Special

MmuINT0093774 @ mm9

Intron Retention

Gene
ENSMUSG00000040488 | Ltbp4
Description
latent transforming growth factor beta binding protein 4 [Source:MGI Symbol;Acc:MGI:1321395]
Coordinates
chr7:28112280-28112806:-
Coord C1 exon
chr7:28112657-28112806
Coord A exon
chr7:28112532-28112656
Coord C2 exon
chr7:28112280-28112531
Length
125 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
AGATGCTCTTTCTTTACCAGGCT
3' ss Score
7.92
Exon sequences
Seq C1 exon
AGGGTTTTCGGGAGATCTGTCCAGCTGGCCCTGGCTACCACTATTCAGCTTCTGACCTCCGATACAACACCAGACCCCTAAACCAGGATCCACCTCGAGTGACCTTCAATCAGCCACGTGTTCCACCAGCCACCCCTCGGCCACCTACAG
Seq A exon
GTGAGCTGGAACCTGGATGGAGGGCGTGCCATCTCCCAGGTGCTGTTGGGAGCAGATAGAAAACCATGGCGAGGAGCAAGCATACCCAAATTTAGAACCCTGGACAGATGCTCTTTCTTTACCAG
Seq C2 exon
GCTTTCTGCCTACTCGTCGACCTGAGCCCCGCCCTGACCCTGGGCCACAGCCTGAACCCCGGCCTCGGCCTGAACCCCGGCCTCGGCCTGAATCCCGACCTCGGCCTGAACCCCGGCCTCGGCCTGAACCCCGGCCTCAGCCTGAATCCCAGCCTAGGCCTGAATCCCGGCCTCGGCCTGAATCCCAGCCTTGGCCTGAATTTCCCCTGCCCAGCATCCCTGCTTGGACCGGTCCAGAGATTCCTGAATCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000040488-Ltbp4:NM_001113549:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.667 A=NA C2=1.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0068312=TB=PD(11.6=9.8)

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000037536





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000104006, ENSMUSP00000113523, ENSMUSP00000113674, ENSMUSP00000113746, ENSMUSP00000127897
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr19:40608370-40608483 
ALTERNATIVE
HsaINT0097602
(LTBP4)
Human
(hg19)
chr19:41114276-41114389 
LOW PSI
HsaINT0097602
(LTBP4)
Rat
(rn6)
chr1:84139742-84139870 
LOW PSI
RnoINT0087591
(Ltbp4)
Cow
(bosTau6)
chr18:50184404-50184528 
BtaINT0087937
(LTBP4)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
TCAATCAGCCACGTGTTCCAC

				
R: 
CAGGGGAAATTCAGGCCAAGG

				
Band lengths: 
254-379

			

		

	





	
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






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