Special

MmuINT0063796 @ mm9

Intron Retention

Gene
ENSMUSG00000026835 | Fcnb
Description
ficolin B [Source:MGI Symbol;Acc:MGI:1341158]
Coordinates
chr2:27935421-27936141:-
Coord C1 exon
chr2:27936106-27936141
Coord A exon
chr2:27935454-27936105
Coord C2 exon
chr2:27935421-27935453
Length
652 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
TCTTTTCTCTCCCCACACAGGAG
3' ss Score
10.63
Exon sequences
Seq C1 exon
GAAACCAAGGAGAAAAAGGAATACGTGGAGAAAAAG
Seq A exon
GTGAGTCTCTGTATTGTGTCTTGGGGAGGTGTGCGCAGCTCTGTGTAGAGAAATTTCTTCCATGCCCAGACATACCTAGGGAGAGGGGCCTCAGCCTGAGGTCCTATTGTCTGGGCAGTGGGTAGAGTAGGTGGCAGGGGCCAGGATATTCAAACCCTGAGGCTCACATTCTAGAACCTGTAAGTGGTCTGTCTGAGTGGTTAGCAAAGCTGACTTGAATTCTTTTCTAATTGAAGCTTATTTTTTTTAATTATGAAACTTTAAGACATAATCTCATGCTTTCTTTATAATCAAGGGGGCTCTACCTGAGTTTTGAATGCCAAGGACATCCCTCACCCACAAGGCCTCCTGGGTAGACACTTTGGCAGAGCATAGTCTAAGCGCACTTGGAGCAAAGCATTCTGGGAGCAAAGAGGGGCTACCCACTCTTTTTGGTACACAAGGCCTCAAGATGGGTGCTGTCAGGGACAGTGCTTACCACAGCTGTGGAGGGAAAGCCAGGCAGCTGGAATGTGTACTCCAGGAGGAGGGCCTAGGCGAGTCCTGGAATTATTCAGCTCAATTATCATGTATTTGCAGGGTTGTAGGGACCAATAGGGATGTAGTTGATGACCTCACACTTATGACCAGTGTCTTTTCTCTCCCCACACAG
Seq C2 exon
GAGACTCTGGGCCCTCTCAGTCATGTGCTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026835-Fcnb:NM_010190:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=1.000 A=NA C2=0.944
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0139113=Collagen=PD(4.5=10.0),PF0139113=Collagen=PU(53.3=80.0)

							
A:
NA

							
C2:
PF0139113=Collagen=PD(13.1=66.7),PF0014713=Fibrinogen_C=PU(0.1=0.0)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000028179





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000112625, ENSMUSP00000119098
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr9:134913614-134914384 
LOW PSI
HsaINT0063312
(FCN1)
Human
(hg19)
chr9:137805460-137806230 
LOW PSI
HsaINT0063312
(FCN1)
Rat
(rn6)
chr3:6621220-6621817 
LOW PSI
RnoINT0060322
(Fcnb)
Cow
(bosTau6)
chr11:106828074-106828269 
LOW PSI
BtaINT0061828
(FCN2)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
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






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