Special

MmuINT0077493 @ mm9

Intron Retention

Gene
ENSMUSG00000006611 | Hfe
Description
hemochromatosis [Source:MGI Symbol;Acc:MGI:109191]
Coordinates
chr13:23799897-23802680:-
Coord C1 exon
chr13:23802496-23802680
Coord A exon
chr13:23800161-23802495
Coord C2 exon
chr13:23799897-23800160
Length
2335 bp
Sequences
Splice sites
5' ss Seq
CGCGTGAGT
5' ss Score
8.4
3' ss Seq
ATGTCTGCTGACTTCTCCAGGTT
3' ss Score
9.13
Exon sequences
Seq C1 exon
CTGAGAGGTCTGGAACCTCAGCAATGGCTACAGGGTGACTTCTTGGATCCTCCACGTTTCCAGATCCTAGTGAAGACCGGTGGACCCAGCTGAGGACATGAGCCTATCAGCTGGGCTCCCTGTGCGGCCGCTGCTGCTGCTGCTGCTACTGCTGTGGTCCGTGGCCCCGCAGGCACTGCCACCGC
Seq A exon
GTGAGTGCGGGAGGAAAAAGGTGGGGGTGTGGGAAGCAAAACCGAAAGTGGCTTCCTTGGCGCCTGGTGTTTCTCTCTTCGAAGGCGAACTACTTTCTCTCTGATCTCTTCCAGCTCTCAGCTTGCAGACCCCCAGAGGGAACACCTGCCACACCACTAGCAGCCTAGGGCACCTCTGCCCCTGCTCTGTCAGAGTGTTACTAGCGAGGAGTCACGTTGGCTTAGCTGAGCCTGGGTCTCCAATCTCTGCTTTAGTGTTTATATTTTGGACTGTGTTACCCTACCTCCCTAACTAACCGGAGATCTGAAATTTCTCACCAAGAGTGACCAACGTCGTCCTTTGGCATTTTCTCTTCAGGGTGCTGGGAAAGGGGCTGAGATGTTTTCCTTGTGAGCACTAGGGGTGCTGGGTCGCACTCCCACTGTGTTAATTTTGTGTGTGTATGTGTGAGACAAAGCAAAGGTCACTTGGAGCCAGGGGCGGGGGGGGGGGGGGGAGCGGGGCGGCGGAGGTCAGGGTCGGGGGTTAGACCTCTCCTCACTCTTGACAATTGTTCTTTCATCATTTCAAATGGATGTAATACTGTAACCAAACATTTTAGGGCAGAAGGCCAGGACTCTGGCAGCCCTTGTGGTTGGCAACAGTGTTCCAATTAAAAAGCCCAGTAATAACGAAACAGTTCTATTCAGTGTTGTCATACTGGGAAGATCAAGTGACCCAGCAAAAGAGTCCATTTTCAGGGTCCTGCCATGACATTTAGATTTAAAGAGAAAGGAACGGATTTCTCTGGATAGACCGCCCTGGAGCCTGCATCCGAGTCCATAAATTGTTCATCTGTTTGTTGTTAGGGCACAATGGAGCAATTTCTTCTGCCCCAACGTGCTGCCTAGACGTCATAGATAATTGCTTTAGTGTGATGGGGGTGAGAAACAGGGTGACTCCTGTTCTGAGGCGTTGATGGTATTCCTGTAATCCAAGGGAACTTCAGGTTTGGGACAATATCTTTGTGTCTTCAGCCTTGGAAGAGGATAAGAGGTTAAGAGAGGAGAGTCCAGCAGGAAGGAGTCTGATGAGACACAGAAGGCAAGCTGAGCACCAGGCCTCCATCCCTTTCACTCACTGTGGGTGATAGGCTGGTGCCCTCTGTCAGTCACCTTCCGAGCACCTGGCGCTCACCCAGTGGAGCTCAACTTTCCTAATGTTGCGACCCTTTAGTACAGTTTCTCATGCTGCGGTGACCCTAACCATAAAATTATTTTTGTTGCTATTTTATGAGTTATTTTGCTCTTATGAATTGTAATGTAAATATTTGATATGCAGGGTATCTGAGAGATGTGACCCCAAGGGTAGACCACTGCTCTACAGGATCTTGTTCAGCAGGGCTTTGCTGATTTGCAAATTAAAAAAGAATTAACAGGCCGTTTCTAAAGGATACCAATGTGCTGCTTAATGCACTTTAATAACACTAGGATCTGTGATCCTTTTTGACTAATCATGCCCTGGGAAACAGCAGTTACTGCTAGTTAACTAGCTCAGATCTTTCCTCAGGTCACAAAGAATATACACTTAAATCTGATCTTTTTTTTTTCTCCTAGAAATTCTGAGGTGCGGTGTCTCCCTGTGTAGTTCAGACTGGGCTACAACTCACCTATGCATATCAGGATGGACTCAAAGCTGAGACAATCCTCCTGCCTCAGTCTCCAGAGTATTAGGGTCAGAAGTGTGAGCCACTACTCCAAGGCAACAAACATTTGTGACACGCTGGCCCCGTGCCAGGTGCCATTTTAAGCACTAAAGCTGTGCCCTTGAGCAACCTTGTTCTGGAATCGAGGGAAAGTAATGGGAAAAAACCCATGCTGAGAGTGGCTGTCAGCTCCCTTTCCTGGAAGTCCTCTGTTTGCTGACAGGTTGTCCTGAGTTATGTGTCAGGACACTCACCAGCATTTTTTAGCCAACATCTGCACTTGATAATGTTCAGAGATGGAAGTGGAGAAAGCCCAGTACCTCCAATCCTTAGGACTTTCATCTTAATGGATTAAACACCAACTCTTAGCTTAGCCTACATAGCTAGAGAAACCCAAACACTTTCCAGAGTCTGTGTCTAAGGTGGGGTGGGGAGGATAACCTATCCACTCAAATAGAGAACATCAAGATGGTGAACAGAATAAGAGCGAACAGCCAGAGCAGCCAGGGCTGTGCAGGGAAGAGAACTAACTGTGTCACTCCACAGGGGAGGACTCACTCTCTGGCAGCAGGAGGTAACCCAGGGCTGTAGGGACCTCTGCATCCTGATTGGGCTGGCTGCCCATTCTGAATGTCTGCTGACTTCTCCAG
Seq C2 exon
GTTCACATTCTCTAAGATACCTCTTCATGGGTGCCTCAGAGCCAGACCTCGGGCTGCCTTTGTTTGAGGCTAGGGGCTATGTGGATGACCAGCTCTTTGTGTCCTACAATCATGAGAGTCGCCGTGCTGAGCCCAGGGCCCCGTGGATCTTGGAGCAAACCTCAAGCCAGCTGTGGCTGCATCTGAGTCAGAGCCTGAAAGGGTGGGACTACATGTTCATAGTAGACTTCTGGACCATCATGGGCAACTATAACCACAGTAAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000006611-Hfe:NM_010424:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion (1st CDS intron)





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0012913=MHC_I=PU(0.1=0.0)

							
A:
NA

							
C2:
PF0012913=MHC_I=PU(47.6=98.9)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000089298





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000089298f6122A
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr6:26087517-26090840 
ALTERNATIVE
HsaINT0075829
(HFE)
Human
(hg19)
chr6:26087745-26091068 
ALTERNATIVE
HsaINT0075829
(HFE)
Rat
(rn6)
chr17:43661447-43665689 
ALTERNATIVE
RnoINT0070508
(Hfe)
Cow
(bosTau6)
chr23:31614377-31617684 
ALTERNATIVE
BtaINT0071803
(HFE)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
chr16:282272-287828 
GgaINT0123450
(F1NFX9_CHICK)
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"