MmuINT0114659 @ mm10
Intron Retention
Gene
ENSMUSG00000003437 | Paf1
Description
Paf1, RNA polymerase II complex component [Source:MGI Symbol;Acc:MGI:1923988]
Coordinates
chr7:28395043-28395539:+
Coord C1 exon
chr7:28395043-28395135
Coord A exon
chr7:28395136-28395417
Coord C2 exon
chr7:28395418-28395539
Length
282 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGA
5' ss Score
9.79
3' ss Seq
AGTCATGTTTTCCCTTCTAGGTT
3' ss Score
10.65
Exon sequences
Seq C1 exon
GTCTGGAGTAGTCTGCCGAGTCAAGTACTGCAATAGCCTTCCTGACATCCCATTTGACCCCAAGTTCATCACCTACCCCTTCGACCAGAACAG
Seq A exon
GTAGGACTGAATTCAAGAATGGAAAAACTACTAAAAAATAGTTCATTGATGGCAAGGACTGCTTATTTCATTGCCTCAACCTTCCTCGGACTGGCACATAGGAGGTGCTCAGTAACTACTAATAGAGAAAGCAGTATGCAATACCCTTCTTACTCAGAAGTTGCCAATGCTGGACGCTTGCATTCAGAGTTCCTCTCCATAGAAGCTTAGCTTCTAGGAAGGGAGCATGTTGGGGCGTGAGGGTGGATCATAAAACTGTAACAGTCATGTTTTCCCTTCTAG
Seq C2 exon
GTTTGTTCAGTACAAAGCAACCTCCTTGGAGAAACAGCACAAACATGACCTCCTGACTGAGCCAGATCTGGGGGTCACCATTGATCTCATCAACCCTGACACCTACCGCATTGATCCCAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000003437:ENSMUST00000003529:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.119
Domain overlap (PFAM):
C1:
PF039858=Paf1=PU(7.1=93.8)
A:
NA
C2:
PF039858=Paf1=FE(9.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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:
GTCTGGAGTAGTCTGCCGAGT
R:
TGGGATCAATGCGGTAGGTGT
Band lengths:
212-494
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