Special

HsaINT0132650 @ hg19

Intron Retention

Gene
ENSG00000110844 | PRPF40B
Description
PRP40 pre-mRNA processing factor 40 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:25031]
Coordinates
chr12:50030499-50031367:+
Coord C1 exon
chr12:50030499-50030632
Coord A exon
chr12:50030633-50031252
Coord C2 exon
chr12:50031253-50031367
Length
620 bp
Sequences
Splice sites
5' ss Seq
CAGGTATCT
5' ss Score
7.33
3' ss Seq
ACTGGCCTCTCCCTGCTCAGACC
3' ss Score
9.21
Exon sequences
Seq C1 exon
ACATGGACAAGGAAGATGCACTGATCTGTTTTGAGGAGCACATCCGAGCTTTGGAGAGGGAAGAGGAGGAGGAACGGGAGCGGGCCCGGCTTCGGGAGCGACGCCAACAACGCAAGAATCGGGAGGCCTTCCAG
Seq A exon
GTATCTTTGCTGTCCTTTCTAGATCAGAGCTCAGCTCTGCCCTAGAGCACAACCTCTTCACCCATTCCCTGCCCCCTTCTGGATACGCTGCCTGTTCTTTCTGTGCCTAGCCCTGTCCAAGCTCTATGAGACCTCTCTCTGCCTGCAGTCTGTTTCTGCTGTACCTCCTCAATTCTGGACTGTGCTCTTCTAGGGAGACTAGATGTATGCACCACCCAGAAACTGCCAGTAGAGAGCACCCTACAGGCATGACTTGGCAGCTAGGCCATGTTTATTTCCCTTGGTGGGGCACCCGACAGGCAGAGTTTATTCCCTCAGCTTGGGGGTGGCAGTGGTGGTGGTAGTGCTAGGGGTTACTGCAGGCAGGTTTCTGTTTCTTTGCATCCCGGGACTGGCTTGTTCTCACCTTTTTGTTCTGTCCCTCTCTGTGTATTTACTTTCTCTCTTTTTGCATTGTTCTCAGCCTTCCATCTGCATCTCTTCATCTCTGCCTCTCTTGCCTGCATTTCCTCAATCTTGATTGTCCCTGCCTCTTCCTCTGCCATTCCCTCTCTTCCCCCTCAGTCTGTGGCTCTGCCTCCCTGTCTCACTCTCCCTATAACTGGCCTCTCCCTGCTCAG
Seq C2 exon
ACCTTCCTGGACGAGCTGCATGAGACAGGGCAGCTGCACTCTATGTCCACCTGGATGGAGCTATATCCAGCAGTCAGCACTGATGTCCGCTTTGCCAACATGCTGGGCCAGCCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000110844-PRPF40B:NM_001031698:15
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact

ORF disruption upon sequence inclusion

No structure available
Features
Disorder rate (Iupred):
  C1=0.333 A=NA C2=0.000
Domain overlap (PFAM):

C1:
PF0184614=FF=PD(23.2=28.9),PF091066=SelB-wing_2=PU(46.3=42.2),PF0184614=FF=PU(10.7=13.3)
A:
NA
C2:
PF091066=SelB-wing_2=PD(48.8=51.3),PF0184614=FF=FE(67.9=100)


Main Inclusion Isoform:
NA


Main Skipping Isoform:


Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
ALTERNATIVE
Chicken
(galGal3)
ALTERNATIVE
Zebrafish
(danRer10)
LOW PSI
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACATGGACAAGGAAGATGCACT
R:
AGCATGTTGGCAAAGCGGA
Band lengths:
238-858
Functional annotations
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