Special

MmuINT0139064 @ mm9

Intron Retention

Gene
ENSMUSG00000038371 | Sbf2
Description
SET binding factor 2 [Source:MGI Symbol;Acc:MGI:1921831]
Coordinates
chr7:117590528-117593517:-
Coord C1 exon
chr7:117593409-117593517
Coord A exon
chr7:117590642-117593408
Coord C2 exon
chr7:117590528-117590641
Length
2767 bp
Sequences
Splice sites
5' ss Seq
CTTGTAAGT
5' ss Score
8
3' ss Seq
ATTTTAAAATTCTTTTTTAGTTA
3' ss Score
7.76
Exon sequences
Seq C1 exon
TTACCCGTATATCCCCATTCTTCCGGCTCAGCTCCTAGAAGTTTTGAGTTCTCCAACTCCGTTCATTATTGGCGTACACTCCATCTTTAAAACTGATGTCCATGAGCTT
Seq A exon
GTAAGTACCCAGATGTCTAGATCTTGAGTCTTTTGTTTCAGTCTTGCAAGGTTTCCACATCATTATTATTTTCAAATAAGGTGCATTTCCCATAGAAAAGAAAGACTAGAAGGAAAACAACTGTAAGCAATCTAAATATATTTAATTTTGCAAGTATGGGAGTTTAAAGAAGAAATTATGTATTCATTTATATATTTATTTATGAATAAGATGACTCAGTGGGTAAAAATGCTTAGTTGAGTTTATTGAATTTTTTGTAATTCCAACACTCCTGCTAGAAACAGAGGAATCAGCTTGAAGGTTACAGGTCAGCCAGGCTGATGTGAACAGAAGCAGAAGAGAAACCCTGCTTCAAACAAAGTAGAAAGCCAGAATCAGCTCCCGAAAGTTATCTTCTGACATCCGCATGTATATCACGGCCTCTGTCTGTCTGTCTGTCTGTCTCTCTCTCTGCCTCTGTCTCTCTCTGTCTCTCTGTCTCTCTGTCTCTCTCTCTCTCTCTCTCTCTCACACACACACACACACACACACAAACTAACTAATTAATCAACCAACCAATAAAACAAAAAGCAGAGTTTTTCTATGTGGCCTAGGCTAACTTAAAGGTCCTGAGCTCACAACAGTCCATCCACTTCAGCCTCTGAGTATGTCCTGGCATGGGCTACCGTGTCTCACTTTTAAACAACCTTTGTGTACCAGATCAGATTTATTACCATATTTCTCATATGAGAAATTCTGTATTTCTGTAGATCAGTGGTTGTTAACCTTCCTAATGCTATGACCAATTAATACAGTTCCTCATGTTGTGGTGACCCCAACTATAAAATTATTTTTGGCTACTTCATAACTGTAATGTTGCTACTGTTATGAATTGTAATGTAAATACCTATGTATTTTGATGGTCTTAGGTGAGCCCTGTGAAAGGGTTGATCTACCTCTAAGGGATTGTCACAACCTACAGGGTGAGAACAGCTGCTATAGGTGATAATAAATGATTAATAATCCATTGTTTTATTCATACTTTTCTTACTAGCGCTTAACTTATTAGTATTTTAAAATGAGATCTGCCAATATAGAATGCCTGAAAACTAACAGGAATAAAATAGTTTGCAAATAGTTTAAATTCAGTAAAACTCAAGTTCATTTTGAGCTCCCACCAAATTTCTAGTCCATGTGACATTAGAGACGTTAAAGCTAGTTCAAGAATAATTTGTTTACGGATATCATGCTTCTACTGGTACTATAAAAGTGTGCATCAGAAAACTTCAGAATCAAAAGTTTAGGAAACTACTGTTCTCTGAGGAAATTGTCTCAGGTAATAATTTAATACTATTTAATAACTAAATGTTAATAGTTACAGACTAGCATAGGGAGGAAGGAGAAGGTGGTTGTTTGGAGATATATAAACTAAAAACTAACATCAGTGGGTGTAGTATACAGAAACAAATTCCACTGGGTATATTGTCAGATTTAAGATCTGTCAGCTAATGGAGTGGGTGGGGTTCTTGGTGTGAGATGAGGGGTTGTGTTCTGAAGCTCTGTGCCTCAAGTGCAGGGAGCACACCACGTGGCACTTTTCATGGAGTATAAGAAAAGTTCTTTACCAAAAGAATTTTGTTGCATGATATCTGTAATCCACAAGACTTTGTAAGGCTGCTGCTTTTCTAAACGTTAGCAAAAAGGAAGCTTCAGTGTGGCTCACATAGCAACTGCAGCTGGAACCACATCAGAGATGTCATTGACACGATTGAGTGATCAAAGAAGACCCCTGCACATATACCAATCTGTTCTCCTAACATTGTGTTTCAGATCTATCTAGTTCTTTTTAACTCCAGTATCATCATGTTAAAATATATAAGCTAATAAGCATGTTTATTAAAAAGTAGGCCCCATACAATTTGTAAATTATTTTAGTAGTACTAAAGATAGAGATAGGACAAACCAAATGTTGACAGTTGTAGGGTTCTTCACATTTTAATAAAAAGATAAGAATGAATTATAATCACATTACCAAAATCTTCCGTTATTTATGTAAGTTATTTTTAGATATGACCTTTTAGAATGCTACAAATCAGGTTTGGGGTGTTTGTTTTTGTCTTGGTTTTTGAGACAGAATCTAATGTATCACAGGTTTATCACAAACTTGTACTCCTTACATAGCTAAGAATGGCCTTGAACTCATCCTTCTGCCTCCCAAGTACTAGAATTAAAGATGTACATCACCACTCCCAAGCTAGGCTTTACATCTAAACAGTAATTGTTTAATACATATGGCTTTGTGTTTTGATTCATATGGAATGCAAATGCACTAGCTCAGTTAACATGGAATTTTACCATTAATACGCAGCACCTTGTAGAAATTCCTCAATGTGTCGGCGTCGTTTGCTCCATGGCATCCTTTACCATCCAGGCCTCCTTCCTTATGTTTTCTCTATTACAGTCCCCTCAGGTAGTGTCATCATCGGGATGACTAATGCTAGGCCGCTGCCAGTTCATAGTTCCTTCCTATGGAAAGACAGAAGAAGACATAGAAGAGCCTTACAGCTCTCCTCTTCTGAAGCACAGGAGTGCCCATATCATTTTTTCGTCTTCCACTCTTGTACAATACCCAAATTCCAAGGAAGTTGGGACATGTTGTGTAATTAAGAACTCTTACTATGAACCTCTTTCTCAATTTGGTTTTTCTCAGTTTGCGTTAATTAAGGACAATTTGCTTTAAAACAAATGTATTTTATGAATTGTGGTTAATTTTAAAATTCTTTTTTAG
Seq C2 exon
TTAGATGTAATCATAGCAGATTTGGATGGAGGCACTATTAAAATTCCTGAATGCATTCACCTCTCATCCCTCCCGGAGCCTCTTCTTCATCAGACTCAATCAGCACTTTCTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038371-Sbf2:NM_177324:8
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:
PF0214116=DENN=FE(19.7=100)

							
A:
NA

							
C2:
PF0214116=DENN=PD(5.5=26.3)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000033058





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000033058f3819A, ENSMUSP00000081766, ENSMUSP00000125957, ENSMUSP00000126217, ENSMUSP00000129805, ENSMUSP00000132072
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr11:9998380-10000913 
LOW PSI
HsaINT0145204
(SBF2)
Human
(hg19)
chr11:10019927-10022460 
LOW PSI
HsaINT0145204
(SBF2)
Rat
(rn6)
chr1:175225324-175227931 
ALTERNATIVE
RnoINT0130948
(Sbf2)
Cow
(bosTau6)
chr15:43247530-43249761 
LOW PSI
BtaINT0128800
(SBF2)
Chicken
(galGal4)
chr5:8560426-8561108 
ALTERNATIVE
GgaINT0058187
(SBF2)
Chicken
(galGal3)
chr5:10080005-10080687 
LOW PSI
GgaINT0058187
(SBF2)
Zebrafish
(danRer10)
chr7:66783928-66784015 
LOW PSI
DreINT0130999
(sbf2)
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"