RnoINT0086556 @ rn6
Intron Retention
Gene
ENSRNOG00000056184 | Lrp2
Description
LDL receptor related protein 2 [Source:RGD Symbol;Acc:68407]
Coordinates
chr3:55761031-55762541:-
Coord C1 exon
chr3:55762372-55762541
Coord A exon
chr3:55761255-55762371
Coord C2 exon
chr3:55761031-55761254
Length
1117 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGT
5' ss Score
11
3' ss Seq
ATGACTGTTATTTCTTTCAGGTG
3' ss Score
10.96
Exon sequences
Seq C1 exon
TCAGTGCAGCCTCTGTTATCTTCTCCAATGGTCGGGATTTGCTAGTTGGAGATCTTCATGGAAGAAACTTCCGGATTCTAGCAGAGTCTAAGAACCGAGGAATGGTTATGGGAGTGGATTTTCACTATCAGAAACACAGAGTTTTTTGGACAGACCCCATGCAGGAAAAG
Seq A exon
GTAAGTAGAAAATTCAAGGGCATAGCTTATGGGCTGAATGGAACCTAAAGCACAAAGTGTTGATAGCTTTTCATTTTGGGGGGAGGAGTGGGGAAACGCTCCTTTGTTTTCTGACAAGAACAGCCCTTGAGATATTTTATGTTAGTCAGCGTCTTTTCCATGATATACTATTACATGTGAGCTGTGAGACAAAGACAGCTATTATTTGGATTAGCCTTGAGCAACTTTTAATTTTATTCGTAAAGGAGTCCAAAAGGCTAATTAAAAGAAATCATAGATCTTTCAGAACTAGATAGATATTTAGTCGCCATTTTGGAAACTTGATCATTTAAAATATAAAAATACTCTTTTTACTTGCATGATAAAAATCAGATTTTTTTTTTAACCTTCACTTGTTCATGGAATTGTAACTGAAGGTTGGGCAAAAAATTGGCAGGTTTTTTTTATGTGACAGCCAAAATATTACATTGTTTTACTTAGAAATTAAGATTGATTTTTTTGTTAGAAGTTTGTATTAAAAGAGTCATTAAAAGAATTTTGTTTATTCATTTTGCATTTCTTTTTTTTTTTTTTCTTTTTTTTCGGAGCTGGGGACCGAACCCAGGGCCTTGCGCTTGCTGGGCAAGCGCTCTACCACTGAGCTAAATCACTAACCCTTTGCATTTCTTTTAATGTGAAACCAAGTATACCTTTAAAAGAGTCTAATTAGGATAGTACACAAAGTTGAGAATTTTGATCATTAGCAATTCTTGTTTGAATAGAACTAAAAAATTAAAACAAACTATCATCTTTATCAAAACAAAACAAAACAAAACACACTATAAAACTCAACCATGTATTTGCCCTATGTATACTCTGAACAAAATTCATTTTCTTCTGGAAACTTTATAGGGTCGAGATAATTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTTCCATCTACCTATCATCCATCCATCCATCCATCCATCCATCCCTCCATCCACCCATCCATCTCCCTATCTATCTACCTACCTGTCTGTCTATCTACCTATAATAAAATATAGGAAAACAAGGTTCATGCTCTGTTTTAGGAAGTATAATGACTGTTATTTCTTTCAG
Seq C2 exon
GTGTTTTCCACTGACATCAATGGCTTAAATACCCAAGAAATTCTTAATGTTTCTGTTGACACTCCAGAGAATCTGGCTGTGGATTGGATTAATAATAAACTTTATCTGGTAGAGACAAAGGTCAACCGCATTGACGTGGTCAACTTGGAGGGAAATCAGCGTGTTACTCTCATAACTGAAAACTTAGGGCATCCTAGAGGAATTGCCCTTGATCCAACTGTGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000056184:ENSRNOT00000082624:11
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=0.000
Domain overlap (PFAM):
C1:
PF0005812=Ldl_recept_b=PU(26.8=19.3)
A:
NA
C2:
PF0005812=Ldl_recept_b=PD(68.3=37.3),PF0005812=Ldl_recept_b=WD(100=54.7),PF0005812=Ldl_recept_b=PU(0.1=0.0)
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:
CTCCAATGGTCGGGATTTGCT
R:
GCAATTCCTCTAGGATGCCCT
Band lengths:
354-1471
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]