Special

MmuINT0037366 @ mm9

Intron Retention

Gene
ENSMUSG00000063146 | Clip2
Description
CAP-GLY domain containing linker protein 2 [Source:MGI Symbol;Acc:MGI:1313136]
Coordinates
chr5:134975962-134979331:-
Coord C1 exon
chr5:134978396-134979331
Coord A exon
chr5:134976020-134978395
Coord C2 exon
chr5:134975962-134976019
Length
2376 bp
Sequences
Splice sites
5' ss Seq
CATGTAGGC
5' ss Score
2.82
3' ss Seq
TTACAGGACTGTTCTTTCAGGTG
3' ss Score
6.33
Exon sequences
Seq C1 exon
CTGACCACAGTGGCTGAGAAGTCTCGGGTGCTGCAGCTGGAAGAAGAGTTGAGCCTGCGGCGTGGTGAGATCGAAGAGCTGCAACACTGTCTCCTCCAGTCAGGCCCGCCACCCGCAGACCACCCAGAGGCCGCTGAGACTTTGCGGCTGCGAGAGCGGCTGCTGTCGGCTAGCAAGGAGCACCAGCGAGACAGTACCTTGCTCCAGGACAAATATGAGCACATGCTAAAGACCTACCAGACCGAGGTGGACAAGCTCCGGGCGGCCAATGAGAAGTACGCTCAGGAGGTGGCAGACCTCAAGGCCAAGGTCCAGCAGGCCACCACGGAAAACATGGGGCTCATGGACAACTGGAAATCCAAGCTGGACTCGCTGGCCTCCGATCACCAGAAATCCCTGGAGGACCTGAAGGCCACGCTGAACTCTGGCCCAGGCGCCCAGCAGAAGGAGATCGGAGAGTTGAAGGCCCTGGTAGAGGGCATCAAGATGGAGCACCAGCTGGAGTTAGGTAACCTGCAGGCCAAGCACGACTTGGAGACGGCCATGCATGGGAAGGAGAAGGAGGGCCTGCGGCAGAAGCTGCAAGAGGTCCAGGAGGAGCTGGCCGGGCTGCAGCAGCACTGGAGGGAGCAGCTGGAGGAGCAGGCCAGCCAGCATCGGCTGGAGCTCCAAGAAGCCCAGGACCAATGTCGCGACGCCCAGCTGCGCGCGCAGGAGCTAGAGGGACTGGATGTGGAGTACCGTGGCCAGGCTCAAGCCATCGAGTTCCTCAAAGAGCAGATCTCACTGGCTGAAAAGAAGATGCTAGATTACGAGATGCTGCAGAGGGCCGAAGCCCAGAGCAGGCAGGAGGCCGAGCGGCTGCGGGAAAAGCTTCTGGTGGCTGAGAATAGACTCCAGGCTGCCGAGTCCCTGTGCTCAGCCCAGCACAGCCAT
Seq A exon
GTAGGCTGCATTCGCTCCTGTGGGGCTCAGCGGGGATGGAGGGGCCGGGAGGGCGTGGCCTCTGCGCGCCAGTTCCAGAGCATTTTCCTTGTGCCTGGAGCTAGCCAAGGGGGGCTCAGAGGAGGAGGAGCTTCTGTCTCCCTCTGTCAGAGCCTTGGGAATCATCGGGACCACTGTAGACTGAGAGGACCCTACTTGATCCTTTGTGGGCTTTGAGAGCCATTGAAGGCGCCATTTTGTTAGGCCCTAAACTCTGATTGGCCGAGACTTGGCAAATGGCAAGTTCAAGGCCAGACTCAGTACCTTAGTGAGGTTCCGGTTCAAAGTTGTTTTTTAAAAAAGAGCTGAGCAGAGCACTAGAATGCTTCCCTAGGAGAACCTCAGTTCCATCTCCAGCATGACAAAGCAAATACACACCGTCTGTGGCTAGGGCTGCCCAGAGCCGCTTTTGCTCTCTGTACCTGGCACTCAGGTACCACCCACAAGAAAGGCACAGAAACTGTGCCTCCCAGATCCTTGTCTCATCAGACACCTATCCAGGGACACGAAGATGTCCCTTTAGCCTCTAGAAAGGTCACAGCCACCATGACCCGCTTTGTCCCAAGTCTAGAAATGCCTACCTTTATGGTCCTTGCCCCAGATGAGCATGCCCCGTTGGTCCCTGAGGGATGTCAGGGAGTGTAGAGAGCCCCGTTCGTTCTAGCAAGCCCAGAAGGATGTTTTAACTGGCTCTGTGCTCCATATCGTGCACTGGTCCATTTCGAGGTTTATTGTGTTTAACCATGCACAGATATGCACATGTTGCATACCCAATGCCCATGGAGGCCAGGGCTTCCTGTACCCTGGAGCTGGAGTTCCGAGTGGCTGTGAGCCACCTGGCTTGTGTGCTGGGAATTACACTCAAGTAATCTGCAAGCGCAGTGCACACTCTTAACTGCTGAACCGTGTCTCCAGCCCCCAGTAACTCATTTAAAATACCCTTACAAGGGGTCAGCTAGGAGCTTGACTCTCTAATCCATTCACGGTATCTCTCGCAGTGTGGTGTTTAGGGAATCAAGTATCTGTAGCTCCAGGTCTTAGAAGAAAAGACATCTTCCTGCCTTGTTTCTTTCTCTCAGGAAGGAACTTTTTTTTTTTTTCCTTATTTGTTTGTCTGAGATAGGGTCTTGCATAGCCCAGGCTGCCCTCAAACTCGCTCTGTAGCCGAGGAGAACCCTAAATTCTCTATCCTCTTGTCTTTAACTCTCAGGTGCTAAGATTACAGATCTGAGTCACCATACTCCACCTTGCTGATACATGTGTGTATGTATGTGTGTGCATGCTCACGTGTGTGCACATGCGTCTATGGTGTGCATATGTGTGGAGGTCAGAGGTCAACCTTTTTGTACCAACTTTTTATTTTTTTGGACTGGTCTGGAGCACGTGACATAGGTAGGCTAGGTTGAATGGTTGGCCACTCATCACCAAGGATCGGCCTGCTTCTGGTTCCCAATGCTTGGATTACAACTGTGCACCATTGTGGTGTCCAGCCTTTTTTTATGTGGGCTCTGGGGCCCAGACTCCAGCCCCACTGCTTGCCTTTTACCAAGTGAGTCAGCTTCCTGGCTCACCGGGTTTTCTTTTCCAATCAATGTTTTCTTCCTTGGCTTCTGAGTTTACTACTAAGTATTATGAAGAAGGCAAGGCAGTTAAGTCCCTAGATGAGCTGGCCCTAGATGGGCCATCCAGGCTCTGTTGTACACATTGAGTGCTTGTTTTATGATTGAAGAGCTGGGGGCGTGGCTCAGTGGTAGAGCCCCTGCCTAGAATCCCCCAGGGAGGGACTGGGGCATGGCTCAGTGGTAGAGCCCCTGCCTAGAATCCCCCAGTGAGGGGCTGGGGGCGTGGCTCATTGGTAGAGCCCCTGCCTAGAATCCCCCAGTGAGGGGCTGGGGGCGTGGCTCATTGGTAGAGCCCCTGCCTAGAATCCCCCAGTGAGGGGCTGGGGGCGTGGCTCATTGGTAGAGCCCCTGCCTAGAATCCCCCAGTGAGGGGCTGGGGGCGTGGCTCAGTGGTAGAGCACCTGCCTAGAATCCCCCAGTGAGGGGCTGGGGGTGTGGCTAAGTGGTAGAACACTTACCTAATATGAAAAAGGTCCCAAGTTTCACCCTCTGCTCCTTGCTCCCCAAAATAGCAGTTCAGGGGCAGCAGGGGAATTCTTACAAGGCAGCTGGAAGCCAAGTGGGAGCTTCCCTTTTCTCAAGGAGAGGGATCCAAGTGTGTCTGCTCCCCCTGCTGGCGCATTGGGTCCCTGCATCCCCAGGGCCCCTTTTCACAGGTGGAGGTGTGGCCTGGGTGGTATGGCAGGCATGTCCCCTTACAGGACTGTTCTTTCAG
Seq C2 exon
GTGATCGAATCCAGTGACCTTTCTGAGGAGACAATTCGGATGAAGGAGACTGTAGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000063146-Clip2:NM_001039162:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.524 A=NA C2=0.650
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF116003=CAF-1_p150=PD(12.1=7.4)

							
A:
NA

							
C2:
PF123293=TMF_DNA_bd=PU(19.2=70.0)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000098212





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000037431
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr7:74376823-74380805 
ALTERNATIVE
HsaINT0036374
(CLIP2)
Human
(hg19)
chr7:73791153-73795135 
LOW PSI
HsaINT0036374
(CLIP2)
Rat
(rn6)
chr12:25223645-25226325 
LOW PSI
RnoINT0037335
(Clip2)
Cow
(bosTau6)
chr25:33580817-33583424 
LOW PSI
BtaINT0039341
(CLIP2)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
chr19:2746451-2749380 
LOW PSI
GgaINT0131609
(CLIP2)
Zebrafish
(danRer10)
chr5:58793670-58795633 
LOW PSI
DreINT0047575
(clip2)
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"