAAGTGTGCCACTGTGGGGGGCAGGCTTTGAGGTTTCCTATGCTTAAGCTACTCTCAGTGTGGCACACAGTCTCCTCACTGCCCGCAGATCAGATATAGAACTCTCTTCTCCAGCATCATGTCTGCCTGCACGCTGCCATTCTTGGTTCCATGATGATAATGGACCAAACCTCTGAAACTCTACGCCAGCCCCAATTAAATGTTTTCTTTTATAAGACTTTCCCTGCTCATGGTGTCTCTTCACAGCAGTAAAATACTAAGACAACCAGCATTCAGATCTGCCCATATGAATACAGAAAGTCAAATATGGGGGAAAGAGATGTTCTGTCCTTCCCAGTCCAGGTTCCTGTCCATCTCCTGAAGTGTGGCTTCATCCCAGGCCAGAAGCGAGTTGAGGGAGGATCCTATCTGAAGGCTTCATTCACATCGTGTCTTCCCCAAGACTATGATCTTGGGCAAGAAGCATGAAAACAAGGATTAATACCTAGAGGTTAAGATCTTAGGCTGGAAGAGGCAAACAGACCTGAGTTCACAACCCAGCTCCCCCATTTTTACTTTCTCCGAAACTGTCAAAATTATTCTTAAACTTCAACTCTGACTCAAAAAATTGGAAATATTCGCAATGGCTCTACTGCCATTGCTGAATCCAACCCTAAATAAAAGAATGTGTTGCAAATATTAGTGGATTCTGAATTAGCCAGGGCGTTCCTGAGCATCCTAGCTCCCTGTATTGTATGGGTTAGATAGTTCTAAATGACTTTAGCTGATAAACTCAATGTGGCAGCAGATGGGTATTTATAATGTCTTATCCTCATTGGCATCTGTGATGATAAAAAGGTTTTTTAGCTTGTTGAAGACTGAGGAATGGAGATCCGAAATCTGAGGGCTAGATTTCCCAGAAAGATGACTAGCTCTAAAGGAATGTGATTCCAGCCATATGCTTTTCAGAGACTATGTTGTTTCCAAGAAAATTATTTGGGAGCTGGTAAGATGGCTCAGCAGGTAAAAATGCTTCCTGCCAAGACTAATGACCTGAGTTCAGTCCCGAGGACCCACGTGGTGGAAAGAGAGGACCAACTCCTGGGAGCTGTCCTCCAGCATCCATACACAAGTAATGGCGCGCGCGCACTCGAGCACTGGAGCACATACACATATTCAAAATACTCAGATAAAATGTAATTTCTAGCCGGGCATGGTGGCGCATGCCTTTAATCCCAGCATTCGGGAGGCAGAGGCAGGCGGATTTCTGAGTTCGAGGCCAGCCTGGTCTACAAAGTGAGTTTCAGGACAGCCGGGGCTATACAGAGAAACCTGTCTCGGAAAAAAAAAAAGTAATTTTTAGAAATAAGCTGGGTTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTGTTTTTAATCTCTATAGAAAGTAGGTAGCTCAAGATTCTGAGGTCTGCTCACAAGTAAGGTACACTTGTCAGCTTCCCTGGTGAACTCTGAGCAGGAGATAGACCACCGGGACTGCTGTATAAAACGTTCACTTTTCTCCTACCCTGAGGGGGCTTTTTTAAATGTTTGCTGTGCCCATGGCTGTACTGTTTGCTGTGTTGGCAGGACTTAAGTAAGTTCTTGGTTCTGAAACTGTCAACTTCTGTGAGGGATGACAAACTGATAACCTGTACACCAAATGGGACTTGTTATAGTTTACCTACAAAGAATTGTTGTTTGGGATTTGGAGGATTTGCTCTTTGTACTTAAGATTTTCAATTTGAGATTTTACAGAAGTCCCAGGTTTCTGGTGTCTTACTTAGGGTTTCTATTGCTGTGATAAACACCATGGCCAAAAGCGACGCAGAAAGGAAAGAGTTGATTTCACTTCCACTTCCACATCAAAGGAAGTCAGGACTGAAATGTTGAGACGGGAGCTGATACGGAGACCGTGAGGGGACTCTGCTTACCAACTAGTCCTTCATGACTTGCTCAGCCTACTTTATCCCATCTCTGCCTACCTACCCAGGAGCAACACTGTCCACAACTGGCTGGGCCCTCTCAGATCAGTCATCAATCAAGAAAATACCTCACAGGCTTGTCTACAGGCTTGTAGTCTGGTGGAGATGTAGGGGTGCATTTTCTCAATAGAGGCTCCCTCTTCCCAGGTGACTAGCTTATGCCAAGTTTACATAAAAACTAGCCAGCCCATCTGGCTTCTCTTGGAAAAGTCAGAAATGATGAGTCTCCAAGTACCACAGTCTCACACTGAAACATCATCATAGACTGTGCCCTTCAGTTCCCAGTCCCAACCCTCTCCTTATGCACTTTACCTGCTTGTTCCTGAACCATTTGACTCGTGAGCCCAGCGTTAGGATAAGGTAGACTTGCTCTGAACTCACTGAAAAGCATTTCTATGTGTCGGTTTTAATATCTTTTTATTTCTTAAAAGGAGAAACAGCTGCCGGGTGTGGTGGCACACACCTTTAATCCCAGCACTCAGGAGGTAGTGACAGTTGACTCCCTGAGTTCCAGGTCAGCCTGGCCTTCAGAATGAGTTCAGGACAGCCAGGGCTACACAGATCCTGACCCCATGTGTTCTCGTGTTCGTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCACACACACACACACACACACACACACACACACACACACACACACTTCAGAATACTATACACAATAATTGTTTCTTCTCTTTTTCTAG
Seq C2 exon
CTCACTCTTCTGTCTGGGTTCCTGTCCCTAGTGATGAGTGGAATGCTCTCGATGAGGAAGTGACAACCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000030757-Zkscan2:NM_001081329:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.873 A=NA C2=0.750
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0202312=SCAN=PD(0.1=0.0)

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000041821





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000041821f5997A, ENSMUSP00000134381
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr16:25253038-25255205 
LOW PSI
HsaINT0185861
(ZKSCAN2)
Human
(hg19)
chr16:25264359-25266526 
LOW PSI
HsaINT0185861
(ZKSCAN2)
Rat
(rn6)
chr1:193454581-193457658 
LOW PSI
RnoINT0169020
(Zkscan2)
Cow
(bosTau6)
chr25:23100307-23102513 
LOW PSI
BtaINT0164630
(ZKSCAN2)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
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"