Special

MmuINT0153449 @ mm9

Intron Retention

Gene
ENSMUSG00000035459 | Stab2
Description
stabilin 2 [Source:MGI Symbol;Acc:MGI:2178743]
Coordinates
chr10:86310770-86311798:-
Coord C1 exon
chr10:86311679-86311798
Coord A exon
chr10:86310911-86311678
Coord C2 exon
chr10:86310770-86310910
Length
768 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
GTGTGCTTTGTTTCTCTTAGAGC
3' ss Score
9.58
Exon sequences
Seq C1 exon
GAGGTGCTGGTTTTTTCCAGGAGCTCAGCCCAAGGCCGGGCGTTTTTGAAACACCTGACTGACCTGTCCATCAGTGGCACCCTGTTTGTGCCACAGAACAGTGGGCTACCGAAAAATAAG
Seq A exon
GTGAGTGGAATTCCTGGTGCCTACACTTTAGCCAGGAGTGTTATCTGTCACTACCATAACAGGGTACAAATCACTCCACCAGGCCTAACGGTGCAGGCCTGTCATCCCAGCACTTAGGAAGGAAAAGATACAGAAAAACAACAGTCCCTGCCCCAGTGCAGTGGTTGACAGTTATCCAGCACACATCTGCTGAGCAGCCACTGCTTCTGGTCTCCGCACCGCACTATCAGCGGTCCCGGCTGGCCTGTTGATGGCTCTGTCCTACAGGGTTCTCACAACCAGGCAGCCTAACCCGGTCACGGCAAGGAGCAGGAGTGCGGAGTGCTGCTTGGTCCTCTGTTCACATTTGCCAAGGAGTCACCAACCAACAGCTCACAAGGCTGGGCCCAAAGTCAGGGAAAGAGATAAGGGGCCAGAGGCAAGGATCCAGGGAGGAGAGAAGTGTTGAGGCCCCTGGTGAAGTGAGTCTGACACGCCAACCTTCCGCATGATGTGGTTCAAAGAGGACTTGTCCAACTCAGCCCTGGAGGCTGACCAGCAGGCTGTGAGCTCCAGGTACTACCCAATCACAGGGCTGGAGAGAGATGCCTCTGCCTGCCTGGAATGCACAATAGACAACTCCAGAAAACTCGCTTTAGAGAATGAAAATGGCTTCCCTTGTGCTAATTCTCTATGAGCCTTGGGAACGACCCCAAACACCCAAGAAGACCTCACTATGTCCAGCTGTTGCCCAGACCTATGACTGTTCGTGTGCTTTGTTTCTCTTAG
Seq C2 exon
AGCCTGTCTGGGCGGGACATTGAGCACCACCTCACTAATGTCAACGTCTCCTTTTACGATGACCTTGTCAATGGTACCGTCCTGAAGACTAGGCTGGGAAGCCAACTGCTCATCACCTCCAGCCAGGACCAGCTCCACCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035459-Stab2:NM_138673:64
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.067 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0246917=Fasciclin=PU(30.4=87.5)

							
A:
NA

							
C2:
PF0246917=Fasciclin=FE(40.0=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000048309





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000125263
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr12:103758290-103759132 
ALTERNATIVE
HsaINT0160083
(STAB2)
Human
(hg19)
chr12:104152068-104152910 
ALTERNATIVE
HsaINT0160083
(STAB2)
Rat
(rn6)
chr7:27375963-27376715 
LOW PSI
RnoINT0144394
(Stab2)
Cow
(bosTau6)
chr5:67774609-67775382 
LOW PSI
BtaINT0141880
(STAB2)
Chicken
(galGal4)
chr1:54931789-54932656 
ALTERNATIVE
GgaINT0112669
(STAB2)
Chicken
(galGal3)
chr1:56825430-56826297 
ALTERNATIVE
GgaINT0112669
(STAB2)
Zebrafish
(danRer10)
chr4:10761240-10762837 
LOW PSI
DreINT0156764
(stab2)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
TTTTCCAGGAGCTCAGCCCAA

				
R: 
GAGCTGGTCCTGGCTGGA

				
Band lengths: 
243-1011

			

		

	





	
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"