Special

MmuINT0122163 @ mm9

Intron Retention

Gene
ENSMUSG00000034247 | Plekhm1
Description
pleckstrin homology domain containing, family M (with RUN domain) member 1 [Source:MGI Symbol;Acc:MGI:2443207]
Coordinates
chr11:103235254-103238827:-
Coord C1 exon
chr11:103237907-103238827
Coord A exon
chr11:103235400-103237906
Coord C2 exon
chr11:103235254-103235399
Length
2507 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCTG
5' ss Score
4.87
3' ss Seq
CCCATCACCCATTTCCCTAGGCT
3' ss Score
7.92
Exon sequences
Seq C1 exon
GGCTGTCCAACCCATTCCGGGGCCTCATGAAGCTGGGCACAGTGGCCCGGCGAGGAGCCATGGGCATCTGGAAGGAATTCTTTTGTGAGCTGTCCCCGTTGGAGTTCCGCCTCTACTTGAGTGATGAGGAACGCACCTGTGTGGAGAGCTGCTCCCTGCTCCGATGTGAGGCTGTGGGGCCAGCACACAGTGATGGACGTTTTGAGTTGGTCTTCTCGGGCAAGAAGCTGGCTCTCCGTGCCTCCTCCCAAGACGAGGCTGAGGACTGGCTTGACCGCGTACGGGAGGCTCTGCAGAAGGTGCGCCCTCAGCAGGAAGATGAGTGGGTGAATATCCAGTACCCAGACCAGGCTGAGGATGCCCCAGAGGCTCCACCAGACAGCCTCCCCCCCTATTCAACTCTACTCCCCGAGCCTGCGGGTGCCCAGGGCATGCAGTTGGACTGGACATCTGCCCAGGTTCCAGAACCAGATGCTATCAAAGAGTCCCTTTTGTATCTGTATGCAGACCGGACCTGGGTCCCCTATATCTTTTCCCTGTCCTTGGAGTCTCTGAAATGTTTCCGAGTGAGAAACAATGAGAAGATGCTAAGTGATAGCCATGGAGTGGAGACCATCCGAGACATCCTGCCAGACACCAGCCTTGGGGGCCCAGCCTTCTTCAAAATCATCACGGCCAAGGCCGTCCTGAAACTGCAGGCCAAAAACACCGAGGAGGCCACCCACTGGAGAGACCTGGTCCGGAAAGTGCTGGCATCTTACCTAGAGTCAGCTGAGGAGGCTGTGACACTTGGTGGGAGTCTGGATGAAAAATGTCAGGAGGTGCTGAAGTTTGCTACCAGGGAGAACGGCTTCCTGCTACAGTACCTTGTGGCCATCCCGACCGAGAAGGGCCTCGACTCCCAGGGCTGCTTCTGCGCAG
Seq A exon
GTGCTGACTGACTCTCTACCAACCCCAGCCTCCTGTGTTCTTCCTCCTATGGAGTCATCAGTTTGGGCCCCCAACAATACAGCAGACTGGCGCCTACACTGCAGCCTCTGCTCCTCCACAGGGCCCTCTGTGTACAGCCCCTGCCTGTCTCTTGACATCTCCTAATACTGGGTGGGACCTGTGGGTGGCAGTCCTGCTTCCTGGGCCTTCCCGCTTCACTGCTGCACTGCGTATAAGGGTATAGGATTCTTCACAAGCTCGTATGCTTGCATGCTTTTGTAAGGCATGCTGTTCAGTGCTGCCAGTAGGGCTTCTGTAATGATGAAAGTGCCTGGGTCTGTGCTTTCCAACTCTAGTTCCAGGTTACATCCAGCCACTGCGTGCTTAAAGGGGAGCTGTGTATAATTAAGAGCAAAATTTTCCATTTACTTAAGTATAAAGGCAACCTCTGACTTTGAGCCACTGTATTGGACAACATACTAACTACTCCACGATTTGAGGGTTCATCCACCCACATGTCTCATGTAGCCTAGGCTGGCTTTGAACTCTTGGTCCTCCTGCCTTCTAGGTACTGGGATTATAGGCATGTGTTACTGTGCCCCGACACTTTTTTTTTTTTTTTTTTTTGAGTTGCAGTTTCACTATGTAGTCAAAGTTGGTCTTGAATTCTTGCTTCCTTCCTCAGCCTCCTAAGTAGTGGGATTACAGGCATCTGTCACCACACCTCGTTGGCTTTCCTATGCCTGCTTTTCTCTTATGTGAGTGATTCCGTGGGAAGGATTCGGCTGTGTTGGTATCATCATGGGATCTGATCCTGTGCAGGGCACAAAGCCAGACGCTTTGTTTGGATTCTCTCATTTTTTGCTCAGTACATCCTCATAGAGTTAGGAGCTATTATTTCCTCATTTTATGTTATAGGTGAGGAAACTGGAGCCCAAAGCTAGAAGCTTGTCTCAGGCTTTCAGTATATTCAAGAGGCAGAGCTGATGATTGTGTCCTAGAACTTGCCCTCCTTGGCATGACACCAGAGGGCCTCCCAGTCTCGTGATGTCCCACTGTCTTCCTTCCATTGGCACCTCTTCCCACCTGTCCCTGGGACATGCTGTCTGGGAGAGATACCAGCTGCCCTATTGCAGAAGAATAGAGCTGAAAGCTGAGCTGTCCTGATGGGGTGGAGACCACAGAGGAAAGCCTGCCTCCAGTGCCTGGAAGGAAGTGGCCTGTGGCAAGCCCTGGAGGGTGGGCTGAGCAGAGCTTCCTGCAGAAAACACCTGCAAACCTGCCTGCCCCTGCACTCACAATCCAAACTGGGGGGGGGGGGGGAGCTTCTGGCAGTGGGTGTGAGTATTATAAGGAGAACTCATTCCTGCCAGCCTGCTGTCGGCAGAGACTGGTATACCAAGGAGTTCAGGCATTCTACACTGCTGCACTGTCCCATGGCCATGACGATGCCAACCAGAAATACTTGTGTTGGAATTCACAGTTTACAGGGCACTTGTATTAGTTACACTTTGTAATGACCTCACCAGAGCTGGCAGTAGCTAAGGTATACAGTGAGATAGAATCTTAGGAGAATCGGGTGAAGGTGCGGATGAGGCCGCTCAACAGCAAGAAAGCCAGCTCTTTGGCCTGAGACCAAAGGAACCTTTTCGAAACCACACTATCTTTTTGCCTTGGGCACTCCTGATCCTTGACTCTCTGCTCTCTGGTATGGAGACCGTACTGACCACATGGCTAACGCTGTCACTGCCCACTGTCTTGAGATTTGCTGCTGTCGACGCAGATGGAGACCATGTTGTGTCTAGGTCATGCTGTCTTTCCTGCTGGCTTCCTCTCCACAGCTTCCTCACTAGTCAAGGTCCTAGCTTTGTTGCTGGTGTTTGTGAACCCCGGGTGGGGAAGTAGGGGTTCAGGTTGGCAGTGGGGAGCAGGCAGGGAGCGAGTGAACAGAGGTGGCAGTGGAGGAGAATGGTGACTTGTGGCCAAACCCGACTTGGAGTGCCACCTGTCACTTAGTCTTGGTGGGACCTGACAGATCCCTCTCGGTGAGTTTGCTTTGAGACAGTTCTCACTGTGTAACCCTAAGCTGACCTCGGACTCAGAATCCTCCTACCTCGGCTTCCAAGTTCTCCCCGACCCAGCAATAACCATTTAATAATATACTGTGATAATTAACAGTTTTTCTAGGTGTAGTGGTGCACAAAGTGCAAGCCTGTAATCCTCACACTTGGGAGACAGACAGCTGACAGATATCTGAGTTCAAGAGCAGCCTGTTCTACATAGTAAGACCCTGTCTCAAAACTAACAAAATCACAAAAGTTTTTATTGTAAGTGGTGGGGTTGTGTGGTTAGAAATGCTTATATATTTATTCATTGAGAGAGGGAAGGTCTGAGGAATCGGTTCTCTATTTTTGTATTTGCATGTCTTTCTCACTGGAGCCGACTCTGTGTTCCATGAAGCTGACTCTGGCCCTCACTGCTTATTCACCCATCACCCATTTCCCTAG
Seq C2 exon
GCTGCTCCCGACAGATCGGCTTCTCCTTTGTACGACCCAAGCTCTGTGCCTTCTCTGGCCTGTATTACTGTGACTTCTGCCACCAAGACGATGCCTCAGTGATTCCAGCCAGAATCATCCACAACTGGGACCTCACGAAGCGCCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034247-Plekhm1:NM_183034:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.114 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
PF139011=DUF4206=PU(17.1=71.4)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000047327





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000047327f3242A
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr17:45450764-45453354 
ALTERNATIVE
HsaINT1027368
(PLEKHM1)
Human
(hg19)
chr17:43528130-43530720 
Rat
(rn6)
chr10:91462289-91464794 
ALTERNATIVE
RnoINT0113453
(Plekhm1)
Cow
(bosTau6)
chr19:45729865-45732300 
LOW PSI
BtaINT0113834
(PLEKHM1)
Chicken
(galGal4)
chr27:1590592-1592290 
ALTERNATIVE
GgaINT0143838
(PLEKHM1)
Chicken
(galGal3)
chr27:1495088-1495992 
HIGH PSI
GgaINT0143838
(PLEKHM1)
Zebrafish
(danRer10)
chr12:4915776-4917684 
LOW PSI
DreINT0115985
(plekhm1)
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"