MmuINT0127127 @ mm10
Intron Retention
Gene
ENSMUSG00000023007 | Prpf40b
Description
pre-mRNA processing factor 40B [Source:MGI Symbol;Acc:MGI:1925583]
Coordinates
chr15:99306396-99306931:+
Coord C1 exon
chr15:99306396-99306599
Coord A exon
chr15:99306600-99306804
Coord C2 exon
chr15:99306805-99306931
Length
205 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGG
5' ss Score
9.99
3' ss Seq
GAGTCCCTTCTACTCTCCAGCTC
3' ss Score
4.13
Exon sequences
Seq C1 exon
AAAACAGCAGACCCAGCAACTACAGACACTACAGCCACAACCACCTCAGCCACAGCCTGACCCTCCACCTATACCTCCGGGTCCCATCCCAGTGCCTATGGCCCTCCTGGAACCTGAACCAGGTCGAAGTGAAGACTGTGATGTGCTGGAGGCTGCCCAGCCCCTGGAGCAGGGCTTCCTGCAGCGGGAGGAGGGCCCCAGCAG
Seq A exon
GTATGGGCTGCTCCCCTTTCATTGCAGCCTCAAACTTTCCATCCTTATTCTCTTTAGAGCCTTGGGAGGGACATGTCAAGAGCTGAGCATGACCCCGGAAGGGCTTTCTGGGGAACAAGAAAAGGACAATAAATTGCTGAGAGTGAAGGGCACTGAAAACTGTAAGGATTATGGGCACCGTGGCTGAGTCCCTTCTACTCTCCAG
Seq C2 exon
CTCTACTGGACAGCATCGGCAGCCACAGGAAGAGGAGGAAGCTAAGCCAGAACCAGAGCGATCTGGCCTCAGTTGGAGCAACCGGGAGAAGGCAAAACAGGCTTTCAAAGAACTGCTAAGGGACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000023007:ENSMUST00000145482:10
Average complexity
IR
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:
PF0394210=DTW=PU(33.0=86.0),PF0184614=FF=PU(24.0=27.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGCAGACCCAGCAACTACAG
R:
CTGTTTTGCCTTCTCCCGGTT
Band lengths:
300-505
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types