Special

MmuINT0114455 @ mm9

Intron Retention

Gene
ENSMUSG00000054582 | Pabpc1l
Description
poly(A) binding protein, cytoplasmic 1-like [Source:MGI Symbol;Acc:MGI:1922908]
Coordinates
chr2:163858224-163861118:+
Coord C1 exon
chr2:163858224-163858318
Coord A exon
chr2:163858319-163860980
Coord C2 exon
chr2:163860981-163861118
Length
2662 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGT
5' ss Score
10.29
3' ss Seq
TTCCTCCTCTTCCTCTCCAGGCC
3' ss Score
12.24
Exon sequences
Seq C1 exon
GAAATATGCAGAGTGTGAAGGTGATGAGAGACAGCAATGGGCAATCCCGGGGCTTCGGCTTTGTCAACTTTGAGAAGCATGAGGAAGCCCAGAAG
Seq A exon
GTAGGTGTCTCCATGGTTCTGCTCCAGAAAGGAGCCGCAAAGCCAGGCTTGGGAAGCCAGAAGATCAGGGGCAGGCCTGCCAGCAGAGGGTGAGAAAGCCCCGCCCTCCCCCTGCCCCGCCCCCTGCCCGGAATGGTAGGATTTGGCCTTATCCTTCCTTGTTGGTTTCTAAATCTAGAAGTTCAAAGAATTGAACATTTAGGCATGGAAGCATTCCTCACTGTGTGCAAACACTAATAACTGACTTCTTGGGAAGCCAGAGTTCCCCCTCAAATATTTCTCCCCACGCCAGTAAAAAGTCCTAACCACCGAGTCAGTGTGCACTAGGGTCTGTCTGACTACCATGGCTTTCTGTGGATAAACCGATGGGAAATCAATTCTTCAAGTGGATGTCCTCAGGCAGAAGGTGCAGGATCGTATGCCATGTAACAGGGTCAGGCTTGTTAAGAAGAGAAAACTCTCAGGGCTGGAGAGATGGCTCAGCAGTTAAGAATACTTGCTGCTCTTCCAGAGGCCACTGAGTGCAGTTTCCAGCACCAACATCAGTGGGCTCACAACGGGCTGTAACTCCAGCTCAGGGATCTGCTGCCCTCTTCTGGCCCCTTGAGCACCTGCCCACAGGCAGCACACTCACACACAGATAGACACCATACATTACATCTTTTTCTTATATGCTTTGTAATGTAATGTAAAATATTGAGGTGGCCGGGAGATGGCAGAGTGGTTAACAGCACTGGCTGCTCTTACAGAGGACCTGGGTTCAATTCCCAGCTCTCCCATGGTAGCTCACAACCATCCATAACTCCATGTCCAGGGAATCTGACTCCCTCTTTTGGCCTCCATGGGCACCAGGAACAGACATAGTACACAGACACAATTCAAACTGTTATACACATAAAATAATAAAATAACTTTATTTTTATTTTATTTTTTTATTTATTTATTTTTAGTTTTTTGAGACAGGGTTTCTCTGTGTAGCCTGAATGTCCTGGACCTCACTCTGTAGACCAGGCTGGCCTCGAACTCAGAAATTCGCCTGCCTCTGCCTCCCAAGTGTTGGGATTAAAGGCATGCGCCACCATGCCCAGCTAACTTTAAATTTTTTAAAAAAATATTTTTTTTAAAAAGAAGATAAAGCTGGGTGGTGATGGCACTCTCGGGAGGCAGAGGCGGGCAGATTGCACGAGAGTTCCCAGATAGCCAAGGCTACACAGAGAAACCCTGTCTCAGAGAGAGAGAGAGAGAGAAGAAAAGAGAAAGAGAGGGAGGAAGAAGAGGGGGAAAGTGAGAGGAAAGAGGAAGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGAAGAAAAATCAGGATTGAAGTGCAATGTTTCTTGAACTTATGAAAGCCCTCATGGTTAGCAAAAGGCATTGTTCTGCATTGTAAACTGTACCACGAAGGATTGTGATTTAGACACCAAGCCATCTTGGAAGAACAATGCTTGCTTTGTTCTAATGAGCCCTGTGTGGGGGCGACAGAATACAAGTTTAACTTATTTTCTAATAGACCTTCTAGAGCAGTGTAAAGTTCCTGGCAAAACTGGGTAGATGGCGTAGATGTCCCCCATACCTCTGCCATGCACAGCTTCCCCCACCCTCAGCATTCCCAGCAGGGAGGTACATTTGTCACACTGGCGAATCTACTTCCGCGATGTACCATCATCAACTGGGGGGGGGTGTCTCTGGTTTACTCTGGGATTCATTCTTGGTGTTGTTCACTCTCTGGCTTTGGACCAATATCGAAGTGTATGCATCCACCGTTACCATAGTTTTAGCTCTCTAAAGCCTGTATTCCACTAGTCCTTTACAATCTGCTAGCCTCCTGACCTGCACTGAGTTTCTTACTGGCCTCGAAGTTCTGCCTTTTCCAGACTGTCACCTGGAGAGAGTTAGATGTTCATTAGAGTGAGAGTTAGTTGCATCCTTTACGGATTGGCTTCTTTCAGTGGAATGTGCATTTAAATATTTGGGGCTAGAGAGCTGGCTCAGCAGTTAAGAGTTCCTGCAGAGAATCCAAGTTCAGTTCCCCTGGACTCTACAGTGCAGTAGGAGGCTCACAACCCTCTGTAGCTCTGGGGATCTGATGTCCTCTTCTGGCCTCACTGGGCACTGGCATACAAGCATTCATACCAATGCATACCAATACAATGTACCTACACACGCATTAAACGTCTTTAAATTTAAATATGGAAAACTTAACATTAATTTGAGTTTTGTTTTTCTTTTCGTTTGAGACAGGTTCTTAGCTTGTAGCCACAACTGGCCTGGTCAAAGAGGAAACCAAGTTAGCCCTATACTTACCACAGTTCTCTGTCCCATCTCCTGGATGCCAGGGTTCACAGCCACATTGTCACCACTCAGGCTTCTGTTTATTAAAATAAAGCCTAAATCAAAAATATTAAATCCATCACTTACTCTAGAATCTTGGCCATTTCTTTTAAAATGTGGTTGTCCTGTAAGAGACTTTTCCATGGTATCAATTATTCTCAGCTAAGAAGGCCAGCCTAGTTATAGGTGGTCTCAGCTGGCCCAGGAGTCAGGATTGGAGACAGGGCCACGTGTAGATGGTTCACCAGGGGCTTTCCTCCTCTTCCTCTCCAG
Seq C2 exon
GCCGTGGACCACATGAATGGGAAGGAGGTGAGCGGGCAGCTGCTCTATGTGGGTCGGGCCCAGAAGCGGGCAGAACGGCAGAGCGAGCTGAAGCGCAGGTTTGAACAAATGAAGCAGGAGAGGCAGAACCGCTACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000054582-Pabpc1l:NM_001114079:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.062 A=NA C2=0.391
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0007617=RRM_1=FE(44.3=100)

							
A:
NA

							
C2:
PF0007617=RRM_1=PD(21.4=32.6)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000096701





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000096701f5838A
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr20:44919278-44921593 
LOW PSI
HsaINT0119423
(PABPC1L)
Human
(hg19)
chr20:43547919-43550234 
LOW PSI
HsaINT0119423
(PABPC1L)
Rat
(rn6)
chr3:160419830-160423131 
RnoINT0106589
(Pabpc1l)
Cow
(bosTau6)
chr13:74053143-74055479 
LOW PSI
BtaINT0106813
(PABPC1L)
Chicken
(galGal4)
chr20:5581836-5582131 
ALTERNATIVE
GgaINT0010609
([1])
Chicken
(galGal3)
chr20:5201243-5201538 
ALTERNATIVE
GgaINT0010609
(PABPC1L)
Zebrafish
(danRer10)
chr19:12215163-12215262 
LOW PSI
DreINT0109558
(pabpc1b)
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"