RnoINT0106779 @ rn6
Intron Retention
Gene
ENSRNOG00000019746 | Paf1
Description
PAF1 homolog, Paf1/RNA polymerase II complex component [Source:RGD Symbol;Acc:1306219]
Coordinates
chr1:85363240-85364623:-
Coord C1 exon
chr1:85364495-85364623
Coord A exon
chr1:85363346-85364494
Coord C2 exon
chr1:85363240-85363345
Length
1149 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
GTATGACTACAAGATTGCTCGAGAATATAACTGGAATGTGAAGAACAAGGCCAGTAAGGGCTACGAGGAAAACTACTTCTTCATCTTCAGAGAGGGTGATGGTGTCTACTACAATGAGCTAGAGACCAG
Seq A exon
GTACTCAGCACTGTTGTGGGTTTTTTTGTTTGTTTTTGTTTTTTGAGACCATGAATGAACTACTCTGAAGTCATTTGTACCTAAATATTTGTTTTATGTATCTGAGAGAGCAGCAGGACCCTGCTTATTAATGTAGGCTGGGGGGCTGGGGATTTAGCTCAGTGGTAGAGCGCTTACCTAGGAAGCGCAAGGCCCTGGGTTCGGTCCCCAGCTCCGGAAAAAAGAACAAAAAAAAAAAAAAAAAAAAAATGTAGGCTGGACTTGGCTCTCTGTTCCTAGTACTATAAACCACAAAGAAAATTTTCACACAATGTAGGATGTAAACCTAGTCATTTTTCTGTTCATGTGTGTACATACTGGAGCCAGAGATTGAATCAGCTTTCCTTTGTTGCTCTTATTTTGTGTGCATGCATGAGGAGGTTAGAGGATAACTTGGGTGAAGTTACTCTTTCCTGTTCCCCCATGGCACTTTACCAACTGAACCATCTCCTCCAGGCCTTCAGGTTTTAAATAGTTGACAAAAACTTCAAGAGTGTTACCTCAGAACCTTTCTTTTGAGGGCTGAAAGCTAACTTGTCCTAGGGCCTGTGGTTTGAGTTTCTGTTCAATATGGCTGGAGATGTGAAAACAGACAGTGACAACACCGTTAGTGAGTACTACAATTCAGCTGCAATCCAATGCTTTTCTATTTAAAAGCCAGAAACCCAAATAACTACTGGCTACTCTTCTAGGATGTTTGTTTTTCTTTTTTTCTTTTCTGTTTTTCGGAGCTGGGGACCGAACCCAGGGCCAAGCGCTCTACCACTGAGCTAAATCCCCAACCCTGGCTACTCTTCTAGAAGACCCCAGTTCGTATCCCAGTTCCCACTTAGACAGTTTTGCCCAAAGAATCTGATGCCCTCTTGTGGCTTCTTGGGGTACTATACATACAACATGCAAAACACCCATTCACTTAAAATCTTGAAACAAGAAAAATCCAAAAAACTTAAAAGTTGGGTAAATCAAACCCGTAATACCATCTTTCACGTTCACTGTATGTATACTTTGTTTTCTGGTATGCTGTGGGTCAGATTATTGATAGGGAACTAGGTGTCAAGTTAGACTGGTCCCAGTGGAGCCTAACTCCCCTTCTGCAATTGTCCACTGCAG
Seq C2 exon
GGTCCGTCTCAGTAAGCGCCGGGCCAAGGCTGGGGTTCAGTCGGGTACCAATGCCTTGCTTGTGGTCAAACACCGTGACATGAATGAGAAGGAATTAGAAGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019746:ENSRNOT00000026778:11
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=0.806
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
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:
TGACTACAAGATTGCTCGAGAA
R:
CTGGGCTTCTAATTCCTTCTCA
Band lengths:
232-1381
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]