Special

MmuINT0067615 @ mm9

Intron Retention

Gene
ENSMUSG00000038860 | Garnl3
Description
GTPase activating RANGAP domain-like 3 [Source:MGI Symbol;Acc:MGI:2139309]
Coordinates
chr2:32841886-32845152:-
Coord C1 exon
chr2:32845026-32845152
Coord A exon
chr2:32842351-32845025
Coord C2 exon
chr2:32841886-32842350
Length
2675 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
CAGCAGCTTCTCTCTTCCAGGAT
3' ss Score
7.78
Exon sequences
Seq C1 exon
GCCTCTCTGATGATGGTGGAACCAAAACAGAGGGAGCACCAAGGGCCAAATCAAAAACCCGGAAGCGGTTGGAAGAAAGCCAAGGAGGCCCCAAGCCAGAGACTGTGAGGTCAGCTAGTAGTGACAG
Seq A exon
GTAAGAAGGCCCTGCTCTGCTGGATGGTGGCCAGCAGACGCCAGCATGCCCAGGTGTTATGTTTATAAAAAGAAAGAAAGAGCCAGGATATGTTTGATAGAGACAGGTACTAGTCATACAACAGATACTGTATGGAATAGAGTTTATTTAGGGAATGGGGAGGGGAGTTGAAGATGGAGTAGAAACAGAGAAAGACAGAGAAGAGGGGGTGGGGGGGAGAGACTGGCCAGGAGCATGTGGAGAGAGAGGGGGGATAGGTGGGGAAAGAGGGAGAAGAGGCAGAGAGTAAGAGAGTAAGAGGATAAAAGAGTAAGAAGGGGCAAGCAGCCTCTTTTATAGTGAATCAGGCATACCTGGCTATTGCCAGGTAACTGTGGGGCAAAGCCTAGAAGGAATACTAACACCAAGAGTCTACTAGCCCAGCACCCTACAGGGTCAGTACCCACCCCACTATGAAGGTCCCAGAAAGGACAGCTGACAGCACAGGGCCGAGATAAGAGAACACTGTCACCAGCAATCAAGCAAATGTTCACTAAAATATATTGAGAGACTAGAGGCAGCTCAGCTAGAGCCTTGCCTGACACGCACAAAACTGTGCACATGCACACACACAAATGTACACATGTGTGTGAGAAAAAAACAATACAGAAAGAGATGGGTTTTGTTTTTTGTTTTTTGTTTTTTGTTTTTTTTAGAAAAGGTTGTGGCATGTAGTTTTAAGCTCTAACCGCCTTTACTCCGAGAGGTGATCACAATACCAATCCCTACCCAGCTCCCCTTGAATCCAGGACAAACAATAAACACACAGTTCATCCCTTTTCTACTTGCCTCTGGCACAATTGCTGGGCACTGCTATCTCCCACCTGGAAAACGAGCCTTTATCTATATTCTTAGCTCCATACCTCCCACCTGCCCTAAACTTCAGTGGCTCGTCCCACCTAGTCCCTGCCAATCATCCCTGACCTGTAGTAGTAGCCACAGGCCCCAGTTCCTCCCAAGACCTCAGTTGGTTGCCCAGTTCTCCTCTCTCCAAAGCATCGAGAACTCCGTCCTCCTTCCTTACATCTCCCTCTCTACCTGCAGGGCCCAGAAGTCCCACCTTTACCTCCGCCCAGCAACTGGCCCAAGGCTTTCTGACAGATCAAAAACCAAGTGGGGAACAGGACTTTAACATAAGCACTGCCCCTTACACCTCACCTTTTCTGTCCAATAAAAAATATTTTTAAAAAACTCTTCTCCCAGACATAACAATCATGTAAATTATATAGTATGATATAAAAATGACATCCAGTCCATCATATTTGTTAATTAGATAAAGTACTCTACCATCACTCCTAACTGAAAGAATTATGATTCTAACTGGAGTATGTTAGACTTTAGCTGACAGTGCTATCTGAAAACATGTCTTCCACTCTATAACCTCTCTCCTAATGTTAAACAACTTGAGTATAATTTTGAGACTAAAACTAGTCTTCAGTCCCGTCAGAAATCTGAAAACTATTTAAACATTACCTGGGTATTTAGGAAGCACCAAACATAGCTTCTCAAACAACCGTAGAAACAGCCGACTGCCTGGACAGCCCATTAATTACTCAAAACCTTGTAGCATCAGTCTTTAGCATGCTGGCCCAGGGTCATCTGACAGACCCTAGCAAAATAGAATTACCTGCATACCCTGTCTTGGCAGAGTCAACAGTTGACTATTTTGCATAATGTGTCCTTTTTCTGGATAGTATTTATTCTGCAGATGAAATAGGCAGTTTCCACTCAGTGGCTACCTTGTCACAATAAGCAACCTTGCTTGGATGTGAAGATGCTCAATTCTTCTTTGAACTAAGAAGGGGGTGCTGTCAGGAGTAGATATGTCTCATTGTCAAATTGCCTCTGCCTCTGCCTCTGCCTCTGCCTCCTCTTGAATGCTGGCATTAAAGGTGTGCAGCACCACCACCTAACAAATAAAGAGTGTTAAACAAACAGCAACAAACCCACTGTAAGTAGCTGGGCATGATGGCTCAGGCCTGGAATATCAGCACCTAGGAAGTAGAAACAGAAGAATCATTGTAAGTTCAAGGCTAGCATGACCCTGGTTCACAGTAATAATATTAAGGGGCTGGAAAGATATCTCCGCAGTTAACAGCATTTATTGTTTGATCTTTGAGGACTCAGTTCAGTTCCCAGTACTCACATGGTAGCTCATAATTATCTGTCATTCCAGTTCTAGGGGACCCAATGCCCTCTTTTAGCCTCTCAGGGCACAGAGATGCACAGGTATAAAGATATACATGCATACCAAACATCAATTTGCATAAAATAAAAATAATGATAAACAACAACAACAATAAATCATGGTAGGAAGGCAGGTAGAAGGCCCACTTGGCTAAGGGTCAAGAACAGAGGAAGCAGCACAGGCCTGGCTTGGACCGCATGGTAAGAACGGGCACAGATAACAGGACTCTGAGCCACTGCTCTGAGCACGGTGCATGGCCAGGGACACAGAGAAGAAGGGACCAGCTTCACAGAGTGCTAGGGAGGCCGCAGGAGGTCACGTGGACAGGGTGGAGGGCAGCATTCAGGGCTCTGGGGCATTTGTGGGATCACAGACTCCCTAAGAAGTGAAACCCTGCACTTGTTCACCTCGGTCCTCCCACCCTGTGACAGCAGCTTCTCTCTTCCAG
Seq C2 exon
GATCCCATCAGGAATTTTGGAAAGTCCGGCATCAGAAGCCAATCCCGAGGGCCACAACCACTGGGCAAGTTCTGAGCAGGACGCTGGGGTGGATAAAGAGGGCAGCCCGGGCTCAGGCAGCAGCCCCTTCCAGCTCATGGCCTCCTCAGAGGAAGACATCATTGACTTGAAATAGAGTCTATGCCCTATTGGCCATCCTTAGTTTTCTTACGCAAATTTATACTGTTCAAGCAGCTCCAACGTCCAGTCTCAACACAGCGCGCCTTCGGCCAGGCAGCGATCCACGGACCAAACCTCCTGCGCCCTCAGCCGGTGGGTCACTTCTCCAGTGTCCAGTGCCATCTTTCTCGACCCTGTTTCTTTCCATTCAAGAACCGTCGGTCCCCTTGTAATAAAGGTGGTAGATTTCATTAAGGTTTTAGATCAAAACTTTGAATAAATCAAAAACGTTCATTCTTATTCTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038860-Garnl3:NM_178888:28
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=1.000 A=NA C2=1.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
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)
chr9:127390768-127393082 
ALTERNATIVE
HsaINT0067769
(GARNL3)
Human
(hg19)
chr9:130153047-130155361 
LOW PSI
HsaINT0067769
(GARNL3)
Rat
(rn6)
chr3:12034588-12040850 
LOW PSI
RnoINT0064014
(Garnl3)
Cow
(bosTau6)
chr11:98155945-98157861 
ALTERNATIVE
BtaINT0065569
(GARNL3)
Chicken
(galGal4)
chr17:10442398-10443156 
ALTERNATIVE
GgaINT1013680
(GARNL3)
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
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"