HsaINT0132656 @ hg19
Intron Retention
Gene
ENSG00000110844 | PRPF40B
Description
PRP40 pre-mRNA processing factor 40 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:25031]
Coordinates
chr12:50037006-50037535:+
Coord C1 exon
chr12:50037006-50037180
Coord A exon
chr12:50037181-50037473
Coord C2 exon
chr12:50037474-50037535
Length
293 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
AGGGATTTTTCTATCTCTAGATC
3' ss Score
7.56
Exon sequences
Seq C1 exon
GGCTCTGAGTCAGAAGAAGAGGAGCTGCCCCCACCATCTCTCCGGCCCCCCAAGCGGAGGAGGCGGAACCCCTCAGAGTCAGGCTCTGAGCCCTCTTCCTCACTTGATTCAGTTGAAAGTGGGGGTGCTGCCCTTGGAGGACGGGGCTCCCCTTCCTCCCATCTTCTTGGAGCAG
Seq A exon
GTAAGCAGTTGCTGTGAGCGTAGAAGCTGGAGAACTGTTGTCCCAGACTGAGAGGATGCCCTCCACAAGCCCCAGCTCCTTTGAGGGTAGACTGGATTGGGAGGGCTGCACCTGTGGAAGTAGAAAGAACTTCCTCTACCTGCCCAAGCAAGAAGCTGGAGAAGGAAAACTGGACTTAGACTTCCTCAGAGCATGAGGTTCCTGCCTGTGAAGAATGAACAGAGGGGCTAGAACAAAGAAAAAGAGCCTGTCTTTCTCCTGTTGGGACTTAGTAGGGATTTTTCTATCTCTAG
Seq C2 exon
ATCATGGCCTTCGGAAAGCCAAGAAACCAAAAAAGAAAACTAAGAAGAGAAGACACAAGTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000110844-PRPF40B:NM_001031698:22
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCTCTGAGTCAGAAGAAGAGGA
R:
CGACTTGTGTCTTCTCTTCTTAGT
Band lengths:
237-530
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)