Special

MmuINT0060125 @ mm9

Intron Retention

Gene
ENSMUSG00000026368 | F13b
Description
coagulation factor XIII, beta subunit [Source:MGI Symbol;Acc:MGI:88379]
Coordinates
chr1:141400338-141403528:+
Coord C1 exon
chr1:141400338-141400538
Coord A exon
chr1:141400539-141403342
Coord C2 exon
chr1:141403343-141403528
Length
2804 bp
Sequences
Splice sites
5' ss Seq
ACAGTAAGT
5' ss Score
9.49
3' ss Seq
CATTTACCTTTACAATACAGAGA
3' ss Score
3.99
Exon sequences
Seq C1 exon
AGAAACAGTGTGATTTTCCTACCGTGGAAAATGGAAGGATTGCCCAATATTATTATACGTTTAAAAGCTTTTACTTCCCCATGAGCGTAGACAAAAAACTATCATTCTTCTGTTTGGCTGGCTATGCAACCGAAAGTGGGAAGCAAGAAGAGCAAATCAGGTGCACAGCAGAAGGCTGGTCTCCAAACCCAAGGTGCTACA
Seq A exon
GTAAGTCAGTGCGTGCTGTCAGCACTCGTTCCCGAGAAAAGAATGTTTATTTATATTAAATATGATCACTGATTAAACTTTATATACATAAATAACAAGAAAAGTATGGTTATAAAATACCCTACATAAAATTCTGTAAATGAGCTGCTATTAACAATAAGTCGTTTTATTTGGTTTTAATAGCACTTGGGAAGAAATACCAAAAATGTACACGTAAGCCGGGCGGTGGTGGCGCACGCCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGGTGGATTTCTGAGTTCGAGGCCAGTGTGGTCTACAAAGTGAGTTCCAGGACAGCCAGGGGGCTATACAGAGAAACCCTGTCTCGAAAAACAAAACAAAAACAAACAAACAAAAAAGTACACCTAAGTAGCTAAAAATGTACAGAATAAGAGATTCTTATTTTTACAGAATGAGCCTTCCTAATGTTTATTTGTGTATATTTGTCACTCATTTGTGTGGCCACTTTTCTTTCTCCTACCCACTGAAAGCTGCAGGTGGCTTCCCTCTACTTATGTGAAGTGTCTTGAGTGCCCTGAATTCCTGTTTTCTAGAGTAAGGGGCTTCTATTAAGTTCTTTCTATTTGGAAGAGGCATTTTGGCATGGTAGTAGTTGTGGCTTATATACCTAGTAAACAGAACTGCATAAGATAACCATTCATTCTGTGATTTCAGGACAGACCAGAGTAACTTATAACAGAGTTATAAATGTCATTATAACATCATAGAAAGAAGTCATGTTCCTTGAATTTACTATCTTAAGAGACAGAAAATTGCAGCGATTGGCACGGGAGCATAATCATTAAGACAGAACCTCTGCAGTCAGCTGACTGCGTGTGGTCTCATCTCCATCCTTGTGAAAGTGACATGAAAATTCCTAGCCTGTTTCTTTTCTTTTTCTTTTTAAAAATTCTTTATTATTTTTTAATAGTCCAGACTTTATCCCTCTCCTGGTCTACTCTTTGTTCCACATCTCATACTTCCTCCGCTCACCACGGTTTCCAAGAGGATGTCACCATTTCCCCCTCACCCCACCAGACCTCCCCACTCCCTGGAGCCCCAAGTCTCTTGAGGGTTAGATGCATCTTCTCTGACTGAGTCCAGACCCAGCAGTCCTCTGCTGTATATGTGTTGGGGGCCTCATATCACCTGCTGGATACTGCCTGGTTGGTGGCTCAGTGTCTGAGAGATCTCGGGGGAGTCCAGGTTAGTTGAGATTGCTGGTCTTCCTATGGAGTTGCCCTCCTCCTCAGCTTCTTCCAGCTTTCCCTTAATTCAACCACATGGGTCAGCAGCTTCTGTCCATTGGTTGGGTAAGTATCTGCATTTGACTCTTTCAGCTGCTTGTTGGGTCTTTCAGAGAGCACTCATGATAGGCCCCTGTTTGTAAGTACACCATAGCCTCAGTAATTGTGTCAGCCCCTGAGGCCTCCCCCTGAGATGGATCTCAATTTGGGTCTGTTACTGGACCTCCTTTTCCTCAGGCTCTTCTCCATTTTTGTCCCTGCAGTTCTTTCAGACGGGAGCATTTCTGGGTCATAGTTTTTGACTGTGGGATGGCAATCCCATCCCTCCACTTGATGCCCTGTCTTTCTGCTGGAGGTGAAGTCTACAAGTTCCCTCTCCCCACTAGAGCATTTCATCTATGTTTCTTATGCACAAAATGAAGTAGGGACTTCCTTTGAGAAAGTCTCAGACCTCTCAGTTCTCTGGTGCATTCTAGAGGGCCACCCCACCTCCTTGTCTCCTGAGGTTGCCTGTTTCAATTCTTTCTGCTGGCCTTCAGGACTTCAGTCCTATTCTTCCCCCACCAATACCTGATTATATCCCCCTTTTCTGCTCCCTATTCCATTTCCCACCTAAGTCCCTCCATCCCTCCCCCATCATGTGATTGCTTTCTTCTTTCTTCTTCCTCCCAAGTAGGATTAGGCATCTTCACTTGGGCCCTTTGGTTTGTTAACCTTGAGTTCTATGGATTGAATCTTGGGAATTCTGTACACTTTTTTCTTTGTTTGTTTTGTTTTGTTTTGTTTTTATAGCCCTGGCTGTCCTGGAACTCACTTTGTAGGCTAGGCTGGCCTCAAACTCAGAAATCCGCCTGCCTCTGCCTCCTGAGTGCTGGGATTAAAGGTGTGTGCCACCATGCCTGGCTCTTCTGTATACTTTTTAAGTCTGTTTCTTATGCACAAAATGAAGTAGGGACTTTGACATAAGAGTGCCACACAGCTAGTACTAAATGTTTTTGTGATAATATAAACATATTGGGCAAATTTCTAAACCCTTCTAGATGGCTTTCTCAAAAAGTTCCAATAATATAGCTTATAAGAATTATAATGTGAAGGTTATTTTCTTATGGGTACCTTACTGTTGCACATATTTATCAAAAACTTGATTGTAGACTCCAAGGGTTTCAGGCGCTTATGTATGTCCATATACACTGACTCTTGGATCCCAAAATATTTTCTAGGATAATGAATGAATGAAGGTTTTACAGTAAGTTACTTTAGTATTATTTAATGATTTGTTAAGGATGTCTTTGATTACATTATAAAACAATGGAATAATATGTCAATAGGATAAGAAGAAATTGGCTTTTTTGTGATTACTGGCAACTAGTGAAAAGCTAAAAGATGTGGGAAGAGTAGGAGTGTCTAAGGAAACTAAAATTTGTAGATGCAAAAACAGTTTAGTGAAGTACATAATGTGAATTTTACTATGAAACAGACAGACATGGTAATTTCATCGTGAAACAAAGCACATTTACCTTTACAATACAG
Seq C2 exon
AGAAATGTCTGAAGCCTGACCTAAGGAATGGCTACGTCTCCAATGACAAAGTACTGTACAAACTTCAAGAGAGGATGAGCTACGGTTGCTCTTCAGGATACAAAACCACTGGGGGAAAGGACGAGGAGGTGGTCCACTGTCTTTCTGCAGGGTGGTCTTCTCAACCGTCCTGCAGGAAAGAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026368-F13b:NM_031164:2
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:
PF0008415=Sushi=WD(100=92.6)

							
A:
NA

							
C2:
PF0008415=Sushi=WD(100=88.9)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000027615





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:197061970-197062856 
LOW PSI
HsaINT0059150
(F13B)
Human
(hg19)
chr1:197031100-197031986 
LOW PSI
HsaINT0059150
(F13B)
Rat
(rn6)
chr13:56601850-56603517 
LOW PSI
RnoINT0057501
(F13b)
Cow
(bosTau6)
chr16:77850585-77852740 
LOW PSI
BtaINT0058905
(F13B)
Chicken
(galGal4)
chr8:2632976-2633437 
ALTERNATIVE
GgaINT0035675
(F13B)
Chicken
(galGal3)
chr8:2659267-2659728 
ALTERNATIVE
GgaINT0035675
(F13B)
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"