Special

MmuINT0153437 @ mm9

Intron Retention

Gene
ENSMUSG00000035459 | Stab2
Description
stabilin 2 [Source:MGI Symbol;Acc:MGI:2178743]
Coordinates
chr10:86327737-86329502:-
Coord C1 exon
chr10:86329356-86329502
Coord A exon
chr10:86327794-86329355
Coord C2 exon
chr10:86327737-86327793
Length
1562 bp
Sequences
Splice sites
5' ss Seq
CCGGTCAGT
5' ss Score
7.53
3' ss Seq
TCTCTCATATTGCACCCTAGGGG
3' ss Score
8.46
Exon sequences
Seq C1 exon
GGAGAGCTCTTTCTAAATGGACAAATGTGCAGGATTATACAGCGGAGACTCTTGTTTGACGGAGGTGTGGCCTATGGCATTGACTGCCTGCTAATGGATCCTACCGAAGGTGGCCGATGTGACACTTTTACTACCTTCAATATTCCG
Seq A exon
GTCAGTTCCCAAATTACAAAATACTGAAAGAACCTTGTACCAGAGACCAGCCCTAGTGATCCAGCATAGGCCCCAAGGAAGAGCCTTGATGAGGCCTGGCCCCAAGAAACCCGAGGGCCAGTCGATGGCATTCTTCAAACTCAGAACCAGCAAGCGTCTGCTTAGGCAGTTGCAGGCCTTGAATATTCTTGGTTAGCCATCATCTACCTATGATTCCTTCATCACTAAGGAAGCTGTGCTTGGATACCAAATGTTAGCTTTCTATTGTGTCATTCATTTTCAAATCCATCCTTCCATTTTATTCATTCAACAAACATCGTTTTGAATTCCTACCAGGTTATATCATATATAAATGGCCTACTTGGCAATTAACAAAAATGGTTCCACATATATATGTATGTATATGTATATATATGCATACATACATACATACATATATGCCCTACACACCTCCATTCAATTTCCTATTCATTTTGCATCATATCAGTTTGCAACACTGAATGAATCTGTGTTTCCAGCTCTCCACTCTGCAAAATACGTCCACCATACAAAATGTGTTCTCCTTCCCTCATCCAGCCAGTAATTCCATCAGATGAATGTCAGCTTTGATCTGCTCTGCTCAGTGCTCATCTGACCCCACAGCAACCCAATAATGAGAGCAGTTGCTACCAACTCTGTCATATAGACTTGGAAATGGAGGTGACAGGACTGCACAGCAGAGCTTGTCACTGAGCCATGTCAGCATCTGGCATCTCTCAGACACTTTAATAAACATCTGAAAGAAGGTTTTCCCCCAAGTTTTATCAGGTGTAACTTTCTTAATTTCTAAAATGTATCCGTACACCTTTCCCCAACTAATTAGTTTCTCTTGACAATTCCCCAAAGGTCAAGTGGCAGCAATAAGTCTTGTCTCTATGCTATACTTTCTGAAAACTAAAGTTCAGAATGTATCAGTGATTGGTCAGAAGTCTCACAGCTAACTTAAAATGCATTCCCATGTGCCCACATCCCCGTTGCTACAGTATGTCGATACCATACTTTCTGGGCTCAGCTCTGTACAGCAGGGGACTGCTTTCAAATGGCCATGCAAGACAGACCTTCGGAGTTTTCCAGGGCAAAGTCAAGTGTGTGCATTTATATGATCTTGATCATAGCCATATCTTAATCATTTAATCATGATTCAGTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCACTCGCGCATCTCTTTGTGAAGGTGCATGTAGAATCCAGAGGTCAACCTGGGGTGCCTTTCCTCAGAAGCCATCCACCTTTTTTCTTTGAGACACGGTCTCTCTGTGGAATCTAGGATTCACTGGTCCAGCTGGGCTGGCTGAGCAGCCAGCAAGGCCCCAGTACAGGAACTACATATGTGCACCACCATGCCCGACTTTCTATGGGATTTCTGGGAACTGAACCCAGGTCCTCCTGCTTATGCAGCAAACATTTTACTGGCTAAGCTATCTCCCCAGTCCCAGATTAAGTTCTTTGATTGCCAATATTCTTGATATTAAAGTCTCTCATATTGCACCCTAG
Seq C2 exon
GGGGAATGTGGGAGCTGTTTCTCCACTCCCAGATGCCCACTACAGAGCAAACCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035459-Stab2:NM_138673:53
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:
PF0246917=Fasciclin=PD(24.1=65.3)

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000048309





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000125263
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr12:103737781-103739411 
ALTERNATIVE
HsaINT0160071
(STAB2)
Human
(hg19)
chr12:104131559-104133189 
ALTERNATIVE
HsaINT0160071
(STAB2)
Rat
(rn6)
chr7:27393491-27394953 
ALTERNATIVE
RnoINT0144380
(Stab2)
Cow
(bosTau6)
chr5:67749077-67750341 
LOW PSI
BtaINT0141868
(STAB2)
Chicken
(galGal4)
chr1:54940507-54942008 
LOW PSI
GgaINT0112658
(STAB2)
Chicken
(galGal3)
chr1:56834592-56836093 
LOW PSI
GgaINT0112658
(STAB2)
Zebrafish
(danRer10)
chr4:10755770-10755928 
ALTERNATIVE
DreINT0156753
(stab2)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GGAGAGCTCTTTCTAAATGGACA

				
R: 
TTGGTTTGCTCTGTAGTGGGC

				
Band lengths: 
202-1764

			

		

	





	
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"