Special

HsaINT0132648 @ hg19

Intron Retention

Gene
ENSG00000110844 | PRPF40B
Description
PRP40 pre-mRNA processing factor 40 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:25031]
Coordinates
chr12:50029148-50029776:+
Coord C1 exon
chr12:50029148-50029256
Coord A exon
chr12:50029257-50029625
Coord C2 exon
chr12:50029626-50029776
Length
369 bp
Sequences
Splice sites
5' ss Seq
AAGGTAATG
5' ss Score
8.99
3' ss Seq
CTGATCCTGTGGCTCCCTAGGAA
3' ss Score
10.28
Exon sequences
Seq C1 exon
GCGGGCAGAACAGACCTTTGGGGAGCTGGAGGTCTGGGCTGTGGTCCCTGAGAGGGATCGAAAAGAGGTTTATGATGATGTCCTCTTCTTCCTGGCCAAGAAGGAGAAG
Seq A exon
GTAATGGTCCCTGGGCAGAATCCTTCAGCCCATCTCATCCTGGACTTTCCTTGTCTTTGCTTTGTTATGGACCCTCGCCATTTACTTCTCTACTTCCCCAGTGTCCCAGCTTCTGACTTGGAAGCTGGTATGGGACTTGCACATCTCATTTCTGCTCTGGGCCTATAGTCCTGGGTGTAGCAGGGAGGAGGAGTCTCTGAGAGATGGGTCTGTAACCTGTACTCCCTCCCCTTCCCTGAGACATGAAAGTCTTGAGTATGGCCTTCTTCCTAGGGTTCCCTAGCTACCTTTCCCCAGGTCCTCCTCTGCCCAGGCCTACTTGGGTAGCTCTGGCCTGCCCTGCCTCACCCTGATCCTGTGGCTCCCTAG
Seq C2 exon
GAACAGGCCAAGCAGCTCCGGCGCCGCAATATCCAGGCCCTAAAGAGCATCCTGGATGGGATGAGTAGTGTCAACTTCCAAACCACGTGGTCCCAGGCCCAGCAGTACCTCATGGATAACCCCAGCTTTGCTCAGGACCATCAGCTGCAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000110844-PRPF40B:NM_001031698:13
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.027 A=NA C2=0.196
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0394210=DTW=PD(4.0=13.5),PF0184614=FF=PD(54.0=73.0)

							
A:
NA

							
C2:
PF0184614=FF=PU(75.0=82.4)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSP00000448073





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSP00000261897, ENSP00000369634, ENSP00000369634f2836A
  



Associated events






Other assemblies


hg38




Conservation


Mouse
(mm10)
chr15:99307931-99308190 
LOW PSI
MmuINT0127131
(Prpf40b)
Mouse
(mm9)
chr15:99138362-99138621 
LOW PSI
MmuINT0127131
(Prpf40b)
Rat
(rn6)
chr7:140971930-140972240 
LOW PSI
RnoINT0118343
(Prpf40b)
Cow
(bosTau6)
chr5:30381783-30382139 
LOW PSI
BtaINT0118356
(PRPF40B)
Chicken
(galGal4)
chr7:35055905-35056101 
LOW PSI
GgaINT0048636
(PRPF40A)
Chicken
(galGal3)
chr7:37185259-37185455 
LOW PSI
GgaINT0048636
(PRPF40A)
Zebrafish
(danRer10)
chr9:4736448-4737708 
LOW PSI
DreINT0120521
(prpf40a)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
AGAACAGACCTTTGGGGAGCT

				
R: 
TCTGCAGCTGATGGTCCTGAG

				
Band lengths: 
254-623

			

		

	





	
Functional annotations
(Submit an annotation)

	


There are 0 annotated functions for this event 


		










GENOMIC CONTEXT[edit]












INCLUSION PATTERN[edit]






SPECIAL DATASETS
  • Genotype-Tissue Expression Project (GTEx)
  • Autistic and control brains
  • Pre-implantation embryo development






Retrieved from "https://vastdb.crg.eu/wiki/Special:VastDB"