Special

MmuINT0067598 @ mm9

Intron Retention

Gene
ENSMUSG00000038860 | Garnl3
Description
GTPase activating RANGAP domain-like 3 [Source:MGI Symbol;Acc:MGI:2139309]
Coordinates
chr2:32879009-32881708:-
Coord C1 exon
chr2:32881600-32881708
Coord A exon
chr2:32879055-32881599
Coord C2 exon
chr2:32879009-32879054
Length
2545 bp
Sequences
Splice sites
5' ss Seq
CACGTATCC
5' ss Score
0.74
3' ss Seq
TGCCTTGACTGTCCCCACAGATA
3' ss Score
10.44
Exon sequences
Seq C1 exon
GTGGAAAGGAAGCGCCACATTGGAAACGATATTGTCACCATCGTGTTCCAGGAAGGAGAGGAGTCCTCTCCCGCCTTTAAGCCTTCCATGATCCGCTCCCATTTTACAC
Seq A exon
GTATCCTGGGTCTTCATAAATGCTCCTGCCCACCAGCCTCCTGGGGCCTCCCAGGACATGTAATAGGCAGCGTGACACCCACCTGAGCGGCTAGTCTGACACCCGCCACCGGGCAGTGTGCCCAAGTGCTGCGTGTTTCTTTCTTGCCCGCCTCTGAGGCAGCGGGGAGGAGTCCTCGGGGACTGTTTCATTGTGTTTCTCAATTTATACACACACAAGATCCCTTCACCACACCCTCCACTACCCTCCCATCCTTCCCCTCTTCTGACCACCCCTTCTTCCTAACAAGGCCCCTCTGCTTTCTCACCTGGGTGTGTCCCACCTGTGTCTAACCAGGGATGCAGTTAAAGCCTACGCAGATGGTCATTTATTTGAGTGAGAGCAGCTCATCAGTAGCTACACCACTGAGAAAATGACTTTTTTTTAAATTATTTATGTATGTGAGTTCACTGAAGCTGTATTCAGACACACCAGAAGAGGGCATCAGATCCCATTACAGATGGCTGTGAGCCACCATGTGGTTGCTGGGAAATGAACTTAGGACCTCTGGAAGAGCAGTCATCCACTGAGCCATCTCTCCAGCCCGAAAATGGCTCTTTGTACCCCAGCAGCCATTAACTGCCTATAGCTCTTCAGGGAGGGGCAGGGCCTCAGGAGCCCCTCCCCATCCACAGTGGGATGTTGATGGGCCTAGGCCAGTACAGGTAGGCACTGGCTGTGAGTTTGCAGGTCAGAAGACAGTGTTTCCCAGCTCACTTCCGGCCTGCTGCCTCAGACCTCTGGGTGCTAGGGTTACAGGAGCATGCGACCACACCCACATTGACTTTCAGAATGCCTCCTCTTTCCTCAGGAAGTCTGTGAAGTGAGGCAAGCTTCCTATTATGAACTGGTAATGAACAATTGTGAAGGATAAGTAGTGACCCCTCTGGGAAGTGACGTCAACTATAAAATCTGTTGCCGCATGCCTGTAGTTCCAACACACTGAAGGCCTGGGCCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATCTGGGCATGCAGACTGACACCTGTAATTACAGCACCCGAGAGGCTGAGGCAGGAGTTCACTGTGAGAAATTATTCTAAGCCTGATACTACCTGCTAAGTTGAAGTATGCTGCGGCATGGTAACATTAACAATGTTACGCACATCGCCTAACCCTGCCCAGCTCACTGTCTGTAGATGCCCGTGGTGGGGCTGGCCCTCTCAACATTGCTCAGCCAGACAACCCCAGGGCATGTGTTCGTCCTATCTGCCAGACCTCAGTCACGGCCCACTTACCATGGTTACAGGCCAGGAGAGCCAATCTCAAGGCAGCGGCTCAGAAGGTTGGCCACAGTAAGGAAAGGACATCTAGTGGGCATTCTCAGAATGAAGTTGAGTCTCATTACTCCTGTTCCCAGAGACCCCGGGAAAAACACCGGGGGACAGACCACTGCGCATCAGGTGCCTGCCAATAAAACTGACTTGTCTCAAGTCAGACAACAGAGCTCACAAGGAGGTTTTTAAAAGTTGAAATGGCCAAATTTCTCCCACAAGGGTAGGGGTTATAATTAAGGTGAAGACACACCCTCCTTGGCTCCTCCTACTTACAGCATAATGTCCCCCATTTATTGGGCTGTGGCACTAATATTCCCCTTTTCCTGGTGACAGAAGGCTTCTCTGAGTGAAGCCCAGAAGACAAGGTAGCTAGATAGCTAGAGACACTTTAGGGTGCTCCCTATTAGACATTCTGCACACTGGCCTGAGCACATATGCAGGTGGTCGGTGTGACCTCATCCCGCAGAGTACAGGAGTGGCTGCACCCGAGTGTTGCTGCCTTCAGCCCCAGGCAGCAGCAGGGCTGGAGGTGAGATGTGAGAGCAGGCCAGAGGAGCACTATTGGGTGCGGCAGTTGTGCTCTTTGATTTATTTTTAAAGAGTTGTATTGAGATTGAAGCCCCATAGCATATCATTTGTCCTTTTTTCTTAAACGCTGGTGGAAGCCAGGTCTCCCACAAGTCCCGAAAGTGCTCTGCCACTGACCCACAGCCCGAGCCGCTCGTTGAGCTTCATCCCAAGCACAGGCGCCTCTGCTCAGCAGCTGCCAGCGGCTACACTGGCTCGGTCTGTTTTGTCTGCCAGAGGCAGGAGGAGAGGGAAAGTGTACAGCAGAAACATTTCCATTGTTTCCCCGTGTGGTGGAATAGATGAGTAGCCGGCGCCAGGAGCTGCTGCTCTGGTTCCCTGGCTGCTTGACTGTTTCATGGATTTCCTTATACACTCCCATGACAGCTGTGGAGGCTTCACCTAACCTTTTCCCAGTATAAGACCACACAGATGCTAACACTAGGCACAGGGCTCCCCTGTGTGTGTGTGTCCCTTGTAAAGGGGTGGAGTTTTGTCCCAACTTCAGAGCAGTAGGTACCTAGCCACAGGGAGGCCTGCTCAAGAACACTTCTGCAGGCAGGGTTCTCAGATCCAGCTCTCCAGTGTGAACATCAAGGGTATTGATGAGTTGCCTTGACTGTCCCCACAG
Seq C2 exon
ATATTTTTGCCTTAGTGAGGTATGACCAGCAAAATGACAATTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038860-Garnl3:NM_178888:12
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.027 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0214510=Rap_GAP=FE(19.1=100)

							
A:
NA

							
C2:
PF0214510=Rap_GAP=FE(11.7=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000047283f3900A





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000047283, ENSMUSP00000057582, ENSMUSP00000099874
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
chr9:127336237-127338115 
ALTERNATIVE
HsaINT0067752
(GARNL3)
Human
(hg19)
chr9:130098516-130100394 
ALTERNATIVE
HsaINT0067752
(GARNL3)
Rat
(rn6)
chr3:12076081-12078726 
ALTERNATIVE
RnoINT0063996
(Garnl3)
Cow
(bosTau6)
chr11:98103665-98105805 
ALTERNATIVE
BtaINT0065553
(GARNL3)
Chicken
(galGal4)
chr17:10424034-10426243 
ALTERNATIVE
GgaINT0125905
(GARNL3)
Chicken
(galGal3)
chr17:11154577-11156786 
LOW PSI
GgaINT0125905
(GARNL3)
Zebrafish
(danRer10)
chr5:32787271-32787439 
LOW PSI
DreINT0071455
(garnl3)
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"