Special

MmuINT0007038 @ mm9

Intron Retention

Gene
ENSMUSG00000053297 | AI854703
Description
expressed sequence AI854703 [Source:MGI Symbol;Acc:MGI:2141510]
Coordinates
chr6:48580171-48583687:+
Coord C1 exon
chr6:48580171-48580314
Coord A exon
chr6:48580315-48581538
Coord C2 exon
chr6:48581539-48583687
Length
1224 bp
Sequences
Splice sites
5' ss Seq
TCTGTAAGT
5' ss Score
7.96
3' ss Seq
GTCTCTGCTTCTGTGAACAGATA
3' ss Score
9.21
Exon sequences
Seq C1 exon
CATGTCAGACTTGAAAGCTACTTGGAGAAGGTCACTTGCCACGGTTCCCAGACCCAAGCTCGGTCCCCAAAGCCTCAGCCTCCTGTACCCACTGCCTGGTGGCCTTGAGAAGCCATTCCACTCCATGTCTCAGTTTGCTTATCT
Seq A exon
GTAAGTTGGAGATGAAGATGAAAAACCTTTACCTTTTCCCTGGGGTGCCACGAGGCTTCACTGTTATCAGAAGGTGAAGCCATTTGTCTGGAGTTACTTAAGAAGTCCACACTCATGCCTGGGACAGGGTGTAGGGTATCTGCACAGAGATATGGGCTACTCTGGGACAGCCTGCTCTGAGTTGGGATGGTGTCTGGCTTTACCTAAGGGGCTTTGATGGCTTTGTCCTTAGTTCTAGAGGGACAGGATTTCTGTAGGGAGAGTTGGGAAGCAGAAGGATGGGTTCCGGACAGCAAGGACTAGGATTTGTTCAGAGGGAAGGTACACCAGACATTTGTCATGAGTGCAGGGAGCACGGATCTGTGATTTAGAATGAGAACAGAGGCCCTGGGAGGATGGATGGATGCACAAAGCCTTGAGGCTCATTCAGGTAATGAGAAGGGAGGCCTCAGTCAAGATGGCCAAGGTCGTCTGGTAAGACTGCTAGCTAGGGCTTGCTTGAAGACCCATGTTTACAAGTTGTCACTCGGAGGTACTGGCCTTTTCTGCCATTTGACAAACAAGGAAACCACGATTTGCCCAAACTTGTTCCAAATTACAGCAAATAATTAGCGTCACTATAGCAGGTCAAGTCTGGGCTTTGGTTTTTCATTTTGGACCTGAAAACACGTCAGCTCTATTGTTGAATTATTGAAAATGCAGCTGGGAGAACCTGGGCATGTGGCCAGGGGCCGGGTGATAGGCTATCATGGGCAGGTTATCACTGGGTTTGACAGGTGCAGGGATATGAAGTTAGGAAGCTGCGACCTCTGAGCTGGCCTCTGTTCCCTGAGCCCTTGCTTCCAGCTAGGCCCGTGCTTGGTGCTGGAGGCTGTTCATTGCTTTTGCTCTCTGTCCCACCTCAATGCCATGCGCCTCCTCTGGAATCACTTCTGCCTGAGATCCCTGGGGGTTATTGTAATATTATGGACTAGTATTTAGTGACAGAAAATATTTAACAAGATCCTAGTTAGTCACTCAAGTACCCAGACCCAAGGCATGTCGGGTGTCAACAGGCTAAAACTTGGCGGTGTTTTGTTGGGGAGTGGTAGTAAGAGGGTTCTCTTAAGGTCCCAGATAGACCAAGAGTAGGTCAGGTGAATGTACCCATGTAGTCCAGATGGGCTGGTAGGCAAGGCCATGCTACTACAATGTGCTGACCATAGTCTCTGCTTCTGTGAACAG
Seq C2 exon
ATACGAAGCCAACAGGACCTCATGGCCCAGAACCTGCAGGGCGCATCTGGGCATGGAAACTAAAACTGGAGTCTCGTAGGTCCTGGGTTCCTGACCTGAAGACACGTCTCCTCAGAAGTCCTACCTCTGGAGGTGCCCTGTGTTGGTAGAGCATGGGATTAGAGGCTGATTCCATGCCTTGGTGGGAAGACTCCCCAGATCTGACTTGTCACAGCTGGGCAAGCCTCATTTGGCTTCCTGATCCTAGACCTCAGCTCGGGGGTGGAGGCAGACATCACCTGTGTGGAGAAGTGGCTTCTCTCCTCCAGCCTGGCTCAGCCCTTGGTTGAAGGGCAAGGACAAGGTGTGACTGTTGTGTACCGTTGCAGCAAGTTGATGGCAGACTGGGCTCAAGAGGCAAAACTTCCCTGATGACATGGAGAGCACGTGAAGGCTTCCATGCCCGTTCCCAGCTAGACAGGTGACTGCTTCAGGGGCTTGTGGCCCTTTAAGTGGAGGCTGTGGACCTCGTCCTAGAACTCGCGTACTCATGGAACTCTCAGAGTGCCAAGCAGTTTCAGGAGCCTCTGGACTCCAGCCTAAAGACCTCAGCCCTGGGGAGTCCATCTTCCATCCTTTCCCTACTCCACACAAGTGTGACGCTCTCCTGGTCTCCTCTTGTTTGGGAATAAAGAATTCTGAGGCTGAGCCCCTTTTAGTCCATCCAATCCCTTTCTCTTCAATCTGACAGCACCCCAAATTTCTGGAGCCAGGCTTCCCTCCCCAGACACTGCCCAAGACTGACTCCTGGGCTTGGTTCCTTTTCCCTGTTTTGTGTCGGACAGGATGTAGGGTTTTACAGTGGAGCCCTCTGCTTGCCTTTGGCTCTAACTTCCCTGTGGAGTCTCAAGGGAAGGTTGGCCTGCTGAAGGGATGGTAAATAATTTTCTCTGTGTCTGTTCCTCGGGAAAGGAATCGTACTTCCACTAGCCATATGCAAACAATTGGACCTCCTAGCTGGGCAGGCTTGCAGCTCCAGGCAGGTATCACCTGGGAAGGTGGGGGTTGCAGGGCACCAGAACCCTGCACATGGTGGGTCTAAGCAGTGGGAAAAGCCAGTGGAGGAGTTGCATGTGTCTCCTAAGTAAGCAGGGGTACAACTTGGAGATGAGGGTCTTGGGCCACTGCTGGTCAAGGACTCATATCCTTACATATTAGCCCGTCAGTCGAGAGCCCACAACTGTCTCCCTCCCTTCCTAGAATGAGCCACTCATTAGGAAAGGGGGAGGGGCTTTCTTTTCTATCAGGACTTGGTAGAAACCTCTGGATTCCTGACTTGGGGTCTTACTGCCTGCATTCCCCATGCAGTTTGGGTTACAAGTTCCTACTGAACCCCTATGCCTTATTCTGGGGTCACTGAGTACTCAAAGAGATCAGAGAAAGGGAAGGCGCTACCCATACCATGGGAACTTCCATGCACCCTCTTTTCTAACTTAGGGCGACTTTCACCATGCCTCTCAGCTAACTGCCCAGCTTGTCTCATCCCCACTGTAACTGAGCCATGCCTTCCCTTGTCCTGCTCTGAAATGTTCTTCCCCTAGCCTCTAAACCCACTTATTCACCAGGGCCAAGCCTCTCAGCCTACCCAGCCCATGTTCCTTAACAGTCCTCGTGTTAATACATGGTGTCTCCCTGAGTATCATGTGCTGTTTAATCTTGTGCTTGTTTCTTCTGTGTTTGTGTATGTATACGTGCTGTGTGTGCCCGTGTGCACCTTGAGTCCCCAACTAGACTGTGAGCTCCCTGAGGGCAAGGGGCTGTCATTTCTTCTTCAACTTCTAGTGGGTCTAGCCCAAGAACCTCTCAGAAGACAACTGGATGAAACACATGCTGGAGGTCATCTGAGGTGGAGGGTTGTGTGCATGGGGAGAGTCCACATGGCTTAGCAAGAGGTCTATGCTGTTGGGCTATGGCCTGACCCCTTGGATCAACAATGGATGCTCAAGGTCTCACATCCTTGCAAATTGGAGGTAGTAGAAACAGGAGGGACACCCCCTCCCCCAACACAGATAGACCATGGCTACACCGGAGTGCACATGAATGGTTGGATATTCCCAAAGGTCCCTGATATCTGTTGGAGGAGGTGACTCAAATAAATGTTCTCTACAAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000053297-AI854703:NR_027236:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
NonCoding





No structure available

		

			
Features


			

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

				
Domain overlap (PFAM):

					





						

							
C1:
NA

							
A:
NA

							
C2:
NA

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
NA





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr7:150105577-150107247 
ALTERNATIVE
HsaINT0095237
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr4:113644716-113646050 
Chicken
(galGal4)
chr2:403204-404099 
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GGCCTTGAGAAGCCATTCCAC

				
R: 
GAAGCCACTTCTCCACACAGG

				
Band lengths: 
342-1566

			

		

	





	
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"