Special

MmuINT0127369 @ mm9

Intron Retention

Gene
ENSMUSG00000015476 | Prrt1
Description
proline-rich transmembrane protein 1 [Source:MGI Symbol;Acc:MGI:1932118]
Coordinates
chr17:34768715-34769205:+
Coord C1 exon
chr17:34768715-34768900
Coord A exon
chr17:34768901-34769028
Coord C2 exon
chr17:34769029-34769205
Length
128 bp
Sequences
Splice sites
5' ss Seq
CAGGTGTGG
5' ss Score
6.34
3' ss Seq
CCCTCGCCCCTCCCCGGTAGGTG
3' ss Score
10.04
Exon sequences
Seq C1 exon
CCCTACGCAGGCGGGACCCCCGGGGGTCCTGGAGTGACCTCCACTCTGCCCCCGCCGCCCCAGGGCCCAGGATTGGCTCTGTTGGAGCCCAGGCGTCCGCCACACGACTACATGCCCATCGCTGTGCTGACCACCATCTGCTGCTTCTGGCCCACAGGCATCATCGCCATCTTCAAGGCCGTGCAG
Seq A exon
GTGTGGGGTTGACCAGGGTTTTCTTAGTCTGGGGCATTCTGGACTTATTCTCAGAGGGGAGGCTGTGGCGGGTGAGCAGTGGCTCTCTGACCCCCCCCCCCCCCCGTTCCCTCGCCCCTCCCCGGTAG
Seq C2 exon
GTGCGCACGGCTTTGGCCCGCGGAGATTTGGTGTCTGCCGAGATCGCTTCACGCGAAGCCCGGAATTTCTCCTTCATCTCCCTGGCCGTGGGCATCGCAGCCATGGTGCTTTGTACCATCCTCACTGTAGTCATCATCATCGCCGCCCAGCACCACGAAAACTACTGGGATCCCTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015476-Prrt1:NM_030890:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.403 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF045057=Dispanin=PU(54.4=79.0)

							
A:
NA

							
C2:
PF045057=Dispanin=PD(43.3=66.1)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000015620





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr6:32149399-32149536 
LOW PSI
HsaINT1028182
(PRRT1)
Human
(hg19)
chr6:32117176-32117313 
Rat
(rn6)
chr20:4395047-4395187 
LOW PSI
RnoINT0118641
(Prrt1)
Cow
(bosTau6)
chr23:27040395-27040472 
BtaINT0118680
(PRRT1)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
chr19:27273993-27276401 
LOW PSI
DreINT0120765
(prrt1)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CCACACGACTACATGCCCATC

				
R: 
AGTAGTTTTCGTGGTGCTGGG

				
Band lengths: 
253-381

			

		

	





	
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"