Special

MmuINT0006618 @ mm9

Intron Retention

Gene
ENSMUSG00000035279 | A430110N23Rik
Description
RIKEN cDNA A430110N23 gene [Source:MGI Symbol;Acc:MGI:3606211]
Coordinates
chr7:4884737-4888428:+
Coord C1 exon
chr7:4884737-4885054
Coord A exon
chr7:4885055-4887864
Coord C2 exon
chr7:4887865-4888428
Length
2810 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGG
5' ss Score
8.3
3' ss Seq
CCTCCCTCCCGGTCTCCTAGGGA
3' ss Score
9.49
Exon sequences
Seq C1 exon
GGTCCCCCCAGTTGCGCCTGGTGGCTGGACCCAGCAGGTGCTCTGGCCGGCTGGAGGTATGGCATGACGGACGCTGGGGGACAGTATGTGATGACAGCTGGGACATGAGAGACTCAGCTGTGGTCTGCCGGGAGCTGGGCTGTGGGAGGCCTCGGCAACCAGACCCCGCAGCAGGCCGCTTTGGCTGGGGTGCAGGCCCCATCTGGCTGGATGACGTAGGTTGTATGGGGACGGAGGCTTCACTGTCAGAATGCCCTGCTGCTTCCTGGGGGAAACACAATTGCGCCCACAATGAGGATGTCGGGGTTACCTGCACTG
Seq A exon
GTGAGGATGCACTAGCCACCCACTGGCTCTAGGAGGGCTTCTAAGTGGAAGCAGTGGAGGCTAAAGGTGGTGTTAACTTGACTGAGTACTGCAAGCTCCAGCTCTGTAGTGGGTATTTAGCTCATATAACCTCATTCAAATTGCCTATGTGTAGCCAAAGTGAGGGCTAATTCACATGAACTCTGGCAGTGCATCCCCCCATTTATAGGGGTTGCTTTCCAGCTCCACAGCTAGATACTGAGCTAGGAGCTGGCTGCTCAGAACAGAATGAACATAGTACAGGTCTTTGAGGAGCTCACGCCTCATGGAGAGCAAGGGGAACACAGACAAGCTCTTGCAAACCAGCAGTGTTTGGGAGGTCTCTGAAACCGCACTGACATTCCTTCTGTTGCTAAAGGACTCCCAGAAATGAGAGAGGTGGGGGGTGGTGGGGGGTGGGGGGGGTTGTATTTCAATATACTGAAGATGCAGATTAAGTTCAGCCAAGGGAAAGCAAACACATGTGGAATGGAGTTTAGGTGTGAAGTCCTGGTGTGTGTGGGAGGGGTATAAACGGTGCTGGATTAGCCCAGCAACATGTGTGTGACAACATGAGAGAAGAGCCAGATGTGCTAGTCTTGATGTCTATGGGGATTGATTGTTTGTTTGTTTGCTTATTGGTAGGGGCTTGATTGACCACGTTCAGGGCTGTTCAGAAATCACATTGTCAGTGTGGACTTAACATGGTGCAAACTGCCTCCCCTAAACATATAAAGAGTTTCTTACCAGGCAAGAACATTCCAAGGGCTTAGAGGTCATCTTCCTAGAGCCAGGGCAAAGCCCCCAAGCTTGTCTTGGGCATGATTCGTCCTTGACTGCCTAGGTGGCCTAACCAGAGAGACAGAGTGTGGATATTGGTGACTCAAAGGATAGAGTGAGTCATCAGGATAGTGCCTCTGTCTCCTCTGGGAGCCACCGGAGGACGGGGAGCAGGGGACTGGCTTGTAGGCTTCATGCCACTCTTGAGGGTACTGAATATGAAAGAAAAGGCAGTGGTGATAGAGCAAGCCTGTGGTACCAGCACTTGGAAGGCTGAGGCAGGAGGATTCTTACGAATTTAAGGCTATCCTGAGCTATAGAGTCCTTGTCATGGGAAAACAATCAGGGGCTAAGTGGTTTAAAGTGCTGGCTGATTTTGAAGAGGACCCAGGTTTGAGTCCCAGCACCCACATGGCAGCTCTCTAACTCTACTTGGTGGGTAGGGAATCTGATGCCCTCTTCTGGCCACTGCAGGCACTGAACCCACATAGAGCACAGACATTCATGAAGGGGAAATACATCAAATAGAAGTAAATCTTTAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTAGGCATGGTGGGGCAGACCTATAATCCTAGTTACTTGAGATGGTGTAAGAGGATCACAAGTTCAAGGCCTGCCTGGACAGCTTTGCTCCCGTCTCAGAGTAAAAACATAAGCAGCTGATACATTGCTAAGAGATGAAGCCCTTAAGGCAGCAGTTTTCAGCTCATGGGTTGTGACCCCTTTAGGGGTTGAAGGAGCCTTTCACAGAGGTCACTTAAGTCCTGGAATAATCAGCTAGTTATATAATGATTCATAACAGTAGTAATATTACAGTTATGAAGTAACAACAAAAAATACTTTTATGGTTGGGGTTTACCAAAACTAGAGGAGCTGCATTAAAAGGTGGAAGTGTTAGGAAGGTTGAGAACCACTGTCTTAGGGTGTGTGCCTAGGAGTGGAGTAGCTATCCTGCATTTCCCTATTCCTTGACTTTAAAAAAAATTGACTTTATTATTTTTAACCATGTACATGCATTTGTGTGTATGGCACTCTTCCCTGCTGGGCTGTCCCTCCAGCCCCTAGCCCCAGCTTTTTGTGGAATCTGCACGCTAGTTTCCCAGAGTGGCTACACCACTAGACACTCCCACTAAGCGTGAAGGAGGACTCTGTTTCCTATTGGCTGTCATTTGTTTCCTTGATGATAGTTTTTCTGACTGGGATGAGATGGGATCTCAAAGTAGCTTTAACTGTTGTACCAGGCTCTTAATGACAGTTTTAATCCACCGGTAACGCAGATGACCTCTGATGGATCGCATGACAAAAACCCAAGGTTATGAAGAGGGGAGAGAGGCAGGTAGGGGTGAGAGAGATAATTAGGGAACAATGCACTGTAGACATGCTCGCAATGCTCAGGGGGCAAGCACACTTAGTATAGATTGCCTTTATTTAGTTTTTATTTTATTTTATTTTATTTTATTTTTTGTTTTTTTAGATTTATTTATTATATGTAAGTACACTGTAGCTGTCTTCAGACACTCCAGAAGAGGGCGTCAGATCTTGTTACAGATGGTTGTGAGCCACCATGTGGTTGCTGGGATTTGAACTTCAGACCTTCGGAAGAGCAGTCGGGTGCTCTTACCCACTGAGCCATCTCACCAGCCCTATTTAGTTTTTAAGTGTGCAGGTATTTTGCCTGCAAGTGGATCTGTGCGCCATGTGCTTGTCTGGAGTCCTTGGAGGCCAGGAGAGGCCACCAGACTCTCTGAGATTAGAGTTACAGACAGTTGTGAGCCACTATGTTTGTGCTAAGAATCAAACCCAGGTCCTATGGAAGAGCAGCAAGTACTCTTAGCCACAGACCCATCTCTTCAGTCCAACAGACTTCTATTTTCTTAAGTGAAACGAGGGCGGAGGGTATGGGTTAGCAGGACAGGACGAGACCTTCCCCATGATCTTATCTCTCCTCCCTCCCGGTCTCCTAG
Seq C2 exon
GGACCCCCGGCCTGGATACCATCTCAGACCCTTTCAGTTGGAGCTGGCTCCCTGGGCTGGGTAGAGATCAGGATGCCTGGCTCCCAGGAGAGCTAACCACCAAACCTTCTGCCAGTCTCACCTCCAGTGTGCCACAGAAACCCACAAAGGTTCCAGGGAAAGCTCCCAAGAGTACCAAGAAGTGGGTGACTAAAAATGCAAGGAGACCAACCACTCAGCCCCCTGGGATGCCAACCACCAAACATTCCAGGGCCCCAGGCACCCCAACCTCCCTACATCCAACAGCACGTACCTCTGAGTTACCAAAGAGACTGACCACTGAGGCTCCCCACAGGCAGACCTCACATACCACTGTAAGGCTGACCCCTAGGGTCCCCTGGGAGTGGACCTCAGAGCCTGTGGTGTCACAGTCCACTCAAGGTCCCCAAGAAGTGACCTCTGAGGCCACCACAACGGAAAACCCTCAGACCTCTTTGGAGCCATCGGGTGAGAACACCGAAGGCTCTCTGGAATCATCCCAAGATCCAGCTACCACCCCAACTGCTGGAGTCCCTGTGCCATCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035279-A430110N23Rik:NM_173008:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.280 A=NA C2=0.894
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0053013=SRCR=WD(100=92.5)

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000052126





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr19:55498198-55499815 
ALTERNATIVE
HsaINT0159403
(SSC5D)
Human
(hg19)
chr19:56009565-56011182 
ALTERNATIVE
HsaINT0159403
Rat
(rn6)
chr1:72452594-72455277 
ALTERNATIVE
RnoINT0143839
(Ssc5d)
Cow
(bosTau6)
chr18:62462581-62465108 
LOW PSI
BtaINT0141331
(SSC5D)
Chicken
(galGal4)
chrLGE64:651489-652232 
ALTERNATIVE
GgaINT1001361
([1])
Chicken
(galGal3)
chrE64_random:19467-19799 
GgaINT0000632
([2])
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
No suggested primer sequences

				
R: 
No suggested primer sequences

				
Band lengths: 

			

		

	





	
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"