Special

MmuINT0134149 @ mm9

Intron Retention

Gene
ENSMUSG00000026482 | Rgl1
Description
ral guanine nucleotide dissociation stimulator,-like 1 [Source:MGI Symbol;Acc:MGI:107484]
Coordinates
chr1:154375403-154378725:-
Coord C1 exon
chr1:154378636-154378725
Coord A exon
chr1:154375590-154378635
Coord C2 exon
chr1:154375403-154375589
Length
3046 bp
Sequences
Splice sites
5' ss Seq
CCTGTGAGT
5' ss Score
7.21
3' ss Seq
TGGCATTCTGTCTCCTGCAGGCT
3' ss Score
10.66
Exon sequences
Seq C1 exon
CTACGCCCTCTCGTGTGAGATTGAAGCCGCTGCCGACGCCAACACCACTTCCCCTAAGCCTCGGAAAAGCATGGTGAAGAGGCTGAGCCT
Seq A exon
GTGAGTCCCCTGTCAGGGGTCCTGTCAGAGAGGGGAGAGGACCGTGCATTCAGTAGCTCTGAATGCTCACTTGAAGGGTGCATTTTCTGTCCTGAACACAAACAACTCATTAGATCCATCCGTTCCTGTCCTGGACACGCCAGCAACGGTTCTGCAGTCATCTTACATAGCCTAGTGATCCTTTGAACAGTAGATTATGTCACTTTTTAAAACTCCCAATGGTTTTATTTTGAAATAAAGTCTCAACTCTAGGTCCTAGTTTACAAGGCCTTATGGGGTCTACTCCCAACCTTCCCTCGCTTACAACAGTTCACCAAGATTCACCACACCAGCCTTCTAGCCAACCTTAAACACAGCAGGCTGTTGCCTGCTCAGGGCCTTCACACTAGCCCTTCCTGTGGCTAGCAGTGGTCTTTTTTCCTAGCCAGCTTCAGATGTTAGCATGAATGTTTTCTCCTAAGAGATCTTCCCGACGGTGAGGTCTCCTCTGGTTATTCTCATTCCTATCGGATGCTTCTCACAGTCTAGAGGAAGCAGTGTTATAATAGAAGCATTCACTGCTCATCATGTGTAGCAGACGAGGAGGCCTTCTGTGGTCAACTTTGAAAGACCTCACTCCATTTGGATAACATCCAGAGGCCTTAGACCATCTATAGGACCCCACTGCCCGGAAGCATTAGTACCACCCTGTCGGCCTGGCTCCACCTCTCTGTCCCCTCTTTCTGGTTCACTCCACACTTTGTACTTCAGCTACCTCAAGACCTCCCCACACACCAGGCAGTCGTTTTTAGTTGCTTTTGTTCTACTAACTTTTCTCCCAAAGAGCCACCTGGCTCACTTTCTCACTTCCTTTGGGTGTTTGTAGAAATGTCATCTTGACAAGCGTGTTGGACACTGTAGCCCTTCATCATATCTGTCCTTGACACCCTCCCTTGATTGTCTTCTGTCTTAATTTTTTTTCCATCGCATTATCTTCTTCCGCCATACTGTATACTGTATGCGTCTGTATTGAACTTAAAGTCCATGTAGAGAAGCCTCGGTTGTATTTGTCGCTCAGTTCACAGGGTCTAAATGCTGCCCCCACCCCCAGTAAGTGATTAGTGAGTATGTTTAGAATAGATAAATTGAGCTGAGAGCTAGGACTGTTATAAGAACAATGCATATGTTTATAAAATCTACAACATGATCTAGGAACCAGTTTCTATAATTAGCTCCAATCACAGAGCCCAGGAAACCAAAGTATGGAGAAGGTGGTTCAAGCGCTTCTAATAGAGGACCAGAAAGCATATTCAGATTCAGCTCAGAGTTAAGCTTACAGAAGTTTTACTGTACAGTAAAATTACATTCTGAAGGAAGAGAGAGATGGAAGGTCTAAGGGAGAGGAGAGAGAACCACAGGAGAGGAAAAGGGGACTAGAAAAGGTACTCATAAGCCGGGCATGGTGGCGCATGCCTTTAATCCCAGCACTCGGGAGGCAGAGGCAGAGGCAGGCGGATTTCTGAGTTCGAGGCCAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCCAGGGCTATACAGAGAAACCCTGTCTCGGGGGAAAAAAAAAAAGGCAATCATGTGATGCAGGCTTTGATTGTATCTGTGTCTGTAGCAGCAGCTTGAGAGGACCTACTCTGCTCCATAAAGCTGACCATTAGAATGTGAGGGACCAAAGACGGCAGGCGTTACTTCTAGGACGCTGCGCTCTCACACAGATCCCGGCACTTACACACCTGAGATTGATCTGGGTGATGTTCCCTGCACTTGCTAGGGGCAAACAGGGCAGTCTTTAGGGACCATTGGCCAGTTCTCCATGGTCAAGTAATTTCCCCCGGCACTTGCCAAGCCCACCCGCAGACTTCTCGGTTGTCGTGAGAGTTTGTGATGTGAGAGTTTGTGATGTGAGAGTGCAGTGCCTCCTGGATCCGTGAGCTGTTATGGCTCAGCAGTTCTGGAATCTTCTCAGGCACTGCATCTGTCTGGTCCCTTTGCCAGGCTCAGTGTCTCCTGGCTCTGCTCTTACATGTGCACAGGGCTTTCTGTGTTTTCATTATACCCCTAACCTCTGTTCCCATAGCTTCATGTCCATCAGGACCATCATGCATAGACACATTATTTCTTCTGTATTAATTCAGGCCAGGCCAGGCAGACGTCCCTGTTGTCTCCTGTGTCTGTGGGAAGATACTTTTCTAACCTGTCTCCTTACTGCGGGTAAAGCCCTTTGAGTGCCTGGCTTTATATAGATTAGGTTCTCTCAACCTTACTTTAGTAAGCAGAACCGTCATTTCACAGTGCTGTGTATGTGTTAACTTCATACACATGAATCAGTTCATACTGAAAGCATATATGGAAATATCAATGGAACCCCATTATTACGTATAATTAAATTGTGCTAGTGGTTTTTTTTTTTTTTTAACAATGACTGTTTTGCCAACATTCATTCCTTCTGTTTCCCAACCAGAGCATCTGCAGAAATAGCTCATCAACTTCCGACTTTCAGTTCCCTTTTCTGTAAGGCCTGGCCCACAGGGATTTCCCTTACATATACCAGCTCAGCTCAAAGGGGGTTATAATACTTCCTACCTAGTTATTTTATGGAGAAGGGTTTGGGTTATGTTAGTTTGCCAGATGGCTCAAAGCAGAAGTGTTCTTCCTTGGCTTCTTATTCGGAACACACCCACCTTTTCCAGCTTCACAAAGTTTAAAGTTCATTTTAGGCTAAGAATCAATAAGGGGTGGGGTGCTGTCCATGTAAAAGATGGAGGACCAATGACTTAGACTCTGACCGCATTAGTTAAACAGCCTATGTGTTATTTGAAGCTGGACATAATCAACTGGGACGTATAATTAAATTGACTATCTAGTCAATACTGTTTGTTAGAATATTATAGTATTTTCTAAAGCAATATTTACAATAGAGCATACATGATTGAAAAACATTAAGGGGTTTAATCAGCACACATTATTCAGTCAGTCATGGGTTCTAGGTTTGTAACAGCTCAGATGTGTGGCATTCTGTCTCCTGCAG
Seq C2 exon
GCTATTTCTGGGGTCTGACATCATCCCCGGGAGCACTCCCACCAAAGAGCAGCCCAAGTCCGCAGCCAGTGGGAGCTCTGGGGAGAGTATGGACTCAGTCAGTGTGTCGTCCTGTGAATCAAACCACTCCGAGGCTGAGGAGGGCCCCGTCACACCCATGGACACACCAGATGAGCCCCAAAAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026482-Rgl1:NM_016846:14
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.323 A=NA C2=0.857
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000107490





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000027760, ENSMUSP00000107488
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:183907102-183912081 
ALTERNATIVE
HsaINT0139869
(RGL1)
Human
(hg19)
chr1:183876236-183881215 
ALTERNATIVE
HsaINT0139869
(RGL1)
Rat
(rn6)
chr13:69921623-69923976 
ALTERNATIVE
RnoINT0126445
(Rgl1)
Cow
(bosTau6)
chr16:66422465-66427161 
LOW PSI
BtaINT0124426
(RGL1)
Chicken
(galGal4)
chr8:7700833-7702858 
ALTERNATIVE
GgaINT0035663
(RGL1)
Chicken
(galGal3)
chr8:8040679-8042704 
LOW PSI
GgaINT0035663
(Q5ZIY0_CHICK)
Zebrafish
(danRer10)
chr8:19258034-19260297 
LOW PSI
DreINT0126410
(rgl1)
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"