Special

MmuINT0148285 @ mm9

Intron Retention

Gene
ENSMUSG00000025020 | Slit1
Description
slit homolog 1 (Drosophila) [Source:MGI Symbol;Acc:MGI:1315203]
Coordinates
chr19:41685492-41688989:-
Coord C1 exon
chr19:41688892-41688989
Coord A exon
chr19:41685632-41688891
Coord C2 exon
chr19:41685492-41685631
Length
3260 bp
Sequences
Splice sites
5' ss Seq
CACGTGAGT
5' ss Score
9.3
3' ss Seq
TTCTCTGCCCCCTACCGCAGGTG
3' ss Score
11.18
Exon sequences
Seq C1 exon
GGCCGACACTGTGAGGTGTCTCTGGACGGCTGTTCCAGCAACCCATGTGGAAATGGGGGGACCTGCCATGCCCAGGAGGGCGAGGATGCTGGCTTCAC
Seq A exon
GTGAGTTCCCTGGAGCCTGAGATGGGGTTGGGGACCGCTGCTGGGCCCAGCGTCCAAGTCTCCTCGTGCTGGAGATGAGGCTGGAACAGACCTGTGCTCCAAATTATCGTCAGCGGTTCTTTAAGGCTCCTCTCACCTGGAAGCCCTGAAGGACAGCAGGCACCAGACAGTACAGGTTCACAGGACAGGGAGCTGGGGCTTGGGTGGGGCTGCCTCCTGGTGAAGGTGCCAGGAGTGTCTCTCTGCATGCTGGCAACCTATAGCCAAGAATATACGCCATGGTAGTGGCAGGAAATGGTTGGGGACATCTAAGACTCTTTTAAATTTCCACACACCCTCCTGAGCCTCCACTTTAAGCCGATCAAGTCTCTAGAGGTTATGCCAGGACCCAAGCAGGCCTTAGCCAGCCCTGTGTTATAGCTGAGATGACCAAAAGCGAAGCCACATTCTGGTCACCCCTTCTGGGGTTCTACCTTCACACAACTCTCACTGACTGGCCACTGTAGGGAGGAATCCCACCGTATTTTCCCATGCTCTGAGCACAGCTGTGCTCCCCACATAGTGTATCTGAACCCCTCCAGAGCAGATGTTTTACACACACACACACACACACACACACACACACACACCACACACACACACACACACACACACACACACACACACACACACACACACACACACACGCGCGCGCGTCTGCTTTCCCCAGGAAGCCCCAGCCCCCAGCCCTGGCCTCCCAGAGCTTTTCTGAGGAACACAGTACTTAGTTGCTGGAGATAAATTGCCTACTGAACAAATTGGCTCTTCAGAAAATGATGTTGAATCTACGAGCGGAAATGGCCAAACCTACCTCTGCAGACCCAAATTACCAGATGTAAAAAATAAAGCGCGCTAAGTGCCTCTCCTCCCGAGTTGCCTTGGAAACGCATCCTTACAATAGGCAGGCCCTCCTCAGGGGCAGGCAGCAGCTCAGGCTAAGCTTCCCGCCTGGTCCATTCCTCAGCTCCTACTCAGGGCTGGGATGCCCCTTCAGGGCAGAGGGGACAGGTGGGGTGGCCCTACATATCCAGCAACCGGGCAGCCTATAGCACCAGGTAGGAGGGGAGACCTCCTTTCCACCTCCCTAATGCGTTTAGATTTTGCCAGTAGGGACTTTCTGTATAAATATCCTGTCACCCTAGCTTAAAATCAAACTGCAAAAGGCGGCTGTGGCATAACCTTCAGACCTTTTTACTTGCATTGCCCTCCAGAAAAGATGTAAATGCCATCTGCACAAATTTTCTTAGACCAACAGCTACATTTTTTTTACTGTAAGTTTATTTTTTCATGCAAAAGAGACAGTCTCATAGATATGATAAATATTATTGCCATTTTAAAGTAAAACAACGAGATTAAGCACACGATCCCCACCCTCCTGTGGAAACTGTGAGGATAGCCATGGGGGTGCCACTTTGTTATTTATTCATTTTTTTTTTTTTTTTTGAGACAGGGTTTATTGTGTAGCCGAGGCTGCCCTGGAGTTCTCAATTCTGCCTCCCTTTGGCATCCCAGTGCTTAGATCACAGCTTCTGATACCGCACTTTGCCTGCCTTTTCAAAATGTCACCTGCAACCCCCTCCGTAGCAATGAAGTGACTGTACACCAGGAGCCTCTGTCACCAGCGAGAGTTTAAGGGCTCAAGTTTAATGTCCCTCCTCATTTCTTGTCACCCTAAGCTCCTAATTAGAAGTTTCTTTTGGCTGGGTTTGGTGGTACACATAGGTAATCCTAGGATGCAGGAGTCTGAGGCAGAAGGATTGTGAATTTGAAGCCTGCTTAAGCTAGCTACATAGGGAGATCCGATCTCACAAATTTTATTTTATTAAAATTACTTTGGAAAAAAATTACTTTGGAGCATGGAGAGATGGCTCGGTGGGTAAGAGCACTGGCTGCTCTTCAGAGGACCTGGGTTTGAGTCCCACCACCCACATGGTGACTCCCAACCATCTATAACTCCAGTCTCAGGGAACCGGATGCTCTTTCCTTGCCTCCAAGGGAACCAGGCATGTATCCGGTCCATATACAGACATGCACACAAAACCAAACAAATAAATACAATTACAAAGAAATAGTTTCTTGTGTCTCACTTATCAGTAAGATGACTGATAACACACAAAACAATGTAACTGCTATACATTTCACAGTTATTACCTGTAAGGTAATGTGTGCTGATACTGGACTCCTTTGTGGGGGTGTGTCTGTATTCTTTGCCAGTGGGCCCATGTGTCCCCAGATGGTCTGAGCACGACAGGAGAGGGCAGCTGCCCTGCTGTTTTCTTTGCATGTCTATTTTATTCTGGGAAGGTCTGTTCACACAGATCCACTGTCGGGGTTAGTGGATTCATCATAGACCTGGCACTCAGCTATTGGAAACCCTTACAGTTTATAGGACAAGAATCTCCAGAGTGAGCAGGTGGCAGCAGTATTTCAGTTCGGTTAGAGGCTCAGTTCCCCGAGTCTCCTGCCAGTTATTTTTAATTGTCTGCTTGCTGCCTTCCTTGGCACCTGGAGACACAGCCCCACCTCCTGCTTAGGCAGAGTGCCACCTAAGCATGACAGGAGAGGGCAGCTACCCTGCTATCTGTCTCCAACTCATGGTGATGTTTGAGGAGTTTTATAGGCGTTTGGAAAGCTGGGCGGAAGCCCCCCAGCCCTCTCCCTCTGACCCCCGGGAAAAATCACATGTCCTAAGCTAATGACTACCCTGGTTTGTAAATCACCAACCTCAAGAACCTTCTACAGCCCAGAGATGGCTCAGCCCAGCTCTGTTCTTTCTCTGTCCCTGAAGTCTGTGTCCTCAAGGACGTGAGCTGTGTAGCTGAGCAGGGCCTACCTTCTCACTTCAGACTTCACCCATCCCTCGGTGCCCACTGCCTCCCCTCCCCTGTTGGGACTCTTGCTGAGGCTAACCCATCACCTTTGCCAGGAAGTCTGCCTGACTATGCCTTGGTGAGGAGGAGTTGGGTGTTCTTCTCCCATGCCTGGCTTCAGAGCCTCCACCATCGTGATTGTACTTCACTCTTTTCACTTGGTCTCCAACACCAGACTGCAAGCCAGAGGGTTCCTTGAGGACAGGGCTGGTCTTGTCACCCTTTAATCTGTTTGCCCTCTGGCAAGGGCCTGGTCTAGAGAAGAGCTCCAACCATTGGTGTGGAATAAGGACTCTGGCCAATGGCCACAGGTTTTCCCAGCTCCTCTCCATTCTCTGCCCCCTACCGCAG
Seq C2 exon
GTGCTCCTGTCCCTCCGGCTTTGAAGGGCCGACCTGTGGAGTGGACACAGATGACTGTGTTAAGCATGCCTGTGTCAACGGGGGTGTCTGTGTAGATGGCGTGGGGAATTACACATGTCAGTGCCCCCTGCAGTACACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025020-Slit1:NM_015748:28
Average complexity
IR-S
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:
PF0000822=EGF=PD(6.2=6.1),PF0000822=EGF=PU(64.7=66.7)

							
A:
NA

							
C2:
PF0000822=EGF=PD(32.4=22.9),PF0000822=EGF=PU(90.3=58.3)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000025993





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000128381, ENSMUSP00000129034
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr10:97014159-97018585 
ALTERNATIVE
HsaINT0154485
(SLIT1)
Human
(hg19)
chr10:98773916-98778342 
HsaINT0154485
(SLIT1)
Rat
(rn6)
chr1:260855752-260858841 
LOW PSI
RnoINT0139615
(Slit1)
Cow
(bosTau6)
chr26:18146812-18150116 
LOW PSI
BtaINT0137041
(SLIT1)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
chr13:435384-435683 
LOW PSI
DreINT0152376
(slit1a)
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"