Special

MmuINT0037343 @ mm9

Intron Retention

Gene
ENSMUSG00000049550 | Clip1
Description
CAP-GLY domain containing linker protein 1 [Source:MGI Symbol;Acc:MGI:1928401]
Coordinates
chr5:124030009-124032778:-
Coord C1 exon
chr5:124032729-124032778
Coord A exon
chr5:124030134-124032728
Coord C2 exon
chr5:124030009-124030133
Length
2595 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATG
5' ss Score
9.43
3' ss Seq
TTTTCTTTAAAAAAAATCAGATT
3' ss Score
2.99
Exon sequences
Seq C1 exon
GTAACACTGATGCTCAGGCGGAAGAGGATGAGAGAGCCCAGGAGAGTCAG
Seq A exon
GTAATGCTCTTCTATTACCTTCTGCTGTCTGCATGCCCATTTCCCAGAGTCACTAGGTATCTCCAGAGTATAATGCTGGGCATTAAAGAGTACATAGCAAAAAGCCTTCTGGTCTCCGCTGCTCATTTCCCACATGCTGACACTGTTCCCCGGGGCTCACCTGTTGCAGACATCTTAGGGTTTTGTTGTTTTTGTAGCTGTGGTGTGTGATAGCGCATCCCTAGCTCTGCCACTTGGAAGGCTGAGGTAGAAGAATCAGTGGAGTCTGAGGTCAGCCTGTGGGACACAGGAGCGCCCTGCCTCTCGCAAGCACACTCTAGTACCCTTGAGTTTTACCTTGTTTTGGTTTTGGTTTTGGTTTTGAAGACAGGGTTTCTCTGTGTAGCCCTGGCTGTCCTGGAACTCACTCTGTAGACCAGATCCACCTGCCTCTGCCTCCCAAGTGCAGGGATTAAAGAGGTGCCCACTACCACCTGACTTTTTTTTTTTTTCTTTTTTGAGACATGGGGTTTTATGCAGCCCTTATTGGCCTTGAACTCTGCTGCCCTGCCTCCCATGACTGAAGCACAGCTGCGTAGCACCACCCCAACGGCCCCCTCTGAAGTTGTTTGCTTTGTTTTAAGATTTATTTATTTGATGTATGTGAGCATGCTGTCACTGTCTTCAGACACACCAGAAGAGGGCATCAGATCCCATTACGGATGGTTGTGAACCACCATGTGGTTGCTGGGAATTGAACTCAGGACCTCTGGAAGAGCAGTCAGTGCTCTTAACCTCTGAGCCATCTCTCCAGCCTCCATTTTTTTTTTAAACATTAGTAGCATACCACCTAAATCATTCTATGCTTACCCTTTCTTTAGCTGTGTAGTATTCCATTGTATGGATGTACCATAGTTTAGTCAGTTCCCTTTTGGTGGACAGGACACTGGGATCTGTCTAAGCCTATATTAAAAGCCAGAGCTGTAAGGAATTCCTTTAACCAGCTTTCGGACTCCAGCCGACTCAGTAGTAGCTTTGTCTCAGTGTCTCTGGCGTGGTAAAGAATTAACATTGTTTTCTCTCCCCTTCCCTTCTGCTTCCGTCTGTTTCTGCTGCTGACGCCAACTCTTTCCCTCCCATCAGCAAATGGTTTGTTTTATGCTTCCTAATTTGTGTGCACTCGTGCGTGTGTGATTGTGTGCATGGTCCCCTCATCCCTGGAATGGAGCCTTACAGAATGACTTAGAGGATGCAACCTGCAAGTCAGATGTGGGGGGCTGGGGAGGTGGCTCAGTGGTTAGGAACAGTGGTTGCTCTTACAGAAGACTGGGTTCAGTTCCCAGCACCCACACAGTGGTCCACAACCATCCATAACTCCAGTTCCAGGGAATCCAGTGGCCCCCTCCTGACCTCCACAGCCACACAGGCACAACACTCATACACATAAATCTAGAATAAAAAAAAAGAAAGTCAGGGGTGGTAGTATATCCATGTAACCCCAGTATTCATGAGGCAGAGGCAGAAAGAGCTGTAGTAATTTGAGACAGCTACAGGGTAAGATCCTGTCTTTTAAAAAGAAGTAAAGAAGGAAAGTTCAAGGTGAATTGTGTTTGGGGTTTTGTTTTTTGTTTGTTTGAGGCAGGGACTAACTATATAGACCAGGCTAGCTTTAAAGTAACAGACAGGGCCTGCTCTGCCTCTGAGTGCAGGGACTAAAGGTGTATATCACACAAAACTTAATAGTCCGAGGCCAGCCTGGGATACTTAGCAAGAGTCTATTCAAAAACAGAAGGAAGAACAGCTAAAGTGTATGTATTCAGAGAGAGAAACTTTCCAATTCACAGAAATGAAACCTTTTACTTTGTAAAAGAGGGAAGAATGTTTTGTTTTTAGAGAACCCTTAAAAGACAGGAAGTGTTGGGGACATGTTACTTTTTAGTGGTCACTTTGCACTTTGCTCTTAGACCAAGTTATCCTTCCTGTATGTGTGGGAGCATGCCATACCTGTCCTCAGCAGAAGAGGGGCTTGGCCAGCTCTAGTAAGCTCCTATCTCTCTTCTGAAGACACCCTGGGTACACACGCACGCACACACAATCACACGCAAGCGCGCACGCGCGCGCGCGCGCACACACACACACACACACACACACACACACACGAAGGAAAAACAAACCAAGTATTCAGAAATGTGAGATTTTGACTGTGGATAGTATAAAGTGTTTTGTTTTCTTGGAAATTCTCAGTAGCATTTCACCAGTCCGCAGATTAGTGATTTGAGTGTAATGTCATTTATCTGCATGACAAGTGAAGTTCACCCATTCACAGCTACAAAGACTCAATGACATGAATTGAAAGTGTCTTTTGATACAAAATAGTTTCTTAGTAACAAACACTGAGGGATGGAGAAGGGAAGAAGGAAACCTCCGTGCCTCTCACTAGCTGTGATCTCCCGCCAGCTGCAGTTCACTTCCTCAGCGTCCCTGTCCCTGCCCTGCTGTGACACACGTTTGCAGCTGTGGTGTGAGCGTATCCTTCCCCACTTCTAGACACTGCAGCTGTGACAGGCTCAGATGTCCACATAGCTCACTGCTTCTCTTTTCTTTAAAAAAAATCAG
Seq C2 exon
ATTGATTTCCTCAACTCGGTAATAGTGGATCTTCAAAGAAAGAACCAAGACCTCAAGATGAAGGTGGAGATGATGTCTGAAGCTGCACTCAATGGCAACGGGGAAGACCTGAACAGTTATGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000049550-Clip1:NM_019765:22
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.912 A=NA C2=0.575
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000031382





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000068241, ENSMUSP00000121425, ENSMUSP00000127162
          









    
Other Skipping Isoforms:
ENSMUSP00000107186, ENSMUSP00000107190, ENSMUSP00000107192, ENSMUSP00000122064
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
chr12:122274163-122278153 
ALTERNATIVE
HsaINT0036363
(CLIP1)
Human
(hg19)
chr12:122758710-122762700 
ALTERNATIVE
HsaINT0036363
(CLIP1)
Rat
(rn6)
chr12:38447630-38450286 
HIGH PSI
RnoINT0037325
(Clip1)
Cow
(bosTau6)
chr17:55355063-55357345 
ALTERNATIVE
BtaINT0039318
(CLIP1)
Chicken
(galGal4)
chr15:5811673-5812610 
HIGH PSI
GgaINT1009604
(CLIP1)
Chicken
(galGal3)
chr15:5867480-5867912 
GgaINT0009275
(CLIP1_CHICK)
Zebrafish
(danRer10)
chr5:66511975-66513776 
LOW PSI
DreINT0047565
(clip1a)
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"