Special

MmuINT0115696 @ mm9

Intron Retention

Gene
ENSMUSG00000027168 | Pax6
Description
paired box gene 6 [Source:MGI Symbol;Acc:MGI:97490]
Coordinates
chr2:105520404-105524115:+
Coord C1 exon
chr2:105520404-105520464
Coord A exon
chr2:105520465-105523984
Coord C2 exon
chr2:105523985-105524115
Length
3520 bp
Sequences
Splice sites
5' ss Seq
ACAGTAAGT
5' ss Score
9.49
3' ss Seq
TCTCCTCGTCCTTTCCTCAGGTC
3' ss Score
11.96
Exon sequences
Seq C1 exon
AGCCCCGTATTCGAGCCCCGTGGGATCCGGAGGCTGCCAACCAGCTCCAGCATGCAGAACA
Seq A exon
GTAAGTGTCTCAGGTCTTTCTCTGGACTGTTGGGCTGGAGGCGTGCGGGCCGTGGGTTAGGGGAGCGTACTGAGTCTTGGGTCTTGAGGAGTCCAAGCCACTGGGAGAGAGGGAGGGAGGTGGCCTGGGATCTATCCGGGCAACACTGAGTGAGCGCCAAGTAGCCCGCGAGGAAAAGCTGAGAGACTTTTTTTGCTCTGCTAGGTTCTAGAAGGGCAGAGGCTGGGGCCCTTCAAAACTACTCGCCCGAGTTTTTGAAGCTGCGGTAGAGAAACCCCACCCCCCCACCCCAATCCTGTAACTCATACCCCCTCCCCGCCCCTGCCCGGGCTCTGACCCCAGAGAGAGGGGCTGGGCCGAGCAGGGCGGGGCGAAGCAAAGGCTTCTCCTGAGAAGAGAAGGAGGCCCCTTTGGGCTTGGCCAAGACTGTGCGATTCCTCCGACCCTGAGGGGTGGGGGGGGCTTCCCTCCCTTAGTCAATCTCTGGCCAGCTCCTCCCCTCCCCACCCTAGCTACCGGCCTAGAAGAGAAGGGGAGTGGAGCACCCAGGGCTGGTACCCTAGTGGGGAAGTAAACCTCACAGGGTTTACTGGAAAGGAGGGTTTCCTGGATCTGGGAAGAGAGTGGAAGCTGTGCGGGTCAGGAATTGGATAAACCTTGCACTAGCAAGAGCAACTGAGTGGGTTCTGGATGACCCAGGCCCCTGGTGCCTTTGACCAGGCTCCTTTGTGCCTCTCTTCTTACCTTTGCCCAGGTCCTTTGGGCCCCAACCTTTGTACTCAGCCAATGGTTGCTGGTATGTGATAGAGTTGAGCCACTGAAGCTAGGCCTGGGTAAAGGTGGAGATCTACACTGGCTACAACTATGCTTGGGAGTATGGAGAGGCTTGGGTCTTCTGTGGTTGTGGACTGGCAGAAGCTTAGAGAGACCAGCAGCTCTTGATGCCACAGGACGAGGGGCGCTAAGATCAGGAAAGTGAGCAAAGGTGTATTTGCGGCTGCATTTGTGCAGAACCTGTCAGATCCGTACCCTGGAGCTTGGACTCCTTAGCCTTAGGTTTTCAGGTGGGCCGAGGCGCTCAGTCGCGACCGTTTGCCGCTACACTATGGCCTGGCTGGCAGGCCCAGAGGGGTACGGGTCGCGGGTTGGCCTGTAGGCTTTGTGCCGCTGGTTCCCGGGTGTGCGCGAGGCGCGGAGCATCCAAATTGACACCATATGTTTTCGTATTAGAAGCTTTGCGGTCGAATTCTAGGCGCATAATCATCGCCACTGGGCGAGAACGCCAGCAGTCCCCAGGGAAGGGACACAATGATTGAGGCTTAACCTCTAAAGGGGAATTTAGAGCTATGTTTCTTCGCTGCCATTTCGTTGCTGGCAGAGGCGCCCTGGCCCCGTGTCTTTCAGACCAGCAAATCCGGGCTGCAGCTGTGGAGGTGCTGGGCACGTTAATTTTGCAATAAGGGATAAGGAAGGTCTATGAGGCCTTGCACACTCTGGCATCCGTAGACTGGGAATTACCCTGGCTTTGCTTTTGAAAAGTTTCTCTTCATTTCTCTGGGAAGGCCTTTCTTTTTCTGGGAAGCTTTCTTTTGCCCAGAGATGAGCCTCCATACCTGCATGGTAACTGAGATCTAGAAAGCCAAGGTAGATGATAAGAGAAAATTTAGGAGAAACCGGAAGCGCAAGGTAGGCCTTGCCCTGCTTAAGAAGCCCTCTCTTGCAATGTGCAATGTCCACTCTTGCACTGGCCCGGGACAGCCAGAGCCCAGATCTCTAAATGCCTGTCACTTTTCATCGAATTGAGGCCCCGCCCCCCCTCCGTGAGCTCTAACCCTCCTCCAGCCCCAAGCCTCAAGCTACCCTGAAAACGCAGCTCCCCTCGAAGGGGAGCCGAGTGCAGTTCATTCTCGTCTGAGTGATCTACAAATAGGGACGGAAAGGGTCGTTTTATCACGGTCCCGTTTGTCGTGACGATGCAATTTCCCGGAGCGGAGCACTGTCACAAAGTGACAAGGCTGCCACAAGCGCCCCGACTGATCTTTTCAATTAGCCTTCCATGCATGATCCGGAGCGACTTCCGCCTATTTCCAGAAATTAAGCTCAAACTTGACGTGCAGCTAGTTTTATTTTAAAGACAAATGTCAGAGAGGCTCATCATATTCCCCCCTCGTCTATATTTGGAGCTTATTTATTGCTAAGAAGCACAGGCTCCTGGAGTCAATTTATCAGGAGGCTCCAAGGAGAAGAGAGGAGAAGAGAGGAGACAAGAGAGGAGCTGAGAACCACATTTCCTTGAGAGGGCTTCTGTCTAGACACGGGGCTGCAGGTTGGAGATGTCCGAGGAAGTGGAAAGAGGGGACTGGTTTTTTTTTTTTTTCTATTCCTGTGGTTTCCGAGGAGGGTAAAATCATAGACGCGCTCCTTCCCTCTCGCCCTAGTCTCTACGACAAGACAATGGGATGAGGTTGTGAGACAAGAGTGGAAGGAAGGACCGGTGGCACTGTGATGTGGTCTTTTTCTTTTTCTGGTTTGGGTTTCTGTTAATATTTGTGTCCTTGGCTGAGGGGGAGGGCGGAGTTCAGCAGCGGAAGTAAAGCGAGTAGTGGCGGGTGGGAAGGCTCCAGGCTTCTGAGCACCACTTGGGGCAGGCGGATCACTGTGTGAGTGGGATTTCCAACTCTATGCCTGCTGTGGATGCACGGATTGGGGGGTCACTAGCGACAAATTTATCTTTCTGACTTTTTTCTATTCCACACGCGTGCGCGCACCACACACACACACACACACACACACACACACACACACACACACACACACGGTGCTATGTGCTGTGCACCTCTGCCAGAGTTAAATCACCATGCTAAGGTTTTATAACGTTCTGTAGAGCAGTGCAGGACTTGGGATTTGCAGTGCTGTTCCAACACTGCAGAGACTTCTGTGTGGACTCTGTGGTGACACTCAGAGGTGATGTAGGGAGAAGAATTTAAGAGCTTGACTTTTGCCCCTTGTGGGTTCCAAGAAGGGCTGGGGGTGCGTATGAAGGGGGCAATAGACTCAGGGATGATGGTATTGGGTGGATATGTTCCTGTGTATTCTCCCAGGTCTGACAACAGTCCAGTGGGCAGGTTCAAATTGTATTTGAGGCTGGGCTGCCCAGTATACTGCATGGCTGGTGGTTCTGTTATTGGGTGTTTTTTTTTTGTTTGTTTGTTTTTTTGTTTTTTTGTTTTTTAAAACCAGGACCTAATTGCTGAGGTTCACACAGGTTGGCAGGGAGCTGAGGTTGCATTGTGGTCTTTTCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTCTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTTCTTCTCCTTCTTTTTCTTCTTCTTCTTCCTCTTCTTCTTCTCTGCTCTCCTCTCCTCGTCCTTTCCTCAG
Seq C2 exon
GTCACAGCGGAGTGAATCAGCTTGGTGGTGTCTTTGTCAACGGGCGGCCACTGCCGGACTCCACCCGGCAGAAGATCGTAGAGCTAGCTCACAGCGGGGCCCGGCCGTGCGACATTTCCCGAATTCTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027168-Pax6:NM_013627:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion (1st CDS intron)





