Special

MmuINT0036601 @ mm9

Intron Retention

Gene
ENSMUSG00000039205 | Ciz1
Description
CDKN1A interacting zinc finger protein 1 [Source:MGI Symbol;Acc:MGI:1920234]
Coordinates
chr2:32226384-32227277:+
Coord C1 exon
chr2:32226384-32226928
Coord A exon
chr2:32226929-32227155
Coord C2 exon
chr2:32227156-32227277
Length
227 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
GAACGTATATGTCATTTCAGACC
3' ss Score
4.84
Exon sequences
Seq C1 exon
CTCAGAGGAGTCCACCGAGAAAGGCCCTACAGGGCAGCCACAAGCAAGGGTCCAGCCTCAGACCCAGATGACAGCACCAAAGCAGACACAGACCCCGGATCGGCTGCCTGAGCCACCAGAAGTCCAAATGCTGCCGCGTATCCAGCCACAGGCACTGCAGATCCAGACCCAGCCAAAGCTGCTGAGGCAGGCACAGACACAGACCTCTCCAGAGCACTTAGCGCCCCAGCAGGATCAGGTAGAGCCACAGGTACCATCACAGCCCCCATGGCAGTTGCAGCCACGGGAGACAGACCCACCGAACCAAGCTCAGGCACAGACCCAGCCTCAGCCCCTCTGGCAGGCGCAGTCACAGAAGCAGGCCCAGACACAGGCACATCCACAGGTACCCACCCAAGCACAGTCACAGGAGCAGACATCAGAGAAGACCCAGGACCAGCCTCAGACCTGGCCACAGGGGTCAGTACCCCCACCAGAACAAGCGTCAGGTCCAGCCTGTGCCACGGAACCACAGCTATCCTCTCACGCTGCAGAAGCTGGGAGTG
Seq A exon
GTGAGTGTGGACTCCCGGCCTGATCCAGGTCTGCCAAACTCTTCTTTGTCTGTCTGATCTGGCATTGTTTAGTCTTGACTGAGGGTTGGGCCTGGCATACAGATCTGGGACCATCCCCGTCTTGGATTCAGGTTAATATCTGGACAGAGGAGCCAGCTCTTGTATCCAGATCTATCTGGACCCCAAATGGTAGACACTGTGGGAAAGGAACGTATATGTCATTTCAG
Seq C2 exon
ACCCAGACAAGGCCTTGCCAGAACCAGTAAGTGCCCAGAGCAGTGAAGACAGGAGCCGGGAGGCGTCCGCTGGTGGCCTGGATTTGGGAGAATGTGAAAAGAGAGCGGGAGAGATGCTGGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000039205-Ciz1:NM_028412:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=1.000 A=NA C2=1.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000048428





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000048428f3938A, ENSMUSP00000048974, ENSMUSP00000108957, ENSMUSP00000108958, ENSMUSP00000108960, ENSMUSP00000108962, ENSMUSP00000108964, ENSMUSP00000119429, ENSMUSP00000120019, ENSMUSP00000122469
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr9:128178491-128178708 
LOW PSI
HsaINT0035587
(CIZ1)
Human
(hg19)
chr9:130940770-130940987 
LOW PSI
HsaINT0035587
(CIZ1)
Rat
(rn6)
chr3:11400792-11401012 
ALTERNATIVE
RnoINT0036652
(Ciz1)
Cow
(bosTau6)
chr11:98814750-98815009 
LOW PSI
BtaINT0038729
(CIZ1)
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: 
CACAGGCACATCCACAGGTAC

				
R: 
AGCATCTCTCCCGCTCTCTTT

				
Band lengths: 
295-522

			

		

	





	
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






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