MmuINT0114655 @ mm9
Intron Retention
Gene
ENSMUSG00000003437 | Paf1
Description
Paf1, RNA polymerase II associated factor, homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1923988]
Coordinates
chr7:29181840-29183572:+
Coord C1 exon
chr7:29181840-29181968
Coord A exon
chr7:29181969-29183466
Coord C2 exon
chr7:29183467-29183572
Length
1498 bp
Sequences
Splice sites
5' ss Seq
CAGGTACTC
5' ss Score
7.04
3' ss Seq
TCTGCAATTGTCCACTGCAGGGT
3' ss Score
7.59
Exon sequences
Seq C1 exon
GTATGACTATAAGATTGCTCGGGAATACAACTGGAATGTGAAGAACAAGGCCAGTAAGGGCTATGAGGAGAACTATTTCTTCATCTTCAGAGAGGGTGACGGAGTTTACTACAATGAGCTGGAGACCAG
Seq A exon
GTACTCGGCACTGTTTCATGACTTTGGCCCTTTGTGGTCCCCCCCCCCCTTTTTTTTGAGACAGGGTTTCTTTGTGTAGCCCTGGCTGTCCTGGAACTCACTTTGTAGACCAGGCTGGCTTCGAACTCAGAGATCCGCCTGCCTCTGCCTCCCAAGTGCTGGGATTAAAGGTATGCACTACCACGCCCCCCTCTCCCCCCTTTAAAGACCATGCTAGGACAGCTACAGCGTACTTACATATAATAAATAAATAAATAAATCTAAAAAAAAAAAAAAAAAAAAAAAAAGAGAGCAGCAGGAGCCTGCTTATAAATGTAGGCTGGACCTGGCTGTGGTCTTAATGCCATAAACCAGAAAGAAAATTTTCACATAATGCAGGATATAAATCTAGTCATTTTTCTCACACATGATAGGCAAGTGCCCTCCTGTATGATACATTCCTAGTCTCAACAGTTTTTTTTTTTTTTTAAAAGATTTATTTTATTAATATATGTAAGTACACTGTAGCTGTCCTCAGACACTCCAGAAGAGGGAGTCAGATCTTGTTGCGGATGGTTGTGAGCCACCATGTGGTTGCTGGGATTTGAACTCTGGACCTTCGGAAGAGCAGTCGGGTGCTCTTACCCACTGAGCCATCTTACCAGCCCGTCTCAACAGTTTTAATAAGCTTTTTGTATGTGACATGTTTATGTTCATGCGTGCACATACTGGAGCCAGAGGTTGCAATCAGTTTTCCTTTGTTGCTTTTATTTTGTGTGCATGTATGCATATGTATATAGTCATATGCATGACCTGGCATGCACTTGGATGTTAGAGGATAACTTGGGGCAAGAGTTATTCTTTCCTGTTCCACCATGACACTTTACCAACAGAACCATCTCCTATACCCTTCAGCAGGTTTTAAATACTTGACACAACTTCAAAAGTGTGCCCTTGTTGTGTGACCTCAGAACCTTTCTCTGAGGGCTGAAAGCTAACTTGTCCTAGTGCCAGTGGTTCAATATGGCTCTGATCCTGTTGTCTGGCTGGAGATGTGAAAACAGGCAGTGGCATCACCTTTAGTGAGTACTACAATACAGCTGCAAGTCCACTGCTCTTCTATTTAAAATCCAGAAACACACGTTTGCCATTTTCTTGGTTTTATGCTTTGGATAAGAGGCCTTGGAAAATGACTTAGCAGTGATGAACACTGGCTGCTCTTCAGAAGACCTCAGCTTATATCCCAGTTCCCAAGAGATTCTGATGCTCTCTTGCGGCTTCTTGGGGTACTACAACACAACACACATACAGGCAAACCACCCATTCAATTAAAATCTTGAAACAAAAAAAACCCTGAAAACTTAAAAGTTGGGTAAGTCAAACCCGAAATACCATCTTTCACATCCACTGTATGTATACTTTGTCCTCTGTTATGTTCTGGGTCAAATATTGATAGGGAACCAGATGTTAGACTGGTCCTAGTGGAGCCCAACTCCCCTTCTGCAATTGTCCACTGCAG
Seq C2 exon
GGTCCGTCTAAGTAAGCGCCGGGCCAAGGCTGGGGTTCAGTCAGGTACCAATGCCTTGCTTGTCGTCAAACACCGTGACATGAATGAGAAGGAATTAGAAGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000003437-Paf1:NM_019458:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.778
Domain overlap (PFAM):
C1:
PF039858=Paf1=FE(10.2=100)
A:
NA
C2:
PF039858=Paf1=FE(8.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGACTATAAGATTGCTCGGGAAT
R:
CTGGGCTTCTAATTCCTTCTCA
Band lengths:
232-1730
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: