Special

MmuINT0036767 @ mm9

Intron Retention

Gene
ENSMUSG00000033392 | Clasp2
Description
CLIP associating protein 2 [Source:MGI Symbol;Acc:MGI:1923749]
Coordinates
chr9:113805760-113808717:+
Coord C1 exon
chr9:113805760-113805903
Coord A exon
chr9:113805904-113808573
Coord C2 exon
chr9:113808574-113808717
Length
2670 bp
Sequences
Splice sites
5' ss Seq
AAGGTTTGT
5' ss Score
7.81
3' ss Seq
CTACTGTTTGTTCTTTCCAGGCA
3' ss Score
10.17
Exon sequences
Seq C1 exon
GTAAAGGTGGCTATCCTTAAGTACATAGAAACTCTGGCAAAGCAGATGGACCCAAGAGATTTTACAAATTCCAGTGAAACTCGCCTGGCAGTGTCTCGGGTCATCACTTGGACGACAGAGCCCAAAAGCTCTGATGTTCGGAAG
Seq A exon
GTTTGTTTGAGTGGGATGGAGAGATATTTTAAGTATTTTTTTAAACTGCTCTTTTGTTAGCTACGAGCCTTGTGTTTATTGACACCACTGAGGACGTGCCTTCCCCTGTGCCTGTCCCTATCCTTTCCAGCAGTCCCTACAATCCGTGACAATCAACACTTGCCTATGTGGACATTGACCTTTTGTTTTGTTTTGCCTTCCAAGTTCTCACTCCTGTGCCCAGTGATTTGCTAACTGCCTCCTTTCTTAAAGAAGTTCTGTTCTTAGAGCTAATGTCTGCATTGCTTTTCATGTTCTGGAGTTTTGTCTTAGAGTTTATTGTCTTGATTTTCATTTTCTTGAGTTATGGTGTTTTGAGACAGTCTTACATACCCTGGGCTAGCCTGGAACTCTTACATACCCTGGGCTAGCCTGGAACTTACTCTAGCAGATGACATTGAAGTCCTGGTCTTCCTGCCTCAACCTCCTGGGTATCAAGAATTCTGCCACATCCATCTTGCCTAGCTTGAGCTTTTAAATATGTCTTGTTTAGTATATGTTAATAGTTAGTGTATATGCTAATATTTTTAACATTTCTGCCTAGGGCTTATGGCTAGTATTTTCTATTGACTCAAAAATATGTAAGTTGTTTATGCTAGGAAATTACTCCATTGATAAAGGACGTAAGAACTCGAGTTTATATTCCTAGCACCTACATTATAAAAAATCGGGCATGGTAGCACATGCTTGTAATCTGGGTGCTGGAAAGGTGGCAGATTGAAGGCAATTGCTAGGGTTCACTAGCCAGCTAAGCTTTCCTTGTCATTGAACTTCCAGTTGAGTGATGGATGATCTCAAAAACTAAAGGGGAGTTGGGGATATTGGGACACACCTTTAACCCCAACACTCGAGAGGCTGAGGCAGGCAGATCTCTGAGTTAAAGCTAGCCTGACCTTTGGCCTCACATGTGGACACACTTTAGCACGTGTATATATACATGCACAGCTGCACACATGGACACAAGCACATGTATGTACCATAAAACAAAAAAGAAAATACACTAAATTGAATAAAAGTGAAGACATGGCATAATAAAACTCGGAGACGCAGCAGAAGCTGCATCTTGAAGAGAGCTCAGGGTACATAGCCGTATGTGCAGTCAAACACCCATGCATACGGTAGTCGGTGAATAAGATAGAAGCTAGGCTGGCACACACCTTTAATCCCAACAGCTCAGAAGATAAAGGCAGGTCTACTTAGTGTGTTTCAGACCAGCCAGTACTACAGAGTGAGACCTCTTTTCAAAGGAAAAAAACAACAACAAAGAAAACTGCGACTGACTGCACCCAACAGTGCTGTGTGACCCGCTGCCTGGTGCTTCCACTTACCTGAGAATGACCTCTGCCCTTGTGCTGGGAGCCAGAGTAAACCCTTCTGCCCTTCAGTTGCTTTGTCAGATACTTTATAACGGCAACTAATTCAGAGCTTGTAATAAGAGGAAACATTTAAATCGGTTATCTAATCAACCATCAAAAGACAGTGAGTCAAAAGGCAAAGCAAACAGAAATTTGTAGCTGAGAATATGGAAGAAAAGCAGAGACCATACATGGTGTTGCCCAAACCTCTAATCCAGCTCTTAGGAGGCAGAGGTGGGCAGATTTCTATGGATTCAAGGCCAGCCTGCTCTACATAGTGAGTTCCAGGACAGCCAGGACTTTGTACAAAGGCCTGGTGGGGTGAGGTGCAGCAGGGCTGGTGAGGTGTCCAGCACTCACGAGACCCTCATGGCAGCTCACAAGTGGCTGTGATCCTACATACCAGGAGACTGTTGAGTAGTGTTGTGTTATCTGAATACAGCATGCTTTAACCACTCTACTGTTGTATAGTGAGACTCTAAACATAGAACACCGAGGTCTTCATAGGTGAGATCAGAAACAGTCCAGAACAAGGTGTGTGCACTGGACATGGTCCTGTCACTGTGCTTCATTTCGTCCTATATTCTAAATGATTTGATTTTACTTTAGATTCTTCAAAATACCTGACTAACCTTATCTTGAGATTAACTGTAGACTTTTAGATTAGCTGCTTAAGAAAAGACTAGATCTTGCTAACACTTAAGGAGCAGAGGTGGGAGGGTCACAAACTCACAGCCTTCAGGACTACATAGTACAGTCATGCTCTGTTTTGTTTTGTTGGTTGGCTTTTTTGTTTTTCCCCTTCTGCTGTTTTTATTTTTTAATTATCATACGAAGTAACATGTTTCCATATGGCATTATCATGTGTACTTTGGTTTTGTTAATCTTCCCCTCTTCCCATTCCTACCCTTACCCTGTGTTGTCTGCTGCCAATGTATTTTTCAATATTAAGAATGCTTAATTTTAGCATTAAGTCACTGTCCTTTATGTCCTTTATAGGGAAACCTAAAACAGTAATGTGTGTTGACGGGATAACCCTGCAATGTTTGTCATGTTACACTTTCATAGTCCCTTTTTAACTTTAGAAAATAAATGGTAGTTGAAAGGGTTTTATCCTCCCAAAAAGAAAGAAGTTATGAAAGTTAAGGCTTGACCATCACATTTCCTTCTCCATGGGAGAGATTGTCGAACCCTGTGCCTGTGAGCAGAAACATAAGAAGAAACGGACACGCCTGCGCAGCCAGGATGCGTCTCACCTACTGTTTGTTCTTTCCAG
Seq C2 exon
GCAGCGCAGTCAGTGCTGATTTCTTTATTTGAACTCAATACCCCAGAGTTTACAATGTTACTAGGAGCTTTACCAAAAACTTTCCAGGATGGTGCTACTAAACTTCTTCACAATCACCTCCGGAACACTGGCAATGGCACCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000033392-Clasp2:NM_001114347:30
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (disopred):
  C1=0.188 A=NA C2=0.350
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF123483=CLASP_N=FE(20.7=100)

							
A:
NA

							
C2:
PF123483=CLASP_N=PD(15.9=75.0)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000128343f3126A





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000035089, ENSMUSP00000107469, ENSMUSP00000128343, ENSMUSP00000128460, ENSMUSP00000128535, ENSMUSP00000130201
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr3:33544842-33551251 
ALTERNATIVE
HsaINT0035768
(CLASP2)
Human
(hg19)
chr3:33586334-33592743 
ALTERNATIVE
HsaINT0035768
(CLASP2)
Rat
(rn6)
chr8:122158391-122161038 
ALTERNATIVE
RnoINT0036800
(Clasp2)
Cow
(bosTau6)
chr22:7831063-7835266 
LOW PSI
BtaINT0038889
(CLASP2)
Chicken
(galGal4)
chr2:45267401-45272218 
ALTERNATIVE
GgaINT0099692
(CLASP2)
Chicken
(galGal3)
chr2:44715078-44719895 
LOW PSI
GgaINT0099692
(CLASP2)
Zebrafish
(danRer10)
chr19:43221141-43221736 
LOW PSI
DreINT0047221
(clasp2)
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"