Special

MmuINT0148334 @ mm9

Intron Retention

Gene
ENSMUSG00000031558 | Slit2
Description
slit homolog 2 (Drosophila) [Source:MGI Symbol;Acc:MGI:1315205]
Coordinates
chr5:48580668-48583570:+
Coord C1 exon
chr5:48580668-48580831
Coord A exon
chr5:48580832-48583431
Coord C2 exon
chr5:48583432-48583570
Length
2600 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGA
5' ss Score
8.24
3' ss Seq
TCTCTCTTTTTATCCTTTAGGTC
3' ss Score
13.15
Exon sequences
Seq C1 exon
TCGACTCCACTCGAACAACTTGTACTGCGACTGCCACCTAGCCTGGCTCTCAGACTGGCTTCGCCAAAGGCCACGGGTGGGCTTGTACACTCAGTGTATGGGCCCATCCCACCTGAGGGGCCACAATGTAGCAGAGGTTCAAAAACGAGAGTTTGTCTGCAGTG
Seq A exon
GTAAGATCAGTGAGGTTACAGTATTGTTTTTACACTATTGTGTGAGGTGCAAGAAATTCAAACATTCACGATACAGATGTGCTTTCCAGTGAGTCATCCTCACTCATTGCCATGGAGACCCTCTTTCTCACTGAGAATAGTAGATTTTAGGGTATATGTACCTTGGGCAATTATCTGATCACTTGGATGTAAAACATGCCCATTTTCATCCCATGGGAATATAAGAAATTCCTAGATTATAGCAATGCTTGTGAATTACTATTTTCACTTTTATTAATGACTATTACCTACTTTTAGACTAACTAATGAAAATGAATAGAAAATCCCCAAATACTTACTTGAAAATTCAGTATAACTCAATTCTAATTATAAAATGTTAAACACTTTAGAGATGTATGCTTCTAATGACTGAATTAAATATATATATACCAAAATGTATCCAAGTACCAAATGTCTCCAAGCCAAATTTATCAGTAGCTAACATTTGCTCTTTTCTGTTTGTCTAAATAGTATTAATCTAAATATTTCACATATAGCCGCCTTATTGCAAGACTTCTGAAACAACTACATGAACAATATCAATTAATCTCTATATTGGAGATTGAAATATGGCAAAATTAGGACGGTTTTTGAATTTCATATGATCAAGTTAAAGGATCTCAACACATATAGTCTGGATATGCATACATATGTATATACATATATACACAAATATATTATATAAATATATTATTATATACTTATGACTATATGGCTAGAAACATAAATTTTTTATGGTGTTGGGGATCAAACCCAGGTCCTCATTTGTCTTGGCAAGAGTTTGTCCATTGTATTGCATACCAGGTCTTACACAAAGTTTGAAATAACTGTATAATTGGCTTTTCATATTTATGGATTACACAGATATACTTCAACCAACAAAACATTTATAGAATTAAGGTTCAGCACTAAAACTTCACCATCATCTTCTTGTCTTTTATCTGTAAGGAGCTCAATAATATATAAATATTTGTTCATTTAAATTCTCTGTTATAAGTAATCAAAAACTTGGCATCATAGGGTTGACTTGCTTATGCTATATCCAAATGAAATCCCCTTTTATCTAAGATGCTTGTAAGCCCTGACTCTGGTGTCTAATGAAGTCTTATTCTCCTTACTCTTGTTTACCAAGGAAGGAGAATCCCAGGCATCAAAAAACAATTAACAAGATTAAATGACTGAGGAAAATTTCGAGCTCAGCCTTGAACTTTTAAAGCTGTCTTCCAGTGTTTATCTGCATCTGCCACATACTTTTTAATCTAGCTCAGATTTTCCTATAATGCTATCAAATGTTCTCAGTATGTCTGATTGCTAACAGTTCTCTACTAACCTCTGTCTTTCTCTCTTTGCTCTTTCCTTGCTGCCTTCCAGATGAGGAAGAAGGCAAGTTAAATGTGTGTGTGTGTTATGCCCCTCCCCATATTTTTTAGACTTAGAATACTGTTGTAGTTTGAGAACTTGTATGAAGGGATGGGTTTAGCAGCTAGCTCATTGTCTCTTCCTGGCACTTTTTTTCCACTGTGGTGAACCCTTTCCAAAAGATCCCAGAGGGTTTTCATGATTTTCTCCAGAAACCATGGATAAGCAGGTGCCTGTTTGATGCAGCCTGGCTGATGATGTTCTGGTTTTCATTAGTCAGGTCATGAAATCTGATTTCAGAATACTTGTTTTTTTTTTTTCAAATACTGAATAGAGAAATTACACAACTGCAGGTGACTGATTATAGCAAAAGGATCTACCAGAGGAAATCCTGAAAAGAATCATTTCGATGAACAATTACAGAATGATATCTCAAAAATTACTATAATAACTTCAAAGAAAACAGCAATTTTGAGTCTATACAGACACCAAAGTTTTATTATGTAGTTTTCTCCTGCATTTGTTGGCATGGGATAACTTAATTCGGTCAACGGTTATGTCAACCAAGATGGAAGTTTTCTGATTTTTTTTTTTTTAGAGACAAGTAAATTATACTGCAAGCTCCATTAATCTTATCAGAAATAATTTAAATTATTTTGAAGTAGCTACTTATTTTGAAACTAGAATTCAGGTCTTGGATCTAAGTTCAGTTTTACTAATATTTTTCAAGTTCTAGAAGTCTTACAATTTGGGGCTGGAGAGATGCCTCATGTTTAAGAGAACTGACTGCTCTTCCAGAGGTCCTGAGTTCAATTCTCAGCAACCACACAGTGGCTCACAATCATCTGTAATGGGATCTGATTCACGCTTGTTTGTCTGAAGACAGTTGCAGTGTATGCCTTGTATAAAATAAATAATTCATTTTTAAAAAGAAAGAAAAATCTTACAATTTTATGGCAATTTATTAAACCTCAAGAGACAAATGCACTACATCTCAAGATATTGATGCATATATTCCACAAATATTATGGACGCTTATTTAATGAAGAAGTGAGATAGAATTTGAACTGTGTCTCCTGCTTTCTTAGCTGAGTAGAGTCTGCATGTTTCTCATGTCTATTGTGAACTTCAAGAGAAAAATCTAACTGCCATTGATTTCTTTTCTCTCTCTCTCTACCTTTCTCTCTCTTTTTATCCTTTAG
Seq C2 exon
GTCACCAGTCATTCATGGCTCCCTCCTGCAGTGTGCTGCACTGCCCCGCTGCTTGTACCTGTAGCAACAACATTGTAGACTGCCGAGGGAAAGGTCTCACTGAGATCCCCACAAATCTGCCTGAGACCATCACAGAAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031558-Slit2:NM_178804:8
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:
PF138551=LRR_8=PD(11.5=12.5),PF0146319=LRRCT=WD(100=44.6)

							
A:
NA

							
C2:
PF0146213=LRRNT=WD(100=59.6),PF138551=LRR_8=PU(8.2=10.6)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000133840





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000133912, ENSMUSP00000134263, ENSMUSP00000134393
          









    
Other Skipping Isoforms:
ENSMUSP00000033967, ENSMUSP00000127615
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr4:20488983-20491760 
ALTERNATIVE
HsaINT0154535
(SLIT2)
Human
(hg19)
chr4:20490606-20493383 
ALTERNATIVE
HsaINT0154535
(SLIT2)
Rat
(rn6)
chr14:66955379-66956523 
LOW PSI
RnoINT0139666
(Slit2)
Cow
(bosTau6)
chr6:41509677-41512186 
BtaINT0137091
(SLIT2)
Chicken
(galGal4)
chr4:74639586-74641780 
ALTERNATIVE
GgaINT0077282
(SLIT2)
Chicken
(galGal3)
chr4:77802552-77804759 
GgaINT0077282
(Q90XG3_CHICK)
Zebrafish
(danRer10)
chr1:23162591-23162957 
LOW PSI
DreINT0152445
(slit2)
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"