HsaINT0132646 @ hg38
Intron Retention
Gene
ENSG00000110844 | PRPF40B
Description
pre-mRNA processing factor 40 homolog B [Source:HGNC Symbol;Acc:HGNC:25031]
Coordinates
chr12:49634538-49635263:+
Coord C1 exon
chr12:49634538-49634602
Coord A exon
chr12:49634603-49635098
Coord C2 exon
chr12:49635099-49635263
Length
496 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGC
5' ss Score
9.88
3' ss Seq
ACTCCTACCCTCTATCCCAGTGC
3' ss Score
7
Exon sequences
Seq C1 exon
GCTGTCCCCTCCAATGCCTCATGGGAACAGGCCATGAAGATGGTGGTCACCGACCCCCGTTACAG
Seq A exon
GTAGGCCTGGGCAGAGGGAGCCAGGCCCTGTTCATGAGAGCAGCTGTGCTAGGGACTCCCTAAAAAACCCCAGCTCAACACTCAGCCCTAAGGGAACCAGAGTCAGGACAGTGATAGATTGGGTTGGGGTGCAAGGGGAAGAAAAGCTGGAGGGCCTCCAGGAGAAGGAAAGGAAAGGTATCTGACACAACACGTTCAATAAATGCTTCCTGAATTGAATCAAACGGAATTGAATTAATTGGGGAATGAGGGTGCTGGATAGGGTGACTTGAGAACCCCAAAGGAAAAGGGCCCAGTATTTGCAGTGTCTTGGAGCTGCATCTCTTCCCCTCACTTCCTGTCACCCCTACTTCTCCATGAATGGTGTTCAGATCCCAGACATCTGTGCCCTTGGAGCCCCTGCAGCCTGCAGTGTCTCATGACCCTCCAGTGTGGGCTGTGCAGAGTGGTTCGGGTGACTTCTCTATCCCCACCCCACTCCTACCCTCTATCCCAG
Seq C2 exon
TGCCTTGCCTAAACTGAGTGAGAAAAAGCAGGCATTCAATGCCTACAAGGCGCAGCGGGAGAAGGAGGAGAAGGAGGAGGCCCGGCTAAGGGCCAAAGAGGCCAAGCAGACCCTGCAGCATTTCCTGGAGCAGCATGAACGCATGACCTCCACCACCCGCTACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000110844:ENST00000380281:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.909 A=NA C2=0.875
Domain overlap (PFAM):
C1:
PF0394210=DTW=FE(18.3=100),PF0184614=FF=FE(42.0=100)
A:
NA
C2:
PF0394210=DTW=PD(42.6=87.5),PF0184614=FF=PD(30.0=26.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTGTCCCCTCCAATGCCTC
R:
CGGTAGCGGGTGGTGGAG
Band lengths:
230-726
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