Special

MmuINT0090909 @ mm9

Intron Retention

Gene
ENSMUSG00000026890 | Lhx6
Description
LIM homeobox protein 6 [Source:MGI Symbol;Acc:MGI:1306803]
Coordinates
chr2:35947126-35949953:-
Coord C1 exon
chr2:35949733-35949953
Coord A exon
chr2:35947227-35949732
Coord C2 exon
chr2:35947126-35947226
Length
2506 bp
Sequences
Splice sites
5' ss Seq
ACGGTACCC
5' ss Score
6.32
3' ss Seq
CCGCTTCTGTCGCCCCCCAGGGA
3' ss Score
11.16
Exon sequences
Seq C1 exon
CCGATTTGGAACCAAGTGCGCCCGGTGCGGCAGACAAATCTATGCCAGTGACTGGGTGCGGCGCGCACGCGGCAATGCCTACCACCTGGCATGTTTCGCCTGCTTTTCCTGCAAGCGCCAGCTATCCACCGGTGAGGAATTCGGCCTCGTTGAGGAGAAGGTGCTTTGCCGCATCCATTACGACACCATGATCGAGAACCTCAAGAGGGCCGCCGAGAACG
Seq A exon
GTACCCAATCCGCCCAACCCAGCACCTAATCCCAGTCCTTTCCCAGGTTCCCTAGCACCCAAGTTCGTGGTCCGCACAATTGTACTGGCTGAGCGGTCCCTGGAACACCTGGAGGCAGCATCGGGGTGGGGCTACACGTGGAACATGCGCTCTGGCTCCATCATTTGCATGGGCTACTAAGTCACTACCTAACCTTGTAACAATCTCACATGGCTCCCAGCGGCCTACAAGCTCCGCTAACCCCCACCCCATTCTGCCTGCCAGCTGCCTGAGCAGTCCAAGAGATAAGATGTAGCCCACATTCTTCCCACTTCCTTATGGGCCACACAAAGCCAGAGGCTAAGGGTGGGTCATCTTAGATCTGAGGTTCTGAACATAAAAATTTTAAAGGGACCAGTCCCCCGAGTCTTGGAGACGCGGCTTTACCATACAATGTCAGCAAATGAGGATTTCTTTTTCTCATTGGGCCTCCCTCTTCCCGTCCTACATCTGCTCATGATACCTAGATGTTGGACTAGAATGTTCCTTGAATCTCCTCTGGCTCTGGCACGATTTTCTCAAGACATTTATCCTAGGGTCTTGGTGAAATTCTTCAATGCTGTGCGCAGTGGGGGTGAGAGGGGCGGAGTGGTGTAGAAGAGGAGGTGAGGGAATCCGAATCCTAAAAGGGACTGGAGCTGTGGGCAGAGGCAGCAACCCTTCCCATGGTTCTGCTGTCAGGATCTATGGATACTGCTAACTTCCCTGGAATGTGGTTGGATGTATAAAGCCTTACAAGCCCTTTTTAGGAGCTTTGTGCTATATCCCTATTAGTAGCTAGAAAAGCGGCAGAGGTTATTTGCAGTACGTACCTTGTCAAAGCTTACATCTAGTAGGTCTGTTCGGAAGCTCAGTATCTTACCTATCATAATACAGAACACTACACACAGCATGCTATATCCCCTTGGCTTCAGGAGGCTCCGGGGATGTGGTTGCCTCTGAGTTTCATTTTTCCATCTAGAAAACTAGGCACACTAACTGTTATCCTGCCTGCTTTTCTAGGAATATTAATGTCACACAGCTTCTCCCTACCTCAATTTCTAGGCATCAGTGGGAGGGCTAGTAAGGAGCCAAAAACGTGTTAGTGGGTATGTCCTCACCAAGGTCATCATTTTCTCCTGCTAGGATCAGTAGCTAAGTAGGGAGCAACTGAACTTGGTGCACGCTGAAGTTGCCTGTGTTGCTTGGCAAGTCAGCAGAAGAGGAGGGCTCAGGAGTCAGAGCTTCCTCTCCACCTTGGTTAATCAGTAAACCACAGCCTCCTTTCACTCCTGGACCACCCAGGGCCAACATTAGCCATGGCCTTGCCAAAGACAGCCTATTCAGGGAAACTTGAACGCCTGGGGCTTCAGGTCACTGACCGTCATCAGCATTAGCTATTGCTTTTCTTTTAAACAAAAACAACACACACACACACACACACACACACACACACACACACACACGTTCATTATAGAAAAATGAGGAGGCATGGTTAAAGAAAAAGTTGAAATTATTCTGCATGTCATTATCTCCCTGTTTACATTTCTATTTTTCCCTTTGTACATGTAGTTTTCCCCCCTTTCTGCATAGTTTTCCCCCCTAATTAAAACATTACAGCAAATTGTAAGCAGTAGTTATCCCTGAGTGGTGGAGTCACTGGTGACTTTCTCCCTCTTTGTGCTTGTCAGAATCGTCAGGCTTTTGGTAAGAACAGTGTATTATTTTTGCATTCAGGAAAAACGAACTGCTAAAATGGGAATATATTTGCTGGATTACAATCATAGGAACCAAAGTATTATAAAATGGACAGGCAACACTTAAGATATATCCCAGTCAATAAAATATACTTTGGAGAAGGTAAAATGCAATTGTTTTAAATACGTCAAACGTTGCTGAGGTGGCACACCTTTAGTCCCAGCCCTCTGGAAGCAGAGTCAGGTGGATCTACGAGTCAAAGGCCAATCTTATCTACATACAGAAAGAGTTCCAGGACAGCCGGGGCTACACAGAAAAACACTGTCCCCAAAAAAATAAAAAAGGGGGGGGGGAAGTTATAGCTTCAGCAACCCATGCTGTTGTTGCTGCTGCAGCTTCTTTTCCTCCTCCCCCTTCCTCTCCCTTCTCTTCCTCCTCCTCCCTCTCCCCTCGCAGCCCTCCTCTCTCTTTTTAAATCTCCACGGTGATTTCCCCCCAGCTCAGCTAAGACAGAGGTTAGGGTCAGCTCGGTTCCAGTTCAGAGGCAGAGCATTTGGGGTTCCCAGTCAGGAGCTTTCCTCTCTCCGCTCCTTAGTTTCCTCTCTTTAAAAAAAAATGGGTGATAGTATAGAAAGGAAGCTCTGGGCTCGGGGACCAGGGCCCTGGGATCCCCGCTCCCAGCCACTCGCTCCTGACCCTTCCAGGGACAAGCTCCCCCCCACCCCGTCCTTTCCAGGCTGCCACTAGAAGAGATGGGGACGCGTGGTCAGCCGCTTCTGTCGCCCCCCAG
Seq C2 exon
GGAACGGTCTCACGCTGGAGGGGGCAGTGCCCTCGGAACAGGACAGTCAGCCCAAGCCAGCCAAGCGCGCGCGGACGTCCTTCACCGCAGAGCAATTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026890-Lhx6:NM_001083127:4
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=0.824
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0041217=LIM=PD(3.4=2.7),PF0041217=LIM=WD(100=77.3)

							
A:
NA

							
C2:
PF0004624=Homeobox=PU(21.1=35.3)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000108584





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000108584f2023A, ENSMUSP00000108585, ENSMUSP00000108587, ENSMUSP00000108590, ENSMUSP00000108591, ENSMUSP00000135693
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr9:122214384-122217067 
ALTERNATIVE
HsaINT0091738
(LHX6)
Human
(hg19)
chr9:124976663-124979346 
ALTERNATIVE
HsaINT0091738
(LHX6)
Rat
(rn6)
chr3:15419780-15422310 
ALTERNATIVE
RnoINT0085185
(Lhx6)
Cow
(bosTau6)
chr11:93078722-93081200 
ALTERNATIVE
BtaINT0085454
(LHX6)
Chicken
(galGal4)
chr17:8725895-8727873 
ALTERNATIVE
GgaINT0124505
(LHX6)
Chicken
(galGal3)
chr17:9434138-9436116 
ALTERNATIVE
GgaINT0124505
(F1NLU0_CHICK)
Zebrafish
(danRer10)
chr10:9555274-9555354 
LOW PSI
DreINT0089070
(lhx6)
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"