Special

MmuINT0085918 @ mm10

Intron Retention

Gene
ENSMUSG00000059022 | Kcp
Description
kielin/chordin-like protein [Source:MGI Symbol;Acc:MGI:2141640]
Coordinates
chr6:29504233-29504567:-
Coord C1 exon
chr6:29504399-29504567
Coord A exon
chr6:29504310-29504398
Coord C2 exon
chr6:29504233-29504309
Length
89 bp
Sequences
Splice sites
5' ss Seq
GTGGTCAGT
5' ss Score
4.85
3' ss Seq
CATTGCTGTCTCCACCTCAGGCT
3' ss Score
7.64
Exon sequences
Seq C1 exon
AACAGGGAGCTGCAAGCCAGGGTGGTGCAGCTGGAGTCCTGTGAGTGCTGGGGGCCAGGTCACACCTGTCCCGAAGGAGCTCGCTGGGAGCCTGATGCCTGCACAGCCTGCGTGTGCCGTGATGGAACGGCGCACTGTGGCCCCCAGCCCAACCTGCCCCACTGCCGTG
Seq A exon
GTCAGTATCCTCCCATCCATCCATCGTGACTATTTGGGGACCTGGAGAAGGCACTGGGGTCTCAGGTGACATTGCTGTCTCCACCTCAG
Seq C2 exon
GCTGCAGCCACAATGGGCAGTCTTATGGTCATGGGGAGACCTTCTCCCCAGATGCCTGTACCACCTGCCGCTGTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000059022:ENSMUST00000101614:3
Average complexity
IR
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:
PF086146=ATG16=PD(16.9=22.8),PF0497710=DivIC=PD(29.8=24.6),PF0009313=VWC=WD(100=87.7)

							
A:
NA

							
C2:
PF0009313=VWC=PD(0.1=0.0),PF0009313=VWC=PU(82.8=92.3)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000099135





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000077251, ENSMUSP00000088954, ENSMUSP00000124097
  



Associated events






Other assemblies


mm9




Conservation


Human
(hg38)
chr7:128907178-128907263 
LOW PSI
HsaINT0084811
(KCP)
Human
(hg19)
chr7:128547231-128547316 
ALTERNATIVE
HsaINT0084811
(KCP)
Rat
(rn6)
chr4:56783137-56783225 
ALTERNATIVE
RnoINT0078157
(Kcp)
Cow
(bosTau6)
chr4:93681624-93681703 
ALTERNATIVE
BtaINT0079957
(KCP)
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: 
CTGGAGTCCTGTGAGTGCTGG

				
R: 
CCCATGACCATAAGACTGCCC

				
Band lengths: 
174-263

			

		

	





	
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
  • Ribosome-engaged transcriptomes of neuronal types
  • Neural differentiation time course
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types





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