Special

MmuINT0154664 @ mm9

Intron Retention

Gene
ENSMUSG00000026797 | Stxbp1
Description
syntaxin binding protein 1 [Source:MGI Symbol;Acc:MGI:107363]
Coordinates
chr2:32658274-32661669:-
Coord C1 exon
chr2:32661589-32661669
Coord A exon
chr2:32658413-32661588
Coord C2 exon
chr2:32658274-32658412
Length
3176 bp
Sequences
Splice sites
5' ss Seq
CAGGTACGA
5' ss Score
10.03
3' ss Seq
GCAAGGTGTGTTTTCTACAGGAC
3' ss Score
7.18
Exon sequences
Seq C1 exon
TATTCGACTCACCTGCACCTTGCTGAAGACTGCATGAAGCATTACCAAGGCACTGTAGACAAACTCTGCCGCGTGGAGCAG
Seq A exon
GTACGATTTCTTCCTTTCCTTTTTGCATGGCAAAACTTCTGCCCGACCTATTCACCTCACTGAATCTTAACCTCTGACCTTGAACATCTTACAGAATCGTAGGATCTAGAGAAGGGAGAGCCCATGACCCCGGGTTGTCTCAGCTGTGGGGCCAGTGTGGAGCCGCTTTGGTGGGTAGGGCCAAGATAGTTCTGGAGTGCTGTGCAGTTTGGATCTTGCATGCCTGGCTCTTTCCAAAGGCTCTGTTTTTCCTGGAGTGACAGACCTGACCGTGGCAGGGTTGGCTGGTGTTTATGCTCTGATGTGTTTTGATCCCGCTATGACCAGACCAGCTTCAAAGCCCGGGCTGCAGCAGCAGGGCATGAGTCTTCCAGCTTTTCTAACCTCAGGCCTGGATGGGACTCTGCCCTCACTGGTACTTGGTGTCCCTGCTCCCAGCACTGATGTCATTGTCACCTTGTGTAGAGTACCAAAACCATAACTGTGGCAAAACTGCTAAGCTGTGTGGCAACTGTCTTGTTGTTGCTTTCAATCCCCTTGGATTGATCTCAAGAGATCAGACTCAGGGCTGCGGACGAGGCCCTCGAACACCGAGCAGGTTCTGAGGGGAGGAAGAAGATACTGAAAGATTTCAGGGTGCCAGGCTTGGTGGCTCAAGCCTAGGTATTTATAAATCAGACAGGGTTTCTCTGTGTAGCCCTGGCTGTCCTAGAACTCACTCTGTAGACCAGGCTGGCCTGGAACTCAGAAATCTGCCTGCCTCTGCCTCCTAAGTGCTGGGATTAAAGGCATGTGCCACCACTGCCCAGCTGCAGATCAAATATTTACATTACAAAATTACATTAGCAAAATTACAGTTATGAAGTAGCAACAAAATGATTCTATGGTTTGGGGGCCACCACAACATGAGGAACTGTATTAAAGGGTCGCAGCGTTAGGAAGGTTGAGAACTGCTGTGCTAGTCAGTAAGAAGCAAGTTCAGATTAACTGCCTAGAAGGCTGAGCCAGGAGGACCATAGGTTTTAGGCCATCCTGGCAGCTTAGTGACAGCCCATCACACTTAGCACCACCACAGCCATGGTAGAGCCTTAGCGGGAAGTCTCATATTCCAGGAAGCATCAACTCAGGCTCAGTGTGAGCTGAGAGTCTCACCCTTGGCTTGCAGTAAGAGGCTCAGTGGAGACGTGCATGCTCTGTCCAGTAGTGTTGGCTGGGTCGGAAGGGAAGCAGCCCTCCCTCTGAAAGTACCCTGCTTCTCAGGCACCCTCCTCAACCTCACAGCTTCTCCCCAAGAGCTCAGCCTGCCAAAGCAGGAGCTGGCTAGTCCACTGTTTCTCAACCTGTGGGTCACAAGCCCTCTGGTGGCTGAACAAGCCTTTCCCAGGGGTCACATCAGACCTTTACATCACGATTCATAACAGTAGCAAAATCACAGTTATGAAGGAGCAACAAAATAGCTTTATGGTTGGGGGTCACCACAACATGAGGAACTGTGTTAAAGGGTCATGGTGTTAGGAAGGTTGCCACCCACTGTGCTCTCAGATTAATTTTGGAAGCACAGGTTGTTTTGTCTTTTGAAAGTGATTTAAAACCATAAGTGTTAAGCTGGCTGTAGTGCGGCAGACCTGTAATCCAATCCTAGCACTGAGGAGGCAGGAGCCGGTGGACTTCTGTGGACTTGAGGCCAGCCTGGTCTATATAATGCATTCTGGGACAGCCAGGGCTATTTTGTGAGACTCTGTCTCTAAAAACTACCCAAAAAATTGAATTAATTGCATTTTAGTGAGCTTAGAGAGTGTGCTCTAGGGCTGGCAAAATGGCTCAGCAGGCTTGCAGCCAAGCCTGACAACCCGAGTTTAATCCCTGGAACATGTGTGAAGGAAGAAGAGAACCAACTCCCCAAGTTGTCCTCTGACTTCCAATGTGTATCATGCATACACACTAACACAATAAATAAATGTATGTGTGTGTTTTCTTTTTTTTTCAATTCACTTTCTATCCTAATATCATTCCCTTCTACTCCCAATACCCCCTCACACAGATCCTTTCCCCATTTCCCCCTTTCTCTAAGAAGGGGGAGTCCCCCCCAGGCATCACCCTCACCCCCTGTGTATTTTTTTTTTTTTAGTGAGACTGGGTGTGATAGCTCACACTTTAATCCTAGCATTCAGAAGGGAGAGGCAGGAGGATCTCAGAGGTTGAGGCTAGCCTGGGCTATATATAGTGTGTCCCAGGCCAGCCAGAGCTACATGGTGACCCTATCTCAAAAACAAAACAAAAACAAATTGGGGGAGTGGGTGGTGCTAGTTTCTTCCTGCTGGAGCACACATCTGCTGGAGCTGTTGAGAGGACTGGGAGGGAAGTGTGCCTTCCTCAGACCATGTCAGAATGTGAGGTCACCATTTGGGTAAACTCTTGGGGTACTGATAGGAAGAGGAGTCCCAGAAACCCTTCTAGGAGTCCCAGAGAAAGCAGTGGCTGTGTCAGATCTAAAGTCAGTGCTCTGGCTTGCTGAGTGCAGTACGCTGCCCGTGGGGTATGTGACACCTGCCCTGGCTGCCCATGGGGTGAGTGGCACCCACCCTGGCTGCCCATGGGGTAACTGAGTGGCACTCTCTATGGGTGTCCGTGGAGTGGGTGGCACACACCATGGCTGTGTTCATTTTTGTCTTCTCACCTCAGTTTCCTGTCACCTTTCTGTCCTCCACCTCCCAGGCTTGGGAGTCCTTCCTTGTTTCTCCTCAGCCTGTGGAAAGCTATAGGGAGATTAAAACCAGAGGTGAAGCTCAGAAGAGTTAAACCTTAGTGTGCCTTTCATGCCAGGAGAGCCAGGGTGGAAAGAATCCAGCCATGCAGGGGCCCTTGAGATGCCCAAGTTTTCATGAATGGGAAGCGAACCCTGAGTCCCTCAGCTGGGCCGTGTATGTCACAGGTGGGGTGCCCTGGCATCCACCTACAGTCTGATCAGGTACTGTGCCTGCTTTGGAAGGACTCTCAGGGCTCTCGTGCCTGGCCATCTTAGGATTCTATGTCAGCCCGATGCTGCAGGAGACTTGTTCACAGCCTGCTCCCACAACACCACAAAGTCAGGCATTTGTAGGGCGTGAACTTCCTGAGAACTGTCACCTTCCCAGACTTGTCACAGACATAGGACCAGCAAGGTGTGTTTTCTACAG
Seq C2 exon
GACCTGGCAATGGGCACAGATGCTGAGGGGGAAAAAATCAAGGACCCCATGAGAGCCATTGTCCCCATCCTGCTGGATGCGAACGTCAGCACTTACGACAAAATCCGTATCATCCTTCTCTACATCTTCCTGAAGAACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026797-Stxbp1:NM_009295:13
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=0.085
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0099518=Sec1=FE(4.7=100),PF140711=YlbD_coat=FE(26.0=100)

							
A:
NA

							
C2:
PF0099518=Sec1=FE(11.0=100),PF140711=YlbD_coat=PD(1.0=2.1)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000089051f1999A





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000052440, ENSMUSP00000089051, ENSMUSP00000108848
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr9:127673262-127675803 
ALTERNATIVE
HsaINT0161387
(STXBP1)
Human
(hg19)
chr9:130435541-130438082 
ALTERNATIVE
HsaINT0161387
(STXBP1)
Rat
(rn6)
chr3:11837526-11840166 
ALTERNATIVE
RnoINT0145620
(Stxbp1)
Cow
(bosTau6)
chr11:98376499-98378385 
ALTERNATIVE
BtaINT0143042
(STXBP1)
Chicken
(galGal4)
chr17:2443382-2443470 
ALTERNATIVE
GgaINT0126181
(STXBP1)
Chicken
(galGal3)
chr17:2830407-2830495 
LOW PSI
GgaINT0126181
(STXBP1)
Zebrafish
(danRer10)
chr21:13805851-13809379 
LOW PSI
DreINT0158004
(stxbp1a)
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"