Special

MmuALTD0003270-2/2 @ mm9

Alternative 5'ss

Gene
ENSMUSG00000049550 | Clip1
Description
CAP-GLY domain containing linker protein 1 [Source:MGI Symbol;Acc:MGI:1928401]
Coordinates
chr5:124077303-124081178:-
Coord C1 exon
chr5:124080462-124081178
Coord A exon
chr5:124080234-124080461
Coord C2 exon
chr5:124077303-124077419
Length
228 bp
Sequences
Splice sites
5' ss Seq
AAGGTTTGT
5' ss Score
7.81
3' ss Seq
CATGTAACTCGGTGTGTTAGGCT
3' ss Score
4.29
Exon sequences
Seq C1 exon
AACACTTCGGAGCTCGAGAGGAGGCGTTTCAGAAGGAGATCAAGGCTCTGCACACGGCCACTGAGAAGCTTTCCAAAGAGAACGAGTCCCTGAGAAGCAAGCTCGACCACGCTAATAAGGAGAACTCCGATGTGATAGCTCTATGGAAGTCCAAACTGGAGACCGCCATAGCATCCCACCAGCAGGCAATGGAGGAGCTGAAGGTGTCCTTTAGCAAAGGCATTGGAACGGACTCCGCTGAATTTGCTGAGTTAAAGACACAGATAGAGAGACTGAGACTAGATTACCAGCACGAAATAGAAAGTTTACAGAGTAAACAGGACTCTGAGCGGTCTGCTCATGCTAAAGAGATGGAGACCATGCAGGCCAAGCTGATGAAGATCATTAAAGAGAAGGAGGACAGCCTGGAGGCCGTCAAAGCGAGACTGGACAGTGCAGAAGACCAGCACCTAGTGGAAATGGAGGACACGCTAAACAAACTGCAGGAGGCGGAGATTAAG
Seq A exon
GTAAAGGAGCTAGAGGTTCTGCAGGCCAAGTACACTGAACAAAGCGAGGTCATTGGTAATTTTACATCGCAGCTCAGTGCTGTCAAAGAAAAGCTCTTGGATCTTGATGCGCTTCGGAAAGCCAATTCCGAAGGTAAACTGGAGCTCGAGACACTTAGACAGCAGCTTGAGGGAGCTGAAAAGCAGATTAAAAACTTAGAGACTGAAAGGAACGCTGAAAGTAGCAAG
Seq C2 exon
GCTAATAGCATTACCAAAGAGCTCCAGGAGAAAGAGCTAGTGCTCACTGGTCTGCAGGACAGTTTGAATCAAGTCAATCAAGTGAAGGAGACTTTGGAGAAAGAACTTCAGACTTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000049550-13-15,14-15-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact





	

	
Protein isoform when splice site is used (Ref)





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.421 A=NA C2=0.220
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0157614=Myosin_tail_1=PU(78.3=82.8),PF127092=Kinetocho_Slk19=WD(100=25.9),PF0017016=bZIP_1=WD(100=16.3)

							
A:
NA

							
C2:
PF0157614=Myosin_tail_1=FE(15.0=100),PF057016=WEMBL=PU(7.9=30.8)

						

					

				








    
Main Inclusion Isoform:
ENSMUSP00000031382





     
                   









    
Main Skipping Isoform:
ENSMUSP00000107190





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000107186, ENSMUSP00000107192
          









    
Other Skipping Isoforms:
ENSMUSP00000068241, ENSMUSP00000115965, ENSMUSP00000121425
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
chr12:122340753-122340847 
HIGH PSI
HsaALTD1018859-2/2
(CLIP1)
Human
(hg19)
chr12:122825298-122825299 
Rat
(rn6)
chr12:38399847-38400646 
ALTERNATIVE
RnoALTD0006946-2/2
(Clip1)
Cow
(bosTau6)
chr17:55309212-55310156 
ALTERNATIVE
BtaALTD0005429-3/3
(CLIP1)
Chicken
(galGal4)
chr15:5835626-5835627 
ALTERNATIVE
GgaALTD0001698-4/4
(CLIP1)
Chicken
(galGal3)
chr15:5891787-5892731 
ALTERNATIVE
GgaALTD0001698-3/3
(CLIP1_CHICK)
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GGACTCCGCTGAATTTGCTGA

				
R: 
GCTCTTTCTCCTGGAGCTCTT

				
Band lengths: 
308-536

			

		

	





	
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
  • 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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