Special

MmuINT0153448 @ mm9

Intron Retention

Gene
ENSMUSG00000035459 | Stab2
Description
stabilin 2 [Source:MGI Symbol;Acc:MGI:2178743]
Coordinates
chr10:86311679-86313408:-
Coord C1 exon
chr10:86313302-86313408
Coord A exon
chr10:86311799-86313301
Coord C2 exon
chr10:86311679-86311798
Length
1503 bp
Sequences
Splice sites
5' ss Seq
ACAGTATGT
5' ss Score
6.05
3' ss Seq
CACTTTCTTCTGTTCCCCAGGAG
3' ss Score
9.46
Exon sequences
Seq C1 exon
ATGTTAACTGCACCTGCAAGGCAGGCTACGTGGGCGATGGCTTCTCCTGCAATGGGAACCTGCTGCAAGTCCTCATGTCCTTCCCCTCACTCACGAACTTCCTGACA
Seq A exon
GTATGTACCCTGTCTGCCTCTGTCCTCACCTATAGGACGGAGGTTCTGACGACGGCAGCCTCCTGGGACGGTTGTGGTCTTTAAACATGTTGGTATTTTGACAGTGTAAGCATGTGGATTGGTAAAGATCTTTTCCCAATCTGTGGGTTGCCTTTTGGTCTTATTGACAGTATCCTTTGCCTTACAGAAGTTTTGCAATTTTATGAGGTCCCATTTGTCGATTCTTGATCTTACAGCACAAGCCATTAGTGTTCTGTTCAGGAATCTTTCCCCTGTGCCCATATCTTCGAGGCTCTTCCCTACTTTTTCCTCTATAAGTTCCAGTGTCTCTGGTTTTATGTGGAGTTCTTTGATCCACTTAGACTTGAGCTTTGTACAAGGAGATAAGAATGGATCAATTCATCAATGCAATGCAGGTATGCCTGTGTTTGCATCTAAAATGGTTTAAGAAACTGACCAAACCAAAGTAAATAGCATGGCTATTTCTTATATCAATAGCACATCATATCAGAAGCAAATGGACACATTTTTGTCCGTCCACAGAATCAGAATTTATTAACGGTAAATTCACAAGCTGTGTCCATTTTATTGGCTGTAATTTACCATGTAGTCAGTTATAGTCTTGATAATATGACCACTGTCAACCACAGGTTCTTTTATTCTACCATCAATACTAACTCTTGGGCCATCTATTATACTTCACACACTAATACACACACATGCACATGACAGATTGGCTACAAAAGAGGCCACAAAGCTCAAAGAGGCCTTATGGAAGGCAGAGGTCTGACTCAGTGCCCAGGCACCTCAAGTGGTTAGATATTAAAAGAACCCGATGACAGAGCCTGGAAGGCAGCCTGGAGGCTCAAGGCAGGTGAGGCTCGGGGTTGGGCAACTCCGGCTGAATGGGCCTCAGTAAGCAAGAGGGACTACCCTGAGCTGAAGACCTGAAACAGTCTGGCATTCTCTGCCCATCAATCATGAGATGCATGCACTGTGCTAGATGGCTGGACGACAGATCAGTGAGGACCAGTGCTAGATGTCTCTTCCTTTATGGGTGAGGAGGTTGTGTCTACATAAAGAGGATGTATCATAAGTACACAGGCGGTTCCTTTTCACACGTATGAATGAGTTGTTTATCAGCCTGTGCATCATGATGTTGGTGTCTTTGTGCATCCGTGAGACACAGAACCACCCTGCCAATGGGTTTACACTCAGCATGGAGCCAGCTGCTGCTCTGTAAGACAGAGCAGTCACCCATGGCAGGACACAAGCACTGTCTCAGACAATGTGCAGTGGAGCAGTACCCAGAGCATCTTAGGACATTAGGACTCATTAGGATGTTAGCCATCCCGATACTCTGCCAAGGCCAGTGATAGGAAGTACAAAGGAAGTCAGACTTTAGCCTAGCAAAAGGGTATTCTCAGAGGCTTCTCCAGCTTCTCCAGCCACCCCAGCTCCCACACCATGGTAGCCCATCTGACACTTTCTTCTGTTCCCCAG
Seq C2 exon
GAGGTGCTGGTTTTTTCCAGGAGCTCAGCCCAAGGCCGGGCGTTTTTGAAACACCTGACTGACCTGTCCATCAGTGGCACCCTGTTTGTGCCACAGAACAGTGGGCTACCGAAAAATAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035459-Stab2:NM_138673:63
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=0.067
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF129472=EGF_3=PD(34.8=44.4)

							
A:
NA

							
C2:
PF0246917=Fasciclin=PU(30.4=87.5)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000048309





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr12:103755719-103758169 
ALTERNATIVE
HsaINT0160082
(STAB2)
Human
(hg19)
chr12:104149497-104151947 
ALTERNATIVE
HsaINT0160082
(STAB2)
Rat
(rn6)
chr7:27376836-27378032 
ALTERNATIVE
RnoINT0144393
(Stab2)
Cow
(bosTau6)
chr5:67770236-67774488 
LOW PSI
BtaINT0141879
(STAB2)
Chicken
(galGal4)
chr1:54932777-54933079 
ALTERNATIVE
GgaINT0112668
(STAB2)
Chicken
(galGal3)
chr1:56826418-56826720 
ALTERNATIVE
GgaINT0112668
(STAB2)
Zebrafish
(danRer10)
chr4:10760239-10761122 
LOW PSI
DreINT0156763
(stab2)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GCAAGGCAGGCTACGTGG

				
R: 
TTTCGGTAGCCCACTGTTCTG

				
Band lengths: 
206-1709

			

		

	





	
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






Retrieved from "https://vastdb.crg.eu/wiki/Special:VastDB"