Special

MmuINT0020602 @ mm9

Intron Retention

Gene
ENSMUSG00000021066 | Atl1
Description
atlastin GTPase 1 [Source:MGI Symbol;Acc:MGI:1921241]
Coordinates
chr12:71033204-71035907:+
Coord C1 exon
chr12:71033204-71033308
Coord A exon
chr12:71033309-71035856
Coord C2 exon
chr12:71035857-71035907
Length
2548 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGG
5' ss Score
9.99
3' ss Seq
CTCGCTGTCCCATCATCAAGGTC
3' ss Score
6.41
Exon sequences
Seq C1 exon
GTTGCAGTGTTACTGATGGATACTCAGGGAACCTTTGACAGTCAGTCAACTTTGAGAGATTCGGCCACAGTATTTGCGCTTAGCACAATGATAAGCTCAATACAG
Seq A exon
GTATGGAATAACACAAATCTATCTGTGGATATTTCTTTAACTAAAATTCATGAATAGTGTTTGTACATACATGTGTCAATGAGACAGAATCGCAAACCATATGTGTTCTCATTCAGCTCCATAAGAGTAGCCATTGTCACTATAGGCTGTGGGAGTCTAGACGTGAATAGTCATTGTCACTATAGGCTGTGGGAGTCTAGACGTGAATAGTCTTTGTCACTATAGGCTGTGGGAGTCTAGCCAGTTATCAGTTTCTACATTGGCTGCTTTAGTCCAAAGTGGCTCTATTATTGTTACTTTTTTCTGTTAAAGTTTAGAATAAATTAAAGTAATAAATTTTATAGCTAGGGGTATAGCTCACCTGGTAGAGTGTTTGCCTTGCATTTACAAGGTCCTGGATTTAGTCACCAGCACCATATGAACCAGGTGTGGTGGAGAATGTCTGTTATTCTGTACTGAGGAGATGGAAGCAGGAAGATCAAGAATTTAAAGTCTGGGCGTGGCAGCGCACGCCTTTAATCCTAGCACTCAGGAGGCAGAGGCAGGCGGATTTCTGAGTTCAAGGCGAGCCTGGTCTACAGAGTGAGTTTCAGGACAGCCAGGGCTATACAGAGAAACCCTGTCTCAAAAAACAAACAAACAAACAAAACCAACCAAACAAACAAAAAAAGAATTTAAAGTCATCTTTGGTTATACAATAAGACTGAGGCTAACCTGGTCTACATGTTACCCTGTCTCAAAAAGAAAAGTGAGATCGCTCAGCAGGTGTAAGTGCTTGCTGTATAAATCTGTTAACCTGACCCAGTCTACAAAATTCGCGCAAAGGTGGGCACAGAGCAGACCCCACGGAGCTGCCCTCTGACCTCCGCACTCAGGTCACAGCACACTTCCCTATGTGCACATACCACACATACCAACAATAATAAATAAGCCAACTTAAAAATCTTATATGCAGATTGGGGACAATCTATTATAATTTATTTAGTGAAACAGGATTTATAAACACACACTGTGTTTTACATTATCAGTGAAGTTATTTCTAAATGTAAAGCTTTACATGTTCATAGCTTTAGAAAACAGTTTAGATGTAACAGCTACATTTATATGTAAACCGTGTGTACTTAAAGCTTTTCCCTTCTTTTGCTCTTTTTTTCTCTCTTTTTAACAGTACTATTGGGTGGGGAGGGAGCTTTATAGACTTTGTAAATTGTTCTGAAAGTTAGTATACAGCTGAAACAAGGTTAAGGACTACTGTTAGATATGTCTGCTTGTCGAAGAGAGCAGGGGGAGAAGACAGTGAAGAAACAAAGCAGAATTTTTTCAAAGGCAAGATAACTTTTAAAGGTGAGAAAGGCAAAACAGGGTAAGTACAGACTGTGATCATATATAGACGGGGACCTAGAGTTACTGAGCAGGTAGCCAGGGTATCTCTGGTCAGCACCTCCCATACCGGTTCAAAGGAAGAGGAAGGGTGGACTGAACTTTCAAATAAATGAATTTAACATAAAAGTTATAGTTACAATCCATGATTGATGCTTCAAGATAAACCTACCTCTTGGGGCTGGAGAGGCGGCTCTGAGGGGAGGAGCACTTACTGCTCTTGCAGAGGACCTGGGCTCAGCTCCCAGCATCACATGGTAGCTCACCTCACAGTCATCCATAATTCTAGTTAGTTCCAGTGGATTGAACTCTCTTCTGACTGCTGCAAGCATCTGGCACAATAGGTGGCACACGTGCACACAAGGAAAAATTCTTACACATAAATGTGAACAATAATTTTTAAAGGATTGCCATCAGAAAGCTTATCTATGAAACACAGGCTTTACTGTAACTCAAAAACCTGCTTCTTCAATGAATCTGTAAAATACAGACTCAGTATCTGTTTTCTTTAAAATCAATAAGAAAGATCACGTGCACAAGCTAATTAAAACCAGTCTAACTTTGCTTTTACCACTCATTATTTATTATTTATATTTGACCTGAAAACATTGAATCTTTTTATAGAAAGTCTGTCAAGTATGACTATTTCAAATTATTACTTGAGAAATTACATTATTTAAATAAGTACAAATGGATACTATTTGTGTCAATATGTAAACATATACAGAACATTAATTTATCTTTAAAGTTACTAATGCTATCACCTCAAGGAAAATGAAAAGAAAACACACGATGTCATCTTAATGCTGTGCTGTAATAGAAGAAAGAGGCAGGAACCTAAAGCTGGGAGCATGACATTCGGAACCTAATAGTGTGTGCGGGGGCTTTCTGTGATATAAGCAAATCAATACATTATGAAGAGGGAATTGTCATTTTCCAAACAATTTTCCAGTTGGGCAGGAAAACGCACTCTGTAAACCCTGTTCTTTGGGGACTAAGGCAGGAAGACTTCAGGCTTGAGCAATGTAATGAAACCTCCTTTCTTGGCTCTCATAACTGTATATGAGAGTTGCTTGTATCATAACTGATATTTCTAAAAACAGCACGACGAAGTTCTTCTAACGATATGGATTATTTTCTCACCCTGCCTCGCTGTCCCATCATCAAG
Seq C2 exon
GTCTACAACTTGTCCCAGAATGTCCAGGAGGATGATCTCCAGCACCTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000021066-Atl1:NM_178628:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

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

				
Domain overlap (PFAM):

					





						

							
C1:
PF0226314=GBP=FE(12.5=100)

							
A:
NA

							
C2:
PF0226314=GBP=FE(5.9=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000021466





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
chr14:50591640-50593845 
LOW PSI
HsaINT0014166
(ATL1)
Human
(hg19)
chr14:51058358-51060563 
LOW PSI
HsaINT0014166
(ATL1)
Rat
(rn6)
chr6:92332385-92334624 
LOW PSI
RnoINT0022638
(Atl1)
Cow
(bosTau6)
chr10:43528466-43532491 
LOW PSI
BtaINT0022816
(ATL1)
Chicken
(galGal4)
chr5:57770390-57771077 
ALTERNATIVE
GgaINT0056646
(ATL1)
Chicken
(galGal3)
chr5:60453269-60453956 
LOW PSI
GgaINT0056646
(ATL1)
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"