No structure available

		

			
Features


			

				
Disorder rate (disopred):
  C1=0.727 A=NA C2=0.127
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0029213=PAX=PU(13.7=61.9)

							
A:
NA

							
C2:
PF0029213=PAX=PU(35.0=97.7)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000087870





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000016435, ENSMUSP00000039112, ENSMUSP00000087878, ENSMUSP00000097236, ENSMUSP00000106711, ENSMUSP00000106712, ENSMUSP00000106713, ENSMUSP00000106714, ENSMUSP00000106715, ENSMUSP00000106716, ENSMUSP00000119375, ENSMUSP00000129344
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr11:31802835-31806401 
ALTERNATIVE
HsaINT0120766
(PAX6)
Human
(hg19)
chr11:31824383-31827949 
ALTERNATIVE
HsaINT0120766
(PAX6)
Rat
(rn6)
chr3:95711678-95715193 
ALTERNATIVE
RnoINT0107702
(Pax6)
Cow
(bosTau6)
chr15:63369366-63372933 
LOW PSI
BtaINT0107937
(PAX6)
Chicken
(galGal4)
chr5:5227321-5228723 
LOW PSI
GgaINT0051382
(Pax-6)
Chicken
(galGal3)
chr5:5264234-5264557 
ALTERNATIVE
GgaINT0051382
(PAX6_CHICK)
Zebrafish
(danRer10)
chr25:14943314-14946103 
ALTERNATIVE
DreINT0110592
(pax6a)
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"