Special

MmuINT0043549 @ mm9

Intron Retention

Gene
ENSMUSG00000034101 | Ctnnd1
Description
catenin (cadherin associated protein), delta 1 [Source:MGI Symbol;Acc:MGI:105100]
Coordinates
chr2:84440938-84443909:-
Coord C1 exon
chr2:84443806-84443909
Coord A exon
chr2:84443061-84443805
Coord C2 exon
chr2:84440938-84443060
Length
745 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAAT
5' ss Score
6.41
3' ss Seq
CTTCTCTTTTTTCCCCACAGCAG
3' ss Score
11.49
Exon sequences
Seq C1 exon
ATAACAACTATTCCACACTGAATGAGAGAGGAGACCACAACAGAACACTGGACCGATCTGGGGATCTGGGTGATATGGAACCATTGAAGGGAGCACCCTTGATG
Seq A exon
GTAAATCCTTGTTATGTATTGCTGTGTATGAGGCTAATACTATTTTGAAACTGTATGATATATAAAATGGGAGGCGGCGGGAAGAAAAAGACAAATCTTTTTGGTAGGTTTTCTTTGATGCATCTTGATGGTTCTTGGGATGTTGCTCATTGGTTGTGTGGATGGATTTTGCAAGCGTTGCTGACGTCACTGACACTAACTAACCTGCTCTCGAGGACATCTCCCTGCTCTTGCACTTACCTGTTTAGGATGTTTGCCCTGTACTCTTAACAGGGTTTGTTCACTTTACAGATGTTGGGATTTCCCTTCCATCTGGCACACACTTAGAAAGTCTTACCTTGGTTCTCTTACTAACAAATTGCATGTGTTCACAGCAGGACGAGGGGCAGGAATCTTTGGAGGAAGAGTTGGATGTGTTGGTTTTGGATGATGAGGGGAACCAAGTGTCTTACTCCCCCATGGTATGTCCTCCAGTCACCCCTAAGATGGTCCTGAGGAAGGAGGTTGCTGTGTGCCTACTCTTTGCCAATCATGCTGATCTGATCAGGCCTGCGATACTTGTTTGAGCCGCATGGTACCCAAGGGTTCTACTTCTGTGATCACGACCTCTTCCCAGGCTGGGATGCAGCGGATGATCTGGTTCTATGTTGTGTGCTGCTTTCCTGCCTCCAGATTTGCTCAGCTGTGTATGTTTCCCCTGTCGTCCTGTCCTCAGCCTTAACAGCCTTCTCTTTTTTCCCCACAG
Seq C2 exon
CAGAAGATTTAGCGCCACTCTACCTGCTCCATATGGGCTTATAATATATTACTTTTATTTTTTGGTGGTGAAATGGACTGATGATTTTTTTCCTTTCTTCGCTGGACTATTGTGCCAACTGCCAGGCTGACTCCTACCCTTGTAGCCCAAATTGGCTGCCGTCATCCGTGAATTACCTACATCTTCCACTGAAGTTTAATTGTCCTATCCTCCCAGACCCTACTTCCAGTTTTCCCCCAAGAAACCTGACTCTGTTATTTGCATATCTTGAGAAACTGCTGCAGATTAGCTCTTTTTGCCAGCCTTCCCTGGAACTCTTGGCCTTGCATAGAGGGAGGGAGAGTGGAACTCTCTACTGGAAGCAATGGGAAGAACTGAAAATTACACACTGTCTGTTCAGCAGTCAGCATTCTGACAAACTGATGACTTTTAATCAAGACTATTTTTTCTGGTGTGGGGGGAACTTTTTATTTTGTTTTGGATGGGGAAGTGTGAGTTCTTCCCTTATCCAGTGGCGATTTTTGAAGCCAAGAAGGCTGGAAACATTGGCACATTCCACCTGGCAAGGGCCCTCAAGTAAGTGAAGTACTCCCCAACCTCAGAGTGAGAACTCTTGTTCCTCCTGTTCAAGGCAGGGACCACAAAGGACCTACAGACTCCATCTCTCTGTCAGCTTCAGGATAACCTTGGGGTGCTGTCCTGACCAAGGCTGTCCTTAACCCTCCTCTCCTACCCTGTGATAAACCTGCTAACTTGACCTGGCTGTTTTGCAAGATGCTTTGTAAAAAGGAGAATGCCATGGAACCCCCTGGTTGAGAAGAAACAGAAAGATTGTCTATTGAGAAGATGAACCTCTAGGAGGAATGTACATGAAGTGGTTAGTCTGAAACTGGCAGGAAGCTTCAGAGCTGGCTTTCCTCAGCCCCCTCACCCCATCTCTCTTCGTCCTTTATAAGCTTGTCCTCCCTCTCCTCCCCTTCCCTGGATTTGTTGGCCAACTTACAAGACTTGTACATAGCTCCTCCCCCTTTGCCCTTGTAAGGTAGGAGTTGCCCTGGCTTTGCCTCTTCTTTGTGCCTTTGGCCTGGGGTGCATCTCCTCCCTCTCTTCCAGGTGCCTTTCTTTGCCTCTGCAGTCTCATTTCTCATGATTTTGCAAGTTAGACCTTGTTATTTTCTTACCCACTGTTGACCCCCAGTAGCTGAAGCAAAGAAGAGGAGTGGTAACTTAGGGAACTTCACGTCCCTACTGGGTGTTGTTAAAGCCTCTGACATAGCCACAACAGGCTTCTGCTTAACAGTGTGCAGTTGGGATTGGTGAAAATCCATCCCGATAAGTCTCAAAGTGAGGCTGTTAGGAGGGAGTGCTGTGACTCTGACTCCTTAGTCGTCCCCAGTTCCCATCATCTCTGAAAGGCTACAGGGAATCAGGCCATGCCTCCATTACACCCTTTTCTGTTGTAGTGAGTGTTACAGCTTGGCTAGAGAAGCAGCTACTATGTGGGTGCAATTTTTTTTAAACATTTTTCCTTATTTTCTTTCCTTAATCTAAAAGCTCTATTCAATGCAACTGGAATTCTTTATCCCTCTTGTCCTGTTCCTTAATATATTGAGGCTATGGGGTAGGAGAAAAGTGCACAGCCCACCAACTCCTTTTCTTATACATTGCAGTCACCCCCTCCCCCCAACCTTTGCTTCCTTCCCATTTCTTCCTAGTCCCGTTTCCCTTTTCTGGCAAAAAGGAGCTCTGTGCTCTCTGTGACCCTCAGAGTACACTGCACAGGGGAGCCTCCCCCACCCACATCTATCTGCCTCTGGTTTTGGGTTCTCTTGTCCTCTTCTGCTCTTCCTGGTGCTCTTTCTTCTCGGTGGGGTGTGGGTAATAGAATAGCCATGGGCTTTGGGGACCTTTAACTGTTTTTTTGTTTGTTTGTTTTGTTTTTCCTTTTTCATTTATAAAAACACTAAACATTCAATTTCAGCAAACCAAAAATCCTACCCTCCCACCGAATACTACTAAGGGGCATATCTTCTGCTCTGTATCTTTTCTCTCTTTCTTTCTCTTGTTAATGCTTTTAAAAACAAATGAGTTTTTTATATAAATAAAAGTTTTTAAAGTGTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034101-Ctnnd1:NM_001085453:16
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





