Special

MmuINT0123172 @ mm9

Intron Retention

Gene
ENSMUSG00000004565 | Pnpla6
Description
patatin-like phospholipase domain containing 6 [Source:MGI Symbol;Acc:MGI:1354723]
Coordinates
chr8:3537969-3541592:+
Coord C1 exon
chr8:3537969-3538085
Coord A exon
chr8:3538086-3541290
Coord C2 exon
chr8:3541291-3541592
Length
3205 bp
Sequences
Splice sites
5' ss Seq
CAGGCAAGT
5' ss Score
3.1
3' ss Seq
CTGACCTCCCGGCTCCACAGCGG
3' ss Score
7.98
Exon sequences
Seq C1 exon
GCTCCCTGTGGCGGTATGTACGTGCCAGCATGACGCTCTCGGGCTACCTACCCCCGCTGTGCGACCCAAAGGATGGGCACCTGCTCATGGATGGTGGCTACATCAACAACCTGCCAG
Seq A exon
GCAAGTGGCTGCCCACTCACATCTGCATGGACACTTATCACCAGACACATGCCCACACTGACTTCTGCACATGCCGACTGGAAGGGACAGGTCTATATGAATGGAGAAGCTCAAGAGGACACACACAGCTTTGCACAGAGTTATAGACTGACACACATGCATGCATGCATGCATATATTCATGCATACAGATATACGAGTGTATGTGGACAGTAACATGAACATTTGAAAAGTACAAACATCAGACACGGTAGCACACACTGTGATCACAGCTCTTGGGAGGCAGAGGCAGGTGGATTATTGAGTTCAAGGCCAGCCTGGTCTACAGAGTGAGTTCCAGAACACCCAGGGGCTAAACAGAGAAACCCTGTCTGAAAAACAAACAAACAAACAAGTTCAAGGCTTTCTTTAGCTACATGATGGATTTAAGGCCATCCTGGGCTGCATGAGACCCTATCTCAAAATATATATTATTTTTAATTAAAAGTAAGATATGCTCATTTGGTAGAGAATTTGCCTAGTATGAGCAGAGGTCTACATTCTATATCCTCTGCTCACACAAAGCCAGGCATGATGCTGCTCACCCATTATCCCAGGATTCAGATTGAAGCAGCAGGATTGGGAATCCAAGGCCATTTTAAGCTACAGAGCAAGTTCCAGACAAGCCTGAGCTACAGGAAATGAAGTGCCTTTCCATTCTCATGTGTCACAGTGGACACAGAGAGGCTGGCATATGAGGGACAAGAGCTGGAGCCTAGTTACACGTGCACATGCATAGAGATCACGCTTCTACATGTGCACACCAGCTCCCTATGCACACCTGTTCTCTCGGGTGCTTACATAGGCAGAACACATGAACATGTGTGAATACACACATACTTGAGATGGAATTAACCACACTGGCCACACCTTCCCTGAACAGTCTATGGAATATGCCTGTATAGACCTGAAGATTGAATAAGGTGCCTATGTGACCAAGATAAGCATTTTTTCACACCCACCAACTTAAAGGTTCTTTTTTGTTTGTGTTTTAGACAGGATCTAGTGTAGTTCATGGTAGCCTCAAACTTGATAGGTAATCAGAGATGATCTTGAATTTCTGATCCTCCTGCCTCCACGTCTGGGCTGCTGGGATGACAAATGTGCTCCACCATGCCCCGTTTGCATGGTGCTAGGGATGGAATCCAGGGCTCTTGTGCTGCACAGACACTCTACTAACTGAGCTACATTCCCATCCTGCTGCTGACGTCACACACATAGGTGGGAGGTCGATGCAAGTGCAGCTCTGAGAAAACCTCATTCTCTTTGTGGCTGCACAACCTTTAATGCCAGCACTCCAGAGATCTCTGAGTTCGAGGCCAGCCTCATCTACGTAGTGAGCTTCAGAACAGCCAGGGCTACACAGAGAAACCCTGTTTCAAAAAACAACCAACAAACCAAAAGAACTCGGTCTCAGAAGTGTATGCTCCAGAAACATAAGTTAGTTACACACAGACACACATGCTTGATCTCATAGACCAGGATCTGGCCAGCTATAGCACACTGTGTGCATCTGGGCCTGTGCTTGACTTTATGAATAAAGGATTTCTTTATATTTACATATGTATTTGTGACCACAACACATGGAGGTTGAAGGACAATTAATAGGAGTTTTCTCATTCTAAAATAACCAGTTGAACTCTGGTTATAATGGTTTGGTAAGTGCTCCACCTGCTGAGTCACCTACATGACCATGTTTAGTTAGTTAGTTAGTTAGTTAGTTAGTTGTTAAACCCGAACTGACCTCTAGCTTCCTACGTAGCTGAGGTTGGTCTTGAATTTATTCCTCCTCTGTCCACTTCCCAAGTGTTGGGATTCTAGGCCTGAGCCTGGCTTAGAAATAACGATTCACTGGGATAGCCATGCCCATGACCCACCTCTCATCTACTGTCTCTGTTGCAGAACAACAGGGGTGAAAACTCAGAGCAGAACTAAAAGCGTTTTCTAATGGTCCTGCAAGCACTGGAAATGTACTATACATGTAAACACTGCCACAGTCCCTCATATGGCGTTCACATAAGTGTTCACAGACCTACAGATAGACACCATACTTGGTTATGCAAACGTAACCTGAGCTCCATCCCAGTACCCATGTAAAGATGGTCACAGCGGAGGACATCCATAGCCCAGCACTTTGGATGGGTGGGGGGAGTAGACTTTAGGATCCCCAGGGCTCACTGGCCAGCCAGTCTAGTGGAACGGATGAACTCCAGGTTCAGTGGGTACCTTTTCTAATTTAAAAAAAAAAAAAAGGGTGCAGTCAGGCTGCAGGCAGTTAAGAATGTGCACTGCTCTTGAAGAAGACTTAAATTCTGTTCTCAGCACCTACATCTTCACAACTACCTGTAACTCCATCTCCAGAGACATCTAATGCCTCTCTTGGCCTCTGCAGACATTGTGCACATATGCACATAAGCACATGCAGGCACACAACTATGTACACAGAAATAAATCTATTATTTGTTTTGTTTTGTGTTTTGAGACAGGATATCTCTGTGTGTAGTCCTCAAGGTCCTGGAATTCATTCTGTAGACCAGGCTGGCCTTGAACTCAGAAATCCACCTGCCTCTGCATCCTGAGTGCTAGGATTAAAAGTGTACATCACTTAATTTTTATTTTTATTATTTTTATTTTTAAGGTGTCAGGTGATAGAGGAAGACACTCAGTGTTAACCTCCAGCCTGCACACAATACACACACAAATACACGCATACACACACATACGGGTGGATATTTCCTGGCATGCATTTAGACCGGCTGAGCGAGAGAGATGCAGTCATAGGAAGACATGGTGCTTCCCATGGGGTCTCAGAGAAGAGAGATGTAAACAGACAATCACAGGCATGTGCAGCTGACATGCATACCCAGCAACATAAACTCAAGGATAACTACACAAAGTTGAATAGGCAGTCAGGTATTTCCTTGGGCTGGGGTTGGCTCTGTAGTACACAGACATACAGACATACAAACATAACTGCCATTCTCACTGGACCATCTTATCTTGGCTTGTTTGCATAAATTTCCATGTCATTTGCATGCTTGTCATTTGTGGTGTTTGCATGCTCCCCACCCCCCAACCCTCATGTGCCCATTTGCATTGTGGTATCTGTGGGTCGTTTGTGTATCCCTGTCCTGCTGGGAGGGGCTGCTGACCTCCCGGCTCCACAG
Seq C2 exon
CGGATATTGCCCGAAGCATGGGAGCCAAAACGGTCATTGCCATCGACGTTGGAAGCCAGGATGAGACAGATCTCAGCACCTATGGGGACAGCCTGTCTGGCTGGTGGTTGCTGTGGAAAAGGCTAAACCCCTGGGCAGACAAGGTAAAGGTTCCAGACATGGCTGAGATCCAGTCCCGCTTGGCGTACGTGTCCTGTGTGCGGCAGCTAGAAGTCGTCAAGTCCAGCTCCTATTGCGAGTACCTTCGTCCATCCATTGACTGCTTCAAGACCATGGACTTTGGAAAGTTTGACCAGATCTAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000004565-Pnpla6:NM_015801:29
Average complexity
IR-C
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:
PF0173417=Patatin=FE(23.4=100)

							
A:
NA

							
C2:
PF0173417=Patatin=PD(2.4=4.0)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000004681





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000106699
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
chr19:7557285-7558849 
ALTERNATIVE
HsaINT0128580
(PNPLA6)
Human
(hg19)
chr19:7622171-7623735 
ALTERNATIVE
HsaINT0128580
(PNPLA6)
Rat
(rn6)
chr12:2091745-2095415 
ALTERNATIVE
RnoINT0114514
(Pnpla6)
Cow
(bosTau6)
chr7:17643546-17645340 
ALTERNATIVE
BtaINT0114800
(PNPLA6)
Chicken
(galGal4)
chr17:1682277-1685308 
ALTERNATIVE
GgaINT0125241
(PNPLA7)
Chicken
(galGal3)
chr17:2081947-2084978 
LOW PSI
GgaINT0125241
(PNPLA7)
Zebrafish
(danRer10)
chr1:45183744-45187955 
ALTERNATIVE
DreINT0116744
(pnpla6)
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"