Special

MmuINT0177503 @ mm9

Intron Retention

Gene
ENSMUSG00000079173 | Zan
Description
zonadhesin [Source:MGI Symbol;Acc:MGI:106656]
Coordinates
chr5:137877806-137879089:-
Coord C1 exon
chr5:137878948-137879089
Coord A exon
chr5:137878066-137878947
Coord C2 exon
chr5:137877806-137878065
Length
882 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
AGCCATCTCTTTCTCCACAGAGA
3' ss Score
9.71
Exon sequences
Seq C1 exon
TTGGGGGAGAGCTGGTACACAGAGAAGACCTGCACCACCCTCTGCACATGCTCAGCCCACAGCAACATCACCTGCAGCCCAACGGCCTGCAAGGCCAACCACGTGTGTTTGCGCCAGGAAGGACTGCTACGCTGCGCTGCAG
Seq A exon
GTAAGCGGTCCGTGCTGCAAGTGATGTCCCTTCAGTCACGAGAAACGGCTCTCCTAGTCCTCCACACCTCCTCCAGGACACCCCTCTGTCGTACTAGCGTCTGACATAGTCTGGCCTTACCTGAAGGACTTGTGGCAGAACTCAAATTGCCATCCCCTACTTCCCACCCTAGTCTGGTCTTGAACTCCTGATCTTCCTGTGCCTACTTCCCGTGTGTTGGGATTACAGGCATGTACCATCATACCTAACCCTTTCTTTCATGCTTTAAAAATTATGTTACTTATCTTGTGTGTGAAGGTGCGCATACATGGAAGCCAAAGGACTACTTATGGGAATCAGTTCTCTTTTTCCACCTTGTGGGTTTGGGAATCAAACTCAGGTTATCAGGCTCGGCTATAGGTTCCCTTACCTGTTCATCAGGCTCACTGGCCCCACACCTGCTCTTCCATAGCATATTTTAATTCCTATCTACCCTCAAGCATTATCCAGAAGATCCTTGGACTTTGATCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTGCCTCCCTCCCTCCCTCCCTCCATCCCTCCCTCCCTCCCTTCCTTCCTTCCTTCCTGTTTTTCAAGACAGGGTTTCTGTGTAGCCCTGGCTGTCCTGGAACTCACTCTATAGACCAGACCAGTCTTGAATTTGGTGATCACCTGCCTCCGGCTCCTGAGTGTTGAGATCAAAGTTATGCACCACCACTACCACCACCACCACCACCGCTTGGCTTAAATGTGTCCTCTCTTTCTTGGGTCTCTCTGGCCTGGACCAGGCGGAGAGAAGGGTACATGGGGTTCCTCTGAGCCTTGGCACCATTCCTCAGCCATCTCTTTCTCCACAG
Seq C2 exon
AGATGGGAGAGTGTCGCATCTCAGAGGATTCCCAGATCGTGAGCTTTGATGATCATAGCCATCCTATCCAAGACACATGTACTTACATCTTGGTCAAAGTATGCCACCCCAACACGAACATGCCTTTCTTCATGATCAGTGCCAAGACCGACATAAACACCAACGGCAAAAACAAGACTTTCGGTGTCTATCAGCTCTACATTGACATCTTCAACTTCCACATCACTCTTCAGAAAGACCATTTAGTCCTCATAAGCTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000079173-Zan:NM_011741:31
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:
PF127142=TILa=PD(78.9=93.8)

							
A:
NA

							
C2:
PF0009420=VWD=PU(51.2=94.3)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000114068





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000106669, ENSMUSP00000114068f5547A, ENSMUSP00000132895
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr7:100773866-100775327 
HsaINT1047018
(ZAN)
Human
(hg19)
chr7:100371488-100372949 
HsaINT0184454
(ZAN)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr25:36377795-36378086 
BtaINT0163470
(ZAN)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
chr7:26078302-26079157 
LOW PSI
DreINT0022886
(ZAN)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
TTGGGGGAGAGCTGGTACAC

				
R: 
TGTAGAGCTGATAGACACCGA

				
Band lengths: 
343-1225

			

		

	





	
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"