Special

MmuINT0090052 @ mm9

Intron Retention

Gene
ENSMUSG00000008206 | Lass4
Description
LAG1 homolog, ceramide synthase 4 [Source:MGI Symbol;Acc:MGI:1914510]
Coordinates
chr8:4523354-4526079:+
Coord C1 exon
chr8:4523354-4523510
Coord A exon
chr8:4523511-4523603
Coord C2 exon
chr8:4523604-4526079
Length
93 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGG
5' ss Score
9.99
3' ss Seq
GGCCCCATCTGTTTTCATAGATG
3' ss Score
6.87
Exon sequences
Seq C1 exon
GGTCATCTACACGTCTGTGTATGACTCCATCAAGAACTCGGGCCCCTTCTTTGGCTACTACTTCTTTATTGTGCTCTTGGTGATGCTACAGATTCTTCATGTGTACTGGTTCTGCCTCATCCTGCGCATGCTCTACAGTTTCCTGCATAAGGGTCAG
Seq A exon
GTATGGAGGCCTGGGACAGGGTCAGCCCCCGGGACCCTTCCTTGGCCCAGAGCTCCTCACTGTTCTGAGCTCTGGCCCCATCTGTTTTCATAG
Seq C2 exon
ATGACAGAGGACATTCGTAGCGATGTGGAAGAACCAGACTCCAGTGATGACGAGCCAGTTTCTGAAGGTCCACAGCTGAAGAATGGGATGGCTCGAGGGTCTAGAGTAGCTGTTACCAATGGCCCGCGGAGCCGGGCAGCAGCATGCCTGACCAATGGGCACACCCGGGCCACATAGACAACCTTGGACTGATGTTGAGGGGTTGCCGCCAGCATTGTGAATATTCAGATGCTGGGCTGGTGATTCTGGGAGACAGGGAGGCCCTACCTCAAGGTAGGAAGAAGACTGATGATCTGTTTCCCTTCTGTTCCTCTCCCTTTATCCTTTTGAGCAGCTTGACAGAACCTGGGGGAGCAGTGGACTCTGCATCTGGCCTGAGCCAACCCCAGGCTGTAGCTTGGGGGCTGTGGGGAGCTTTGGCTCCAAGGACCAATAAAACGTCAACAGCGATGAATTCTCTGCGCCAGAGCTTAAGTTCCCTTCACAGCAGTTCCTCTCCATAACGTACTCTGTTGACAGGATTCCTCACTGCCACATCAAGATTTATGTCAACTCTTGCCTGTATAGCACCACAGCATGAAGATACTCCCTGCTCCTCAGTCAGTGCCTTCACTTTGTTCTACTTCATAGTAGCTCTCCAGGACGTTGGTGGTAGCAGATACAGGCTGACCTGTAGGAAAGAAATTCTTAAGCTTAGATGAAGCCTCTCTGCTGCTGTCCAAGCCAGAGGGTAGAGCAGAAACCTGTGGGTGTCCTTGTAGTCCCTTGCTTAAAGCAACCTGCAGCCCACCCTGGGGTCTTTATATTCCCTTGAGACAGTGGAGACCTAAGATTTGGTGTGCGGTCACTACCTTTAGGAGTGGTATAGGAAAACATCCTCCTCCAAGATGGAGGCTGAGTGACCAGTATTACTTAACGCAGAAACCAAAGCCAGAGGATCCATGTATGGTTAGACCTTGCCATCTTTGGGAGTATGCAAGAGGAACTGAGTGTCATGGAAGAATGAGAATCAGAGAGTGGGGAAAGAGGTCATCTCAGGCAACATCCAAAAATAAAGACTTTTGGTACAAAGAGCAGAGCCTGGCATGGTGACTCATGACTGTCATTTAACACTAGGGAGGAAGAAGCCAATAGACAGGAAGAACATATAAGCCTGGGATACAAAGCAGGGCCCAGTTTCAAAACAAACAATGGGGGTGTGTGCATGTGTGTCAAGGAACAGGTACTGCAGAAGAGAAAACTATACAAAAATCCGAGATAGAAACAGCTGAGAAAAGGAAGGAAAAATGCTGGGGCAAGAATGAGGGCCAACTCTGCGTACAGAACAAGGTAGTGAGATGAGATAGATTTTTGCCTTCTGGAGAAATATGAGAAAAAGGAAGAGAACTGTGGCTTCTGTTGAGAGAACAACAGTTTAGGAGAAACAGAGGGTGCATTGGTAGAGAATGCATAGAGACTTGTGAAAGAGACAAGAAGACAAAGCAACCGATAGGAAAGGAGTGGGTTAGTAGGGATCAAGAAAAAAGAAGAAAAAAAGAAAGAGAAAAAACGCTGTAGATAGTGCATGGATGAGAAAACTGGGAAAGAACAGGAAAGGGTATTCAAGACAGAAGACAGAGGGCCACTGATGAGAGAAACAGCTTCTAGAGAACTTGAGAGATGGAAACAAGGTGTGACCACAAGTCTGAAATCACAGTACTCTGCATGCTGAGGCAGGAAGATTGTAGGTTTGAGGCCAGCCTGGGAAGGAGCACCAACCTAGAAAAACAACTACAACAACAAAAATGCATAGAGTTATGTGGACACAATGGATTGTTTTCTTTCTTTTTTTTAGCTGTAAAGAATAAATCATGATAGCTGCAGAAAAAATGGATATAACTGGAAGTCATGTTTGGTAGAATAATATACAGACAAATGCTTAATGTTTTCTTTTATGCAAAACTTAGATTCAAACGATAAATATTTGTGTGTGTGTTTGCATTTATATATTTATAAGTTATGAAAATATAGGGGTCATGGGCCAGGTATGGTGGTGCACACCTTTAATCCCAGCACTTGGGAGGCAAAGGCAGACAAATCTGAGTTCAAGGCCAGCCTGGTTTTCCAAGCAAGTCCAGGACAGGTCTGTTACATAGAGAAACCCTGTCTTGAAACAAAAATAAAAGAAAGAAAGATAATCGAGTTGAAGAATGTAATCCATGTGACACAGAAATGGAAGAGTAAAGAACCAACCAGAAAGGGACAGTATGGGAGGAGCACAGGAAGAGTAATGAGTGAATGAGCGAGTCATTCGTGTTTATGCGAATGTCAGGACAAAACACATTACCTTTTACGTAATCATAAAATTTAGGACCAATAAACTTAAAATGCACACTGACCTTACTAATAACCTCAGTACAGAGTAATGCTGGGTTCTTAACCTGGTAGTTGTGATAGTTAACCTCCATTGTCAGCTCGATGAAATCTAGAGTCATCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000008206-Lass4:NM_026058:10
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=0.345
 
                        

				
Domain overlap (PFAM):

					





						

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

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000008350





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000008350f303A, ENSMUSP00000135652
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr19:8261845-8261929 
ALTERNATIVE
HsaINT0090835
(CERS4)
Human
(hg19)
chr19:8326729-8326813 
ALTERNATIVE
HsaINT0090835
(LASS4)
Rat
(rn6)
chr12:4441910-4442002 
LOW PSI
RnoINT0034881
(Cers4)
Cow
(bosTau6)
chr7:18162875-18163119 
ALTERNATIVE
BtaINT0037067
(CERS4)
Chicken
(galGal4)
chr28:100255-103854 
LOW PSI
GgaINT0145873
([1])
Chicken
(galGal3)
chr28:66775-70374 
LOW PSI
GgaINT0145873
(E1C668_CHICK)
Zebrafish
(danRer10)
chr19:8856705-8858406 
LOW PSI
DreINT0045443
(cers2a)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GACTCCATCAAGAACTCGGGC

				
R: 
TGGTTCTTCCACATCGCTACG

				
Band lengths: 
171-264

			

		

	





	
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"