MmuINT0127129 @ mm10
Intron Retention
Gene
ENSMUSG00000023007 | Prpf40b
Description
pre-mRNA processing factor 40B [Source:MGI Symbol;Acc:MGI:1925583]
Coordinates
chr15:99307013-99307721:+
Coord C1 exon
chr15:99307013-99307077
Coord A exon
chr15:99307078-99307556
Coord C2 exon
chr15:99307557-99307721
Length
479 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGC
5' ss Score
9.37
3' ss Seq
TCCTCAACTGTCTACTCCAGTGC
3' ss Score
6.63
Exon sequences
Seq C1 exon
GCTGTCCCTTCCAATGCTTCATGGGAACAGGCCATGAAGATGGTAGTCACTGACCCCCGCTACAG
Seq A exon
GTATGCTTGAGTCAGAATGGATAGTTCTTGTTGGTGAAAGCAACTGGGCCAGGAACTCTCTGAGATGTCCCAATTTGAATTGACACTCAACTGAGTTGGCTCCCAATTGGGTGCTGACACTCAGGTCTAAGTGGCTGGGATGGGCTGCAAGAGAAGGAAAAGCTAGAATAGCTCCAAGATGCAAAGAGGGAAATGGTACAGCCATGAGATGCTTAGTAAATGGTTACTGGCTTGAATTAAAATTAGAGAAATAGGGGCCCTAAGGAGACAGATGTCTGATGGTAACTTGAGAACACTGAAGCAACAGGGTCCAGTATTTCTTTCCCTCATGCCTCATCCCTCCCATATTCTCCACACCTGTATGTTAGGTCCCCAATTTGGTGTGGTGGAGACCTTTCCCCCATGTCTGTGACCCTGCTTCATGGGCTAACAGGGTAATTCACGCTGCATCCTCTCCTTTCCTCAACTGTCTACTCCAG
Seq C2 exon
TGCCTTGCCCAAACTAAGTGAGAAGAAGCAGGCGTTTAATGCTTACAAGGCTCAGCGGGAGAAGGAGGAGAAAGAGGAGGCCCGGCTGAGAGCCAAGGAGGCCAAGCAGACCCTGCAGCATTTCCTGGAACAGCATGAACGCATGACCTCCACCACCCGCTACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000023007:ENSMUST00000145482:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.818 A=NA C2=0.875
Domain overlap (PFAM):
C1:
PF0394210=DTW=FE(18.8=100),PF0184614=FF=FE(42.0=100)
A:
NA
C2:
PF0394210=DTW=PD(46.4=92.9),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:
GCTGTCCCTTCCAATGCTTCA
R:
CGGTAGCGGGTGGTGGAG
Band lengths:
230-709
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