MmuINT0114657 @ mm10
Intron Retention
Gene
ENSMUSG00000003437 | Paf1
Description
Paf1, RNA polymerase II complex component [Source:MGI Symbol;Acc:MGI:1923988]
Coordinates
chr7:28398659-28399388:+
Coord C1 exon
chr7:28398659-28398749
Coord A exon
chr7:28398750-28398825
Coord C2 exon
chr7:28398826-28399388
Length
76 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAG
5' ss Score
9.65
3' ss Seq
AGTCCCCTACTTCCTCACAGATG
3' ss Score
7.96
Exon sequences
Seq C1 exon
GAGGCACGAAAGGCCCAGTTGGAAAACCACGAACCAGAGGAAGAGGAGGAGGAAGAGATGGAGGCTGAAGAGAAAGAAGCTGGGGGCTCAG
Seq A exon
GTAAAGGATTAGTCACATCCTGGGAGCCCTGGGAGGGTGGGCATTGGGATCTCACCAGTCCCCTACTTCCTCACAG
Seq C2 exon
ATGAGGAACAGGAGAAGGGTAGCAGCAGTGAGAAAGAAGGCAGCGAGGATGAACACTCTGGAAGTGAGAGTGACCGAGAAGAGGGTGACAGAGATGAGGCAAGTGACAAGAGTGGCAGCGGTGAGGATGAAAGCAGTGAGGATGAAGCACGTGCTGCCCGGGACAAAGAGGAGATTTTTGGTAGTGATGCTGATTCAGAAGATGATGCTGACTCTGATGATGAGGACAGAGGGCAGGCCCACAGGGGCAGTGACAATGACTCGGACAGCGGCAGTGATGGTGGTGGCCAGAGGAGCCGCAGCCAGAGCAGGAGTCGTAGCCGGAGTGCCAGCCCCTTCCCCAGTGGCAGTGAGCACTCAGCTCAGGAAGATGGCAGTGAAGCAGCAGCCTCTGATTCCAGTGAGGCTGACAGTGACAGTGATTGAGCCTCAAGGCTTTCTAATGAGATCAGCACAGACACCATTTTTAGGGCAGGGAAGCACTTTTCTAGTTGTCTGTTTTGTGAGCTTTTGTCACTACCCCTCAATCTTTGCTGTTAATAAACCTAACTTCTCTTGACTTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000003437:ENSMUST00000003529:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF039858=Paf1=FE(7.1=100)
A:
NA
C2:
PF039858=Paf1=PD(12.1=35.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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:
GAAGAGAAAGAAGCTGGGGGC
R:
CGTGCTTCATCCTCACTGCTT
Band lengths:
176-252
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