Special

MmuINT0090069 @ mm9

Intron Retention

Gene
ENSMUSG00000023021 | Lass5
Description
LAG1 homolog, ceramide synthase 5 [Source:MGI Symbol;Acc:MGI:1919199]
Coordinates
chr15:99566023-99569252:-
Coord C1 exon
chr15:99569096-99569252
Coord A exon
chr15:99566868-99569095
Coord C2 exon
chr15:99566023-99566867
Length
2228 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
TTTGGTCCTGTCCCCCTCAGGTG
3' ss Score
10.88
Exon sequences
Seq C1 exon
GATTCTGAACACAACCCTCTTTGAAAGCTGGGAGATTATTGGGCCCTACCCTTCCTGGTGGCTCTTCAATGCCCTTCTCCTGATCCTGCAGGTGCTCCATGCCATCTGGTCCTACCTAATTGTCCAGACTGCTTCCAAAGCCTTGAGCCGGGGAAAG
Seq A exon
GTAAGGATGAAGCATCCTTCTTTGTTTGGACCATGTGGGAACACAGGTTTGACTTTGCAGACCTCTGCCCAGCCTGGGAGCCTCAGCTACACAAGGAGGCTCGGGATGTAGCCCAGTCACCATAAAGCTGCAGGAAGCCCTGAGTTTGATACCAGCACCAGCACGATGGCGTATGTATACCTGTAAACCCTGTGCTAAGGAGATGAAGCAGGAAAATCACAAGTTCGGGTCATCCTTTGCTAAATAATAAGTGTGAGGCCATCCAGGAATACTTGACCAAAAATAATAATAAAAGGGTGGCTATTGATGTGTAGCTGAGCATACAAACTGGCAAGCCTGAGGAATGGTGTGGTAGTCTTTTTTTGTTTGTTTGTTTTTGGTTTTTCGAGACAGGGTTTCTCTGTGTAGCCCTGGCTATCCTGGAACTCACTTTGTAGACCAGGCTGGCCTCGAACTCAGAAATCCGCCTGCCTCTGCCTCCCAAGTGCTGGGATTAAAGGCGAGCGCCACCACACCCGGCTGTGGTAGTCTTCTAGTTAAGCTAAATCAACTTTGCTGTGACGCACAGGATCGGTTTCTAAACATCTGCCTCACTATTTTTAAGCAAGAGTCTTTAGTGAAGTTTTAGTGCAAAAGTCACAAAGATACTCATCTTTTAAGACAGTGTTGGAAGCTGAGTCCAGGGTCTCATGCCTTCTGACTAGCTAATTCTAGCCCTACGGGGGTGTGGGGGCAGACATTTAGTGATAGAACATAATTGAAATTTGCAAGTTCTAAAGCAGTCATACTGGATCAAGGCAGAAAGCTGTCAGTTGTGCAGAATCCCAAGTGGGATAGGCTCTATTAGAGATGCTAGTTCCAGACTGCACAATGGATGTTGCCTGGTTATTTATTATCTCTCTTGTCATTGTTCTTGATGGCTATAATTCGTTTCAGAACTTGTGTGATGTGCCTGTGCATCTTATAGCTACTGGACATCTCTCTTTTCCCCTGCGTTTCTCTCCTGACTAGGTGCTCTCCCAGGAGGGATTAGACCCAGGCTCTGTACCTTCTGCTCTTTCTCACCTCCTTCCTCTTTTCTCTGCCTGGTGGCAGCTGGACAGTTCCATCCTTTGCATGTAAGTGCATCTGGCTTCTAGTGTTGAGAGAAGCACCTGTCTGAACAGCTCTCCTTCCAGCTGTACTTCCTGGTCCCATCTGCCTTAGAACGTGTTCGCCCAGCTAACGTATGTGACTGTTGTTGACTGGAGCTGAGATTACCAGATTCCTTCCCCAAATGAAGTCTAGGCTATAATGTGGTTTGCTTTTGAGCCTCTACCTCACCTACTCTGGAGATATCCCTAGCCCTCTGGAAATTCCCTAGACATTCTGAATTGAGAGTCAACAGCTATAGTCAACTGCAGAGTCACATAACATCTAAAGCAAATGTCCTTCCTTTATAACAACAGCTGGAGCCATGTTCCTTCCCTACTAATGCTCTTTAAATGACATGCATCTGTCACTGTTTGTATGTTGCAGGGGTCATCATCCTAACACACATGTCACTGGGCTTTCTTTATTTTTATGGCCCAATATAGAGAATTTGAAACATTCTGATATGCAGGGTCTCATTGGAAACTGCCACCGTAATCCTAACCTCTCATTGAAAACACAAAACAAAAGCATGGGTAAACGGCAAAGCCGCGGTGTCGGTAGAGCTGGGAAGGCTCAGCTCTCCACGCTGACGCCCACACTCCTGACTATATTTATAGTGTCCTGGGGGTGCCAGAACTCCATGTTGAGGCCAGAGATAGCAGCACCAGGGTAAAGAACTGAGTGCCCACGGTGATCAGCAGATGGAGCCACGACGGCATTCCTGTGTATCGCTTGTGTGGCTTCCCCAGTTCTGTGGTGAAGAGGGAAGAAGTGCTGGAGTTTTCCTCACAACTAAACATGGACTCAGTGTGGCATCACAGCAGCCTTTCTGGTATAGAATGGCATAAATGAAAGCAAAACAGGAAGCAGGCAAACTCTGTTCACAATCACAGCCAGTGACACAGAAGCATTTAAGTCAGTGTCACCGAACCTAGAAACAGGTACACGAGTGGGCTTTCCTAGGCTCTGAGACTCATCTGCCCCGTGAGTCCTAGAAACAGGTACACGAGTGGGCTTTCCTAGGCTCTGAGATCCACCTGCCCCGTGAGTATGAAACGTAGCGTGTGTACTGCATTTGGTCCTGTCCCCCTCAG
Seq C2 exon
GTGTCTAAGGATGACCGCAGTGATGTAGAGAGCAGCTCAGAGGAAGAAGATGAGACAACCCACAAAAACAACCTCTCTGGCAGCAGCTCTAGCAATGGTGCCAACTGCATGAACGGCTACATGGGAGGCAGCCACTTGGCTGAAGAGCAGGGGACTTGTAAAGCCACTGGCAACCTACATTTTAGGGCCTCCCCACATCTACACTCCTGTGACTAGAGGGACTGCAAGGCACTGAGGAGAATCAAAGAAATATTTTTGTGTTTTAAAGAAACTCTGCCGTTTTGTATTTAATGCCCTCTGGTCCTTTCAGTAAGGTTATTGGCTCTGTGTTTGTGTGGTTTTTGTGTGTGATTATACATGTGTATTGTGCATATAAATGAGTTTCATTGACTCGGTTGGGGCACAATTCTGGATTACTAGTCATTGTCTGGTCACTTCTGAGCCCACCTCAAGTCCAGCCCTGGCTGCATCTTGAATTAAGCTGTCTCCAGACCATCTGTGACCTCGTCCCATGGCTCTTGAGACTCTGGGTTCCTGATCACTTAAATAAGTGCTGTCACCAGACTCAGCTCCAGGACTTGAAAATTGTTCTTTTGGAGGAGGAAGTAATATTTCACCTGATGGAACACTACCCAGGATCAACATAGCTCCTAGCTACATGTCCCCTTCCTATCACCTGCTAGTGGCAGGGACAACTACATACCCTGCTGCTTATTTAATGGTATGCAGGGAGGGGGAGGGTAGGAGAGGATGAGCTGAGATTTGGAGAGCAGCAGCCACTGGTTGCGCTGTTAATGATTTTATACTATTGCTTATTCTTCTGTGATTAAATTGTTTCAACCCTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000023021-Lass5:NM_028015:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.281
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0379811=TRAM_LAG1_CLN8=PD(21.6=79.2)

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000023762f1394A





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000104663
          









    
Other Skipping Isoforms:
ENSMUSP00000023762, ENSMUSP00000135074
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
chr12:50130695-50134545 
ALTERNATIVE
HsaINT0090852
(CERS5)
Human
(hg19)
chr12:50524478-50528328 
ALTERNATIVE
HsaINT0090852
(LASS5)
Rat
(rn6)
chr7:141387773-141389474 
LOW PSI
RnoINT0034898
(Cers5)
Cow
(bosTau6)
chr5:29932171-29933015 
LOW PSI
BtaINT0084745
(LASS5)
Chicken
(galGal4)
chrLGE22C19W28_E50C23:282636-285436 
ALTERNATIVE
GgaINT1009237
(CERS5)
Chicken
(galGal3)
chrE22C19W28_E50C23:259200-262001 
ALTERNATIVE
GgaINT0000981
(CERS5)
Zebrafish
(danRer10)
chr22:5728901-5732100 
LOW PSI
DreINT0045494
(cers5)
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"