Special

MmuINT0153443 @ mm9

Intron Retention

Gene
ENSMUSG00000035459 | Stab2
Description
stabilin 2 [Source:MGI Symbol;Acc:MGI:2178743]
Coordinates
chr10:86317845-86319484:-
Coord C1 exon
chr10:86319291-86319484
Coord A exon
chr10:86317987-86319290
Coord C2 exon
chr10:86317845-86317986
Length
1304 bp
Sequences
Splice sites
5' ss Seq
CCAGTGAGT
5' ss Score
8.28
3' ss Seq
TTCCTGCCCTCTTCCCACAGGGC
3' ss Score
13.4
Exon sequences
Seq C1 exon
TCGTGGATTTCTGCAAACAGAACAATGGGGGCTGTGCGAAGGTCGCCAAGTGCTCCCAGAAGGGCACACAAGTCTCCTGCAGCTGCCAGAAGGGCTACAAGGGGGATGGCCACAGCTGCACAGAGATAGACCCCTGTGCAAACGGTGTCAATGGTGGATGTCATGAGCATGCTACCTGCAGGATGACGGGCCCA
Seq A exon
GTGAGTGCCACTTCCCTGGGGACATTTAGTATAGCAGCCCTTTGCACCATGTTAGGCCTAGTGTCCTCAGCTACCTGGCCTCTGCTTCCCCTCTGGCCTCTGCTGCATCATCTTTCCCACCTCAGTGTTTTTCTAGTGAAAGTCAGTGTATTCTCAGCAGAAAAGGATATCACGTCAGATTTAGTGAAATTCACGTAAGGGCTATTGTTTAGTTCATAGGACTATACCAACATCACTTCTTAGCTTCCACTACAGCTAGACGAGACCCTCATGTTAAGGGAAGGCAATAGGCCATAGAGCAGTGGTCCTCAACCTTCTTAACACTGCAACTATTTGATAATTAATCATGTTGTGGTGACCCCTAACCACAATGCTATTTTTATTGCTACTTTATAACTGCAGTTTCACTGCTGTTATGAACCATAATATAAATATCTGTGTTTTCTCTTGGTCTTAGGTGACCCCTGTGAAAGGATTGTTTGACGCCCCCCCAGGGGTCATGACCCACAGGTTGAGAGCCACTGCTAAAAAGGGTTCTCTCTCTCTCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTTCCTTTCCTACTTCCCTATAAGTCTGACTCCAGATATAAAGTTTATTAAGACAAAAGAACTTGGAAATAAACAGCATAAACAGTCTTCAGGAATTGAGTCAGTGCCCCCATTTCTTTGTTGGGAAGAGAGCTGAGGACACAGTGCCCCATACCAGTTACGAACAGATTTACAGCGAGGCAGCCTTTGAGACTTGCTCTGAACATATACAGTATGTAGCTGGAGCTCCCCTGCTTGGAGTCTCTGAGCCTCAGTTTCCCCACATGAAGCAAGCCTAACAACAGAGACATCATGGCATTTGTAACATTAAGTGTGGACACTCTCTAATTGAACCAGTGGTCCCAAAGCAACAACGGAGGACTGTAGCGGGTGACAGAGACAGAGTCCTGTGTGGGAAAGGTGGGCAAGAGGTGCTTCCTGTAGGTCACTTTGCGGGAGGGCTTCTCTGAGAAAGCAACCCTTATACTAATGGCAGCCTATCACCACAAGACTGCACAAGCCCAAGACAACCTTTATCCCGCTTGCATCACCTGGGCATAGTGCCTTTCTGAGTTGTTCCTGTGCCTGATGCGTGTCCTCTGGTGCTTGGGATCATGGGGGGCTTTTCACGGTTTCCTGCCCTCTTCCCACAG
Seq C2 exon
GGCAAGCAGAAGTGTGAATGTAAAAGTCACTATGTCGGGGATGGACGGGACTGTGAGCCCGAACAGCTGCCCCTTGACCGCTGCTTACAGGACAACGGACAATGCCACCCAGATGCCAACTGTGTGGACCTTCATTTCCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035459-Stab2:NM_138673:59
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:
PF129472=EGF_3=WD(100=55.4),PF129472=EGF_3=PU(50.0=29.2)

							
A:
NA

							
C2:
PF129472=EGF_3=PD(44.7=35.4)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000048309





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000125263
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr12:103749157-103750578 
ALTERNATIVE
HsaINT0160077
(STAB2)
Human
(hg19)
chr12:104142935-104144356 
ALTERNATIVE
HsaINT0160077
(STAB2)
Rat
(rn6)
chr7:27382769-27384426 
LOW PSI
RnoINT0144387
(Stab2)
Cow
(bosTau6)
chr5:67761898-67762977 
LOW PSI
BtaINT0141874
(STAB2)
Chicken
(galGal4)
chr1:54934979-54935964 
LOW PSI
GgaINT0112664
(STAB2)
Chicken
(galGal3)
chr1:56828619-56829604 
LOW PSI
GgaINT0112664
(STAB2)
Zebrafish
(danRer10)
chr4:10758993-10759068 
LOW PSI
DreINT0156759
(stab2)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
TGCAAACAGAACAATGGGGGC

				
R: 
ATGAAGGTCCACACAGTTGGC

				
Band lengths: 
318-1622

			

		

	





	
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"