Special

MmuINT0143117 @ mm9

Intron Retention

Gene
ENSMUSG00000037062 | Sh3glb1
Description
SH3-domain GRB2-like B1 (endophilin) [Source:MGI Symbol;Acc:MGI:1859730]
Coordinates
chr3:144359818-144360431:-
Coord C1 exon
chr3:144360342-144360431
Coord A exon
chr3:144359919-144360341
Coord C2 exon
chr3:144359818-144359918
Length
423 bp
Sequences
Splice sites
5' ss Seq
CACGTGAGT
5' ss Score
9.3
3' ss Seq
CCGTAACTTTTCCATTGCAGGCC
3' ss Score
9.41
Exon sequences
Seq C1 exon
TCTGAACAGGAATTGAGAATAACTCAAAGTGAATTTGATCGTCAGGCAGAGATTACCCGACTCCTGCTTGAGGGAATCAGCAGTACACAC
Seq A exon
GTGAGTGTTACATCATTGCCCCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACGCTGAGACAACCCCAGGCAGCTAAGGAGGAGCATGTGCAGGCGAGAGCTTCCTGTGGCATTTACCTCTCAAGGAAAGCTGAAGAGAGTTTACAAGGATCTGAAGAAATGTGTTCATTTTCTCTCACATCTCACCACACATTTTACACATTGCATAAATTTTCCTGCTGGTTTCTATTGGCTAAACAAAGTTTGTCAACATATTGTTCACCAGTAATTCATCTTAGTAAGTCTGATAGGAGTACCCCAGTAATAAGCTTTACAGTAGGTTGCCACCGCTGATTCTCCCTTGTGACAGTGTTAGCCTTTGTTCCCCTTGGCTTGTAGCACTTGAACTTCTGAGAATGACCGTAACTTTTCCATTGCAG
Seq C2 exon
GCCCATCATCTCCGCTGTCTGAATGACTTTGTAGAAGCCCAGATGACTTACTATGCACAGTGTTACCAGTATATGCTAGACCTACAGAAGCAACTGGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000037062-Sh3glb1:NM_019464:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.278 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0311413=BAR=FE(11.8=100)

							
A:
NA

							
C2:
PF0311413=BAR=FE(13.4=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000101816





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000073821, ENSMUSP00000129800
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:86734692-86735078 
LOW PSI
HsaINT0149362
(SH3GLB1)
Human
(hg19)
chr1:87200375-87200761 
LOW PSI
HsaINT0149362
(SH3GLB1)
Rat
(rn6)
chr2:250722201-250722609 
ALTERNATIVE
RnoINT0134713
(Sh3glb1)
Cow
(bosTau6)
chr3:57421874-57422245 
LOW PSI
BtaINT0132576
(SH3GLB1)
Chicken
(galGal4)
chr8:14876129-14876984 
ALTERNATIVE
GgaINT0035641
(SH3GLB1)
Chicken
(galGal3)
chr8:16643343-16644198 
LOW PSI
GgaINT0035641
(SHLB1_CHICK)
Zebrafish
(danRer10)
chr2:16520706-16522776 
LOW PSI
DreINT0134419
(sh3glb1b)
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"