Special

MmuINT0080176 @ mm9

Intron Retention

Gene
ENSMUSG00000025950 | Idh1
Description
isocitrate dehydrogenase 1 (NADP+), soluble [Source:MGI Symbol;Acc:MGI:96413]
Coordinates
chr1:65215073-65217824:-
Coord C1 exon
chr1:65217533-65217824
Coord A exon
chr1:65215179-65217532
Coord C2 exon
chr1:65215073-65215178
Length
2354 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
GTATGTTCCCCTCTTTACAGTAC
3' ss Score
8.46
Exon sequences
Seq C1 exon
CTATGATTTAGGCATAGAGAATCGTGATGCCACCAATGACCAGGTCACCAAAGATGCTGCAGAGGCTATAAAGAAATACAACGTGGGCGTCAAGTGTGCTACCATCACCCCCGATGAGAAGAGGGTTGAAGAATTCAAGTTGAAACAAATGTGGAAATCCCCAAATGGCACCATCCGAAACATTCTGGGTGGCACTGTCTTCAGGGAAGCTATTATCTGCAAAAATATCCCCCGGCTAGTGACAGGCTGGGTAAAACCCATCATCATTGGCCGACATGCATATGGGGACCAA
Seq A exon
GTAAGTCATTTGAGTGAGCATAATTTGATTTTTTCCGTATTTATTTTTCACAGACCTTTAGCTCCAATATCTATGTTTGTTCTTTGGGCATCTACACCCTTAAGAGAGGTCCAACATATATTATGAATAAACTATAGATTTACATATGTTTAGGAAAGTGTAAAAATACAGATAAACTTTCAAATAAATACTCATCTTAACACATTTTCCCCAAATATCCTTTTGTTAAGTTATTCCATATGATATTGCCATTTTTGTATTAGTAAGACCATACGCTCAGATCAGTGGTTTTCAGTGCTGGTTGCGTGCTGGGATCCTTTCATGAGATGTTGCTGTTGGTGGTAATGGTGACGGTTTTATTGCATTGCTGCTTTGGTTTGTTTTGGGTTTTGTGTTTGTTTGTCTTTGTTTAGTTTCACTTCTAGTATTTGAGTCCCACCATAGAGCCAGTGAAATTTGGATTCTGTGAGGATCAGTTTCTTTTAAAAACCCCACCTGATTCTAATGTTCAGCCACATGAAGAACTGCCAGGTATTACATTAAGCTGATCACTTCGTGGATAAAGAGAAAGTCACCCAGTAGTTTCAATCAGAATGCTTGTGAAAGCATTCTGTACGGCTTGGAAGACAAATGTCATTCATTTCTGTACTGGTACAGTTAGTCTCATTGGTGAATTGGGCAGAAAAGTTGCCGACAACACAGATTACAAAGTCCTTAGAAACTGAGGTTTCAGGTTTTAATAGATAGTAGCTTATCTATCAAAAGGAGCCTTAAACAAAACGGAAGCCAGCTAACACCAAGAGGCTGCTATGGACTCATCCCTGGAAACCGTGGCCACAGCAGATGTCTCTGTTCCTGTGACAGGGTTACCGGCATGGTCCTTGATGTGTCCCATGGCTTTTGTTTCACCCTGCAGCTTTTGATAAGTCTTCATCCTGAGCATACTGCCTACTCAGTATTTTTTTTGTTTGTCCTTTTTATTGCTCAATTCTTGTTTCAGTCCCTTGAGGAGTGGATTCTATTTTCTTTTCATCTATTTTTTTTCTTTAAACTAGTGTGTTGACTCACGGTTTAATGTTCATAGATCTGTACAAAGTGTCTTAGGGAACATCGGTGCCTCAGCTGCCTTGGTAGAGAACTTTCGATGACAGCAGTGTTTGGTCTTTTCTGTTATCTGACCTTTTGCACACTGTGGTTAGGATTACTGTAAAGTGGCAGGTGCAGCTGGCACTGCCCATGTCCTGAAAAAGGTCCCGTGCAGCAGTGACCTGTGAGCACCTGGTGTGTCGGGGGCACATGTCTCCACTGTAGAGTGGCTCAGGCCCATCTTGGAGGTGTTAGTAACAGTGATCACCACAGAGGGAGACTGAACCCTGAAAATTTAACAGCACGTCACATCCCACGCCACTTGGCCAGGTGCATTCTTTCCTAGTTCCTTCATGAAAACCTGGTGCCAAAATCAGATGTGTTCAGCATTCGGCTTCTAGATTAGTGTCAGGACGTGACATAAGCTCTTCAGTCATCTTCAGCGGGAGAGCGATGCTGGCATCTATCTCACTCTACCTTTCCCTCTGTTGCCTCATTCTACCCGGCACCCCCCACGCCCATGTTGACATTTAAAACTTCTCCACCTGTGTCTGTCTTTACGCAGCTACAAGCTTCCTAAAGGGAAATGTCTGTGGTGGATAGTTTTGACTGCCATTTTAATAGTCTAGAATCACCTGAGAATGGAGTCTCAAGAAGGAATTGTCTTGATTTAGGTTGGCCTGTTGGCTTGTCTGTGAGGGAATTTTTTGAACCCAGTTAATCTAAGTGGGAAGGTCCTCCCAGAATGTGGGTGGCACCATTTCCCACCAACTGGGCCTTGGATTGGGTGAAAGAAAGAAAGCTGAGCATTAGCGTGTGTGTGCGTTGCTCTCCGTTCCTGACTGTGGTGGTGACATGGCCAGCTTCTGCGGCTGTGACTTCCCCACTGTGGTGGACTGTCATCACCTGGACCTGGCTGAAAGAAACCCTTTTTTTCCCAAATTGCTTCTGTTGGAGTGTTGTATCGCAGCAACAGAAACAAAGCTAAGACAGACAGAAGTTTATGATAGTCTCCATCCTCTCTGACTTAGTGCTCATAACGCTGCTGTCTATTCCACAGGCTTCTGATGAAGAAGATGTGCCATCTTCAACATGCACTGTTACCAACTAGTAGGCCTCCCTCATAGTGGGCCCCACCCACCCCAACCCTAGCTCTTAAAACCAAACAGCCTCAAGTTACACTGCTGGTGTTTGGCTCCAAAATCTATTTTTACCCCTTACAGTTTCTGGTGGGGTACTTTTCCTAATGTATGTTCCCCTCTTTACAG
Seq C2 exon
TACAGAGCAACTGATTTTGTTGTTCCTGGGCCTGGAAAAGTAGAGATAACCTACACACCAAAAGATGGAACTCAGAAGGTGACATACATGGTACATGACTTTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025950-Idh1:NM_010497:3
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:
PF0018015=Iso_dh=FE(24.7=100)

							
A:
NA

							
C2:
PF0018015=Iso_dh=FE(8.9=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000027087





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000095316, ENSMUSP00000117853, ENSMUSP00000127307
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr2:208245425-208248368 
LOW PSI
HsaINT0078768
(IDH1)
Human
(hg19)
chr2:209110149-209113092 
LOW PSI
HsaINT0078768
(IDH1)
Rat
(rn6)
chr9:71892405-71895685 
LOW PSI
RnoINT0072849
(Idh1)
Cow
(bosTau6)
chr2:96950415-96953057 
LOW PSI
BtaINT0074548
(IDH1)
Chicken
(galGal4)
chr7:13305880-13307385 
ALTERNATIVE
GgaINT0045536
(IDH1)
Chicken
(galGal3)
chr7:14893350-14894855 
ALTERNATIVE
GgaINT0045536
(F1NPG2_CHICK)
Zebrafish
(danRer10)
chr9:28305375-28312246 
LOW PSI
DreINT0080024
(idh1)
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"