Special

MmuINT0067564 @ mm9

Intron Retention

Gene
ENSMUSG00000026867 | Gapvd1
Description
GTPase activating protein and VPS9 domains 1 [Source:MGI Symbol;Acc:MGI:1913941]
Coordinates
chr2:34567685-34570850:-
Coord C1 exon
chr2:34570725-34570850
Coord A exon
chr2:34567859-34570724
Coord C2 exon
chr2:34567685-34567858
Length
2866 bp
Sequences
Splice sites
5' ss Seq
AAGGTAACG
5' ss Score
10.19
3' ss Seq
ACTAAATTTGTTTTTGATAGCTA
3' ss Score
5.03
Exon sequences
Seq C1 exon
GTCCTTCCAATCGCTCCAATTCGGTGTCTTCTCTCGACCTGGAGGGAGAGTCTGTATCTGAACTTGGGGCAGGACCTTCTGGGAGTAACGGAGTTGAAGCACTGCAGCTGTTAGAGCACGAGCAAG
Seq A exon
GTAACGTGGTGGAGAACACATCTGTACAGGTAGCAAAGAACGTGCGTGATTTCAGGAAAGGTAGTCTCTTTGCTTGCTGTGAGTTGATTAATGATCATTAAAGTTGCATTTATCCATAGCTCCTTTAGTTTTTAAAAGGTGTTTAGTTGGTAAGTGTATTATTTGGGCTTAAATTATACACAGCAGTATGAGTTACTTTAAATTCTGTAATATTTATTATGTGGTACAATGATAACTACTAAGGGCTCAATAACTTAGGTTAGGGAAAGAACACTACAAATGGTTAAAAGCCCCAAGTTATATGATCTGAGTTTGATCCTTGGAACCCACCTAGTGGAAGAAGAGAGGCAACTCCTATATGTTGTCCTCTGAGCTCCACACACACACACACCATGGCACCAGTGTATGTGTATATACACGCACACATGCAAACAGAAATACATAGGAGGTAGGAGGATGACTCAGTGAGTAAATTGCCTGCCACAAAACATCAGGGCCCAAGTTTGGATCCCCAACAATTAGATAAGAAGCTGGGTTTGTGCACTTAGGTGACAGGTGGGTGATGGGTTGGGAGGAATGGAAGCATGGGAAGATGAAGAGGCAAACACAGGTAGATCCCTGGCTCTCTGACCTCTTGCCTGCACACACATGAGCACTGTACATAAACTCTTAACAAACAGAAGCTTGTTGTTAGGGAGCACATTCACAGCTAAGTGTGATTCTTACACTTTAGTGTACGTGAAAATTACCTAGGGAGCTCTAAGAAAATGTATTTTCCAAGCTGTCCTAGAAATATACTACTGAAAAGGAAAAGAGTGTTACTACTGGAATGTATGGTTTGTATAAATTATTGCCATATTGGCTCCATTTTCAACTTATCGATTAATATTAAATTTATTGCACATAACAGAGAAACCTGAAATTAGTATACAGTCAAGATGAAAAGAATCACATCTTTGACAGGTGTTCTGGGTGATTCCGGTGTAGGAGTGGACAGCCTTCACATGTGAAATACTAAGTTAAGTAAATCAAAGGCTGGAAGTTGGCTCAGTCATTTGTGACAAAACTTTTCCTGCAGAGACACAATACTTGCCTATTCATTCCACTATGGAGCCCACCATAGACCAAAGTCCACGGTGAACCATGACTTTTTTTTTAAAGATTTATTTATTTATTATATTTAAGTACACTGTAGCTGTCTTCAGACACTCCAGAAGAGGGAGTCAGATCTTGTTACGGATGGTTGTGAGCCATCATGTGGTTGCTGGGATTTGAACTCCAGACCTTCGGAAGAGCAGTCGGGTGTTCTTACCCACTGAGCCATCTCACCAGCCTGAACCATGACTTGTATTGGGGTTACTTATAGGAGCAGAAATGATTCAAAGACCACTGCATAAAGCCTACTCTAGCGTGGTTGACAATTCACAAAGTTGGGAGCCTGGAGCACACTGCACAGCCTGCAGGCTGCTTAACAGGTTGGAGAATGTCCTTTCCAAGTGACTCGGTGTACAACTCTCCCAGGCAGTTCAGCAGGTTTGTGCTGCTGCCAGGCAGCTGGTTTGGTCTCAGATTCTTCTTTGCAGCTTGGCTTTTCTTGGTTCCATTCATCTGAGATGAACTGCACTTTTACTGTTTATACTGGCATGGAGGGAGGGGCCTAGTGAATCTGATCAGTCTCAGGAACTTCCTAAAGCAATTTTCAGTTACCTCCTGCTTAGAGATTTCCTGCAGGATACAATGTTTATAATATTATCAAGATAATGTACTGCTCTTGCACAGTACTCTGGTTCAATCCTAGCACCTTTAGGATGGTTTATATGGGCTCTAGACACCAGGCTTGCATGTGGTACACATACATACATACAGGCAAGGCATTAATATAGATAAAATAATAAAATAAATAAATCTAAAAAGAGGGTGAATTGAAGCCTGGGCATGATGATGCATACCTTTAATCCTAGCACTCAGGAAGCAGGCAAGCTAGCTTGGTTTATGTATAGAGACCCTATCTTTAAAAAAAATTAAAAAAACAAGCAAGCAATCAAATTGAGAGCTAGATGTGGTAACCTATGCCTGTAATCCTATTATTGAGAGGGTGAAGTAAGAGGATCATAAATTTATGCTATTTTGAGGCCTTGTCTTATAAACAAAAACACCTACACCAAAACCCAAGTCAAAGTTTTACAAAATGGAAATTGACAAGAATGACTTATGGGTCTAGGTAGAAGCTCAGTGGGTAAGAGTGCTTGCTATGCAAGCATGAGTGCTTTAGTCTGAGTCTCTAGCATCATGTCAAAGCCAGGCGTAGCCATGCGTGCCTATACCCTCAGCACTGGGCCACAGACAGTGCAGGCCTTGAAGCGTGCTTAGCTGAAGGTGCTGAGCTTTCAGTTCAGTGGAAAGTGGAAAGCAGTGGCAGGGGTACCTCTGGCTGCTGAATCCATGTGCACATCATATACACAGAGCAAGCTGAAGAAAAGTGATCTGGGAAAGAAGGAAAACTCTAGAATTTACACTTGAGCTATTGCCAAGTGAAATAGTTTACATATGGGTTTACCACCTAATTATTAGCACAATGATTGGATCTGGTAAGCTACCCCAAATAGTTATTTTTACATTCCTGTCTGGGTTAGTTTTTCTCATTTAGACTGGGCACATCTGTCTCCTTTCAGCAGTGGTAAGGTGGAGGTTGGGAGTGTGTGGGGGAGTCTCTACTAATCTTAACTGGGTTAATTAGTCAGTGGGGAGCAGGCTGGAACTACGTGCTTATTAATGATAAAATGAATAACCTGACAATTTTTTCAGGTTAACCAAGAAGTTGTAGCTGTGCCACCATTTGTAAAGTGACTAAATTTGTTTTTGATAG
Seq C2 exon
CTACAACACAAGATAATCTTGATGATAAACTGAGGAAGTTTGAGATTCGTGACATGATGGGACTAACAGATGACAGGGACATATCCGAGACTGTGAGTGAGACCTGGAGCACTGATGTCCTGGGAAGTGACTTCGACCCGAACGTTGATGAAGATCGTTTGCAAGAGATTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026867-Gapvd1:NM_025709:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.997 A=NA C2=0.912
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF153241=TALPID3=FE(19.3=100)

							
A:
NA

							
C2:
PF153241=TALPID3=PD(3.3=12.1)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000108723





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000028224, ENSMUSP00000099864, ENSMUSP00000108727, ENSMUSP00000108735, ENSMUSP00000120138, ENSMUSP00000129138
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr9:125323924-125326415 
LOW PSI
HsaINT0067743
(GAPVD1)
Human
(hg19)
chr9:128086203-128088694 
LOW PSI
HsaINT0067743
(GAPVD1)
Rat
(rn6)
chr3:13783451-13786182 
ALTERNATIVE
RnoINT0063957
(Gapvd1)
Cow
(bosTau6)
chr11:96178786-96180534 
LOW PSI
BtaINT0065487
(GAPVD1)
Chicken
(galGal4)
chr17:9612517-9613345 
LOW PSI
GgaINT0126490
(GAPVD1)
Chicken
(galGal3)
chr17:10334512-10335340 
LOW PSI
GgaINT0126490
(GAPVD1)
Zebrafish
(danRer10)
chr8:34457480-34457585 
LOW PSI
DreINT0071414
(gapvd1)
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"