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:
ENSMUSP00000064518





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000107305, ENSMUSP00000107306, ENSMUSP00000107307, ENSMUSP00000107313, ENSMUSP00000107314, ENSMUSP00000107316, ENSMUSP00000107323, ENSMUSP00000107324, ENSMUSP00000107325
          









    
Other Skipping Isoforms:
ENSMUSP00000042543, ENSMUSP00000065252, ENSMUSP00000097524, ENSMUSP00000107299, ENSMUSP00000107304, ENSMUSP00000107315, ENSMUSP00000107317, ENSMUSP00000107318, ENSMUSP00000107319, ENSMUSP00000107320, ENSMUSP00000107321, ENSMUSP00000107322, ENSMUSP00000107326, ENSMUSP00000107327
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr11:57815501-57816299 
HsaINT0042889
Human
(hg19)
chr11:57582973-57583768 
ALTERNATIVE
HsaINT0042889
(CTNND1)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr15:82326597-82326857 
ALTERNATIVE
BtaINT0045100
(CTNND1)
Chicken
(galGal4)
chr5:16245534-16245658 
ALTERNATIVE
GgaINT1010763
(CTNND1)
Chicken
(galGal3)
chr5:18129929-18130318 
GgaINT0052797
(Q5ZJ21_CHICK)
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GGAACCATTGAAGGGAGCACC

				
R: 
ATGCAAGGCCAAGAGTTCCAG

				
Band lengths: 
357-1102

			

		

	





	
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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