Special

MmuINT0131349 @ mm9

Intron Retention

Gene
ENSMUSG00000026821 | Ralgds
Description
ral guanine nucleotide dissociation stimulator [Source:MGI Symbol;Acc:MGI:107485]
Coordinates
chr2:28405969-28408602:+
Coord C1 exon
chr2:28405969-28406083
Coord A exon
chr2:28406084-28407611
Coord C2 exon
chr2:28407612-28408602
Length
1528 bp
Sequences
Splice sites
5' ss Seq
ACAGTAAGT
5' ss Score
9.49
3' ss Seq
CCCTGTCCCTCTCCCACCAGAGC
3' ss Score
11.46
Exon sequences
Seq C1 exon
GTGACCAGCCAGGATAAGGCTCCGACTGTCATCCGAAAAGCCATGGACAAACACAACCTAGATGAGGACGAGCCGGAGGATTATGAGCTGGTGCAGATCATCTCAGAGGATCACA
Seq A exon
GTAAGTCAGTCAACTGTAGGCCAGGGCTGAGGGGCGGCTCAGCACCGGCCCCTTCCCCAGAGCCTGCTGCTGGGCCTCTCCATAAGAGACAAGAGTTGAGGAGAGAGGCTCATGCGTGGGCCTGTCAGAGAGGACATTGCCTGGTTAAAATAAGAAAGCAGGTACTTCAGGAAGAATGCTCAGTTTAAAATCCACACACGAGAGGCTGGATGGCTCAGCGGTTCAGAGCGCTGGCTGCTCTTTCAGGGTACCCAGGTTCAGTTCCCAGCACCTACATGGCAGCTCATCACTGTAGCTTCATTTGCATAGATCTGGCACCTTCCTAGCCATACATGCAGGCTAAACACCAACACACACAAAATACAAATAAATACATCTTTAAAAAAAAATCCACACATGAGATGCAAAAAAGCGCACAGACGAGTCAGCATTCTAGAAAGAAGGATGGAGTCACAAGCCTGGGCTGGGGAGTCGGCTCAGTGGTTACAGTGTACAGTGTGCAGTGTACAGTGTACTGTGTGCTGGGCAGACAGCCTAGTGGTTACAGTGTACAGACTACTGTGTGCTGGACAGATGGCTCAGCAGTTAGAACTTGATGCTTTTCCAGAGGTCCTGAGTCAGTACCTAGTACCCACATGGTTACTTATAATCCCCTAAGTGTGTGCTGCTCTTGCAGAGGATCTGAGTTCAGTTCCCCCCTCTCAGCTTCTCCACAGCTGGCTGACAACCTCCTATGAGTCCAGTTGTACAGGATGTGATGCCCTCTTTGGGCCTCCATAGATGCATGAATGTAATTAAAAAGATAAATAGAAAAATCAGGCCATTCTCAAGGATCTTGGAGAATTTCAGGGGCTCTGTGCCTATGTCCTTTTCCCCAAAAGGAGGCTGTGGCCAGCAGCTTAATGTTAGAGAGAGACATCACCACAGAGGCCACCCATGTCTGTCACCACAGACACTGCTGAAGTGAGCTGAACACCCCCATCTCACCATTTGCTGCTGTCTGCAGTAACTCCCAAGATACCTAGATGTTCTACTGCAAACCTCCTCTCAGCTTCTCCACTGTTTTGGTTATATGGACAGGGTGAGGGGGCCCCTTCCTTCCAGAAGGCAGGCCTACAGAGGCTCAGGAACTAGAGGCAGACACGGGGTCAGCAGGAAGTCCCGCTTGGTAATGATGGACAGATTCTAGGCCAGAGGTGACTAGTGGAATGGAACCCAGAGGAAGGTTCTGCCCTCTGCTGGTCCTTGGAGCCTTGGTGAGTAGCAGTGGAGCATCATGGAAGGCAGTGTGGATTCCTGGAAACCTGCTCTGGCTGGAAGTCCTAGCCAGCAGAGAGAGCCGTAAAGGTGGTGTGGAGAGACTTCCTTAGGCTCTCATTGACCTCTACTGGGGTCGCAGGAGAGGTCCTTGTTGGAGCTGGATTGGAGGACTCCCAAGGCCCTGCTGTGGCCTGGCCGGGAGGAGGCTCTCAGGAGGTGGGGGCATCTCAGCCGCATAAAGCACCACTCCCTGTCCCTCTCCCACCAG
Seq C2 exon
