MmuINT0114663 @ mm10
Intron Retention
Gene
ENSMUSG00000003437 | Paf1
Description
Paf1, RNA polymerase II complex component [Source:MGI Symbol;Acc:MGI:1923988]
Coordinates
chr7:28395952-28396202:+
Coord C1 exon
chr7:28395952-28396057
Coord A exon
chr7:28396058-28396133
Coord C2 exon
chr7:28396134-28396202
Length
76 bp
Sequences
Splice sites
5' ss Seq
TCGGTAATT
5' ss Score
7.06
3' ss Seq
CACCCTTTTTGTTCTATCAGATC
3' ss Score
10.04
Exon sequences
Seq C1 exon
GATTGGGGTTTCTGTGAAACAGCAGTTCACAGAGGAAGAAATATACAAAGACAGGGACAGCCAAATCACAGCCATTGAAAAGACTTTTGAAGATGCCCAGAAATCG
Seq A exon
GTAATTGGGGGGAATAGAATAGAGGCAAGAGTGTGGCTCAGGGTCTTCCTCTTTCTCACCCTTTTTGTTCTATCAG
Seq C2 exon
ATCTCCCAGCATTACAGCAAGCCCCGAGTGACACCAGTGGAGGTCATGCCTGTCTTCCCAGATTTTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000003437:ENSMUST00000003529:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.194 A=NA C2=0.217
Domain overlap (PFAM):
C1:
PF039858=Paf1=FE(8.3=100)
A:
NA
C2:
PF039858=Paf1=FE(5.2=100)
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:
TTTCTGTGAAACAGCAGTTCACA
R:
CTTAAAATCTGGGAAGACAGGCA
Band lengths:
167-243
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