RnoINT0086592 @ rn6
Intron Retention
Gene
ENSRNOG00000056184 | Lrp2
Description
LDL receptor related protein 2 [Source:RGD Symbol;Acc:68407]
Coordinates
chr3:55716531-55717275:-
Coord C1 exon
chr3:55717033-55717275
Coord A exon
chr3:55716657-55717032
Coord C2 exon
chr3:55716531-55716656
Length
376 bp
Sequences
Splice sites
5' ss Seq
GCCGTAAGT
5' ss Score
10.11
3' ss Seq
ATCTGGTTGTGTTTTTAAAGCTC
3' ss Score
6.87
Exon sequences
Seq C1 exon
CCTTTCACACCTGCCGATCAACAGCCTTCACTTGTGGCAACGGGCGATGTGTGCCATACCACTATCGCTGTGATTACTACAATGACTGCGGGGACAACAGCGACGAGGCAGGTTGCCTGTTCAGAAACTGCAACAGCACCACAGAGTTCACGTGCAGCAATGGGCGGTGCATACCGCTCAGTTATGTCTGCAATGGCATAAACAATTGCCATGACAATGACACCTCGGATGAGAAAAACTGCC
Seq A exon
GTAAGTGTCTAAAGTCCTTCCTTTGGGGCTCCGTGGTCCTACGTTAGGATGCAGGAGATGGAATCTTTCCCTAAAATCTATTGCTTTCTGAAAAAAAAAAACCTAAGTGGTTTTTTAATCAATTAAATGATATAAAAATATATCTACCTAATATTTGAATTGTTTAATTTGATGGAGATATATATATATATATATATATATATATATATATATATATATATACACCCCAGGAACCAACTTGGGCCTCTCTTTACCTTTGAACTGGTTTGGACCTCTGATTTAGACCCTTCTCTGGGTTGGTTAACGTCGCCATTATTTTTGATATACTTGGTAGGTCTGTTCCAAGTGTCTTTCTTATCTGGTTGTGTTTTTAAAG
Seq C2 exon
CTCCCCACACTTGCCCGCCGGATTTCACAAAATGCCAGACCACGAATATTTGTGTTCCCCGAGCTTTCTTGTGTGATGGAGACAATGACTGTGGAGACGGGAGTGACGAGAACCCCATTTACTGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000056184:ENSRNOT00000082624:44
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=0.000
Domain overlap (PFAM):
C1:
PF0005713=Ldl_recept_a=WD(100=45.1),PF0005713=Ldl_recept_a=WD(100=48.8)
A:
NA
C2:
PF0005713=Ldl_recept_a=WD(100=93.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTTTCACACCTGCCGATCAA
R:
TCCCGTCTCCACAGTCATTGT
Band lengths:
345-721
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]