Special

MmuINT0093764 @ mm10

Intron Retention

Gene
ENSMUSG00000040488 | Ltbp4
Description
latent transforming growth factor beta binding protein 4 [Source:MGI Symbol;Acc:MGI:1321395]
Coordinates
chr7:27308921-27309414:-
Coord C1 exon
chr7:27309286-27309414
Coord A exon
chr7:27309068-27309285
Coord C2 exon
chr7:27308921-27309067
Length
218 bp
Sequences
Splice sites
5' ss Seq
TTGGTATGA
5' ss Score
5.24
3' ss Seq
TTCCTCCCATACTTTCCTAGATA
3' ss Score
8.67
Exon sequences
Seq C1 exon
ATGTGGACGAATGCCAACTCTTCCAGGACCAGGTGTGCAAGAGCGGAGTGTGTGTGAACACGGCCCCAGGCTACTCTTGCTATTGCAGCAACGGGTTCTACTATCACGCACACAGGCTGGAGTGCGTTG
Seq A exon
GTATGAGCCCCACCTTCCCCACCCCCAATTCTGGCCAGGCCAGTCCCCCCTCCAACACCCCACCCCACCCCACCCCCGCCCCAAGTAGGAATGTAGCCAACCCAGCAGGAAGTCTAGACTCTATCCATCACAATGTGAGCTGAGGAAATGTGAACCAGAGTTCATCCTGGTAACTGCCTCCCCCGCAACCCCCCGCCCTTCCTCCCATACTTTCCTAG
Seq C2 exon
ATAATGACGAATGTGCGGACGAGGAGCCTGCTTGTGAAGGTGGCCGCTGCGTCAACACGGTGGGCTCTTACCACTGTACCTGCGAGCCCCCACTGGTGCTGGACGGCTCCCGGCGACGCTGCGTCTCCAACGAGAGCCAGAGCCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000040488:ENSMUST00000038618:28
Average complexity
IR
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:
PF0764510=EGF_CA=WD(100=95.5),PF0764510=EGF_CA=PU(0.1=0.0)

							
A:
NA

							
C2:
PF0764510=EGF_CA=WD(100=82.0)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000037536





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000104006, ENSMUSP00000113523, ENSMUSP00000113674
  



Associated events






Other assemblies


mm9




Conservation


Human
(hg38)
chr19:40623733-40623935 
LOW PSI
HsaINT0097620
(LTBP4)
Human
(hg19)
chr19:41129638-41129840 
LOW PSI
HsaINT0097620
(LTBP4)
Rat
(rn6)
chr1:84121835-84122014 
ALTERNATIVE
RnoINT0087609
(Ltbp4)
Cow
(bosTau6)
chr10:86190511-86190811 
LOW PSI
BtaINT0087898
(LTBP2)
Chicken
(galGal4)
chr5:37215347-37215547 
LOW PSI
GgaINT1017198
(LTBP2)
Chicken
(galGal3)
chr5:40343424-40343624 
GgaINT0059005
(LTBP2)
Zebrafish
(danRer10)
chr18:49017870-49017950 
LOW PSI
DreINT0013908
(LTBP4)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
ATGTGGACGAATGCCAACTCT

				
R: 
CCAGGCTCTGGCTCTCGTT

				
Band lengths: 
276-494

			

		

	





	
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
  • Ribosome-engaged transcriptomes of neuronal types
  • Neural differentiation time course
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types





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