AGCTGAAGATTCCAGAAAACGCCAATGTGTTCTATGCCATGAACTCTACCGCCAACTATGACTTCATCCTAAAGAAGCGGACCTTCACTAAGGGGGCTAAAGTCAAGCATGGAGCCAGCTCCACCCTCCCTCGTATGAAGCAGAAGGGACTCAGGATTGCCAAAGGCATCTTCTAAGGACGTCTCCTGGGACGGGCTGACTGGCTGGAGACTAAGCACTTACAGACTAGAGTGGCCCTGGCCACACAGGTACCTCTGCCCACCTGCCAGTCCAGGCTACCCCCCTACTCCACTTTCACCCTGAACCTCTCCTGCTGCCGGGATTGACACCTGCCACTGACAGGCTGACCTGGCCTCTGGGGACCACTTGCCGCCTTCGGTGCCTTCTGCTCTCTGAAACCAGAGGACTAGCTGACTTTTGCCAAGGAGTGTTGCCAACTGGGCATGGGACCTTGCCTGCCCTGGACACTATCCACCACACTTTGCTGACACCTCCCCAGGTGCAGATCACTGCCACCCATGCTCCCGGATGCTCCAGGACACACATACACCCAGCAGGGCTGCCGACTGCATTCTCTCCTTGTGCCCACAGGCACTGGCCTGGGACTTTCATGGAGGTCCTAGCCTTTCCTCCCACACTCTAGCCTTTCTCAGGCTGCACCAAAGATTCCACCTTCAGGGCCTACAGAGTGAGGGAGCCTCGCCCACCAGGAGCCCAAGCCCTCCCTTGGATCAGAGAGAGAAGCCCTCTCGTGAACTGCCCGGTTGGTATTGAATCCCAGTCCACTGAAAGTGCCATTGACCACCGCTGCATCCGGGCTGTACAAGACGACACGCAGTGGGAGGTTTGTGGGGAGGAGGAAGACAACTGAACATTTGTATAAAACGTAAAAAGTTTACTGATTGGGGTGGGACAATATTTATTTGTTGTAAATAGAAAATGCTAGACTTGAATATTATATTAAAATCCCGTTTCTACTACGGCCTGGTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026821-Ralgds:NM_001145835:17
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.397 A=NA C2=0.034
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0078818=RA=FE(43.2=100)

							
A:
NA

							
C2:
PF0078818=RA=PD(31.8=47.5)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000097812





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000028170, ENSMUSP00000109526, ENSMUSP00000118966
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr9:133098763-133100267 
ALTERNATIVE
HsaINT0137006
(RALGDS)
Human
(hg19)
chr9:135974150-135975654 
ALTERNATIVE
HsaINT0137006
(RALGDS)
Rat
(rn6)
chr3:7127877-7129577 
LOW PSI
RnoINT0123936
(Ralgds)
Cow
(bosTau6)
chr11:103126373-103128327 
ALTERNATIVE
BtaINT0122018
(RALGDS)
Chicken
(galGal4)
chr17:6790333-6790420 
LOW PSI
GgaINT0125410
([1])
Chicken
(galGal3)
chr17:7450260-7450347 
LOW PSI
GgaINT0125410
([2])
Zebrafish
(danRer10)
chr3:13865477-13868476 
LOW PSI
DreINT0018077
(RGL3 (1 of 2))
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CGGAGGATTATGAGCTGGTGC

				
R: 
AGGGTGAAAGTGGAGTAGGGG

				
Band lengths: 
343-1871

			

		

	





	
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"