RnoINT0086630 @ rn6
Intron Retention
Gene
ENSRNOG00000056184 | Lrp2
Description
LDL receptor related protein 2 [Source:RGD Symbol;Acc:68407]
Coordinates
chr3:55770595-55772087:-
Coord C1 exon
chr3:55771938-55772087
Coord A exon
chr3:55770715-55771937
Coord C2 exon
chr3:55770595-55770714
Length
1223 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
TTCTTGCCTTCTCTGTTTAGGTA
3' ss Score
11.5
Exon sequences
Seq C1 exon
AAAGTAACCAGAGTCATCATAGGTGTTACCCAAGAGAATGGGCGTGTCCTGGGTCTGGACGATGCATCTCAATTGATAAAGTTTGCGATGGAGTTCCTGACTGTCCAGAAGGAGACGATGAGAACAACGTCACAAGCGGAAGAACCTGTG
Seq A exon
GTGAGTGTGGAAACTGCATATGGCTTGCTTCCTGATAGCAGTGCTTCTAGAACAGACTTTCAAACGCAGAAAAAAATCAATTGGCATTTGCACAACAAAATTCCTCAGTTCAGTCGCTTCATTGGCAAACATTTATGGTGTCTCATGGTGGGTCTTGCCTACACCAGCCCACTGGCATTTCATGCTAACCCACACGTGGTTTCATGATGGTGGGGAGTAGACCCACCTATCGTTTGAATAGTTTTAAGTCTCTGTAAGCATCATGTTTGCTAATGTATTGACCACAGCATGTCATTTGGGTGAGGACAGAGTGGAACAAAAGTACATACTAATAGGGAAAGTGGTTTTAATATCAATTATGATGATTTTGACATGGGAGTTTTTTTTGTGTGTGATACTAGGGCTCAGACATAAAGATTTATGAGTATTATGTTATACAAATGCCCTACCCACTGAACTTTGCCATCTGTCCTGTTCCATATATTTGATGTCTTATCTTATACTGGTCTTATTTGGCTACATTAAGACAAGCTTCTGATTCCTAGGGTGTATGTTGTCTTCTAGTGGTTCTAAGGATAGGTGATGACATATATAGGTAATAGTCTATGTAGCTATTTGGTATATAGGCACCCTTTTTTTCTCCTCCCCCCCCCCCCCCCCAGTCAGTCCAATTCTGAGAGCATCTCACATCTCAAAGGGGGACAGATTAGAACTTGCCCTCATCATTTGAACACTAACTCAGTCGGTGATTTCAAAGATGAGCACATGTAATTCTAAACTCCAAGGATTCCCCTCTCCCCCAATACTTGTCATATCTAAAAGTCCTTCCGTTCCATTTAGTATAAAAGCTTCAGAATAAACAAATGTTATATAATCAGTGGTCGAAGTTTAGAAAAGAGATATTAACAGAAAAACAAACAAACAAAGCTAATCTCCTGAAAGCCTACTATTGGAAGTCAGCTGTTGTCAGAACTACCAAAGCTTGACCTGATTGTTCATGAATGGGGTTAGTAGCCTTTTATACCTACTCATAACAGCAGTTGTAATATTAAAAGAAAAAGAGGTTTAACAGAAACAAAGCATTTGCTACATAGTATCGCAAGAGGCAGCTGGTTTTCTTGTTTTACTGCATGCTCATTGGGTTTTCCTATATGGAAGTTATTAGGTAAACTAGTCTCGTCCAGGGTCCATCCAGTTAACCGTTTCTTGCCTTCTCTGTTTAG
Seq C2 exon
GTATGGGTGTCTGCTCTGTCTTAAACTGTGAGTACCAGTGCCATCAGACGCCATTTGGAGGAGAATGCTTCTGCCCCCCAGGTCATATTATCAACAGCAATGACAGCCGTACTTGCATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000056184:ENSRNOT00000082624:8
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=86.3)
A:
NA
C2:
PF0764510=EGF_CA=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:
AAAGTAACCAGAGTCATCATAGGTGT
R:
CAATGCAAGTACGGCTGTCAT
Band lengths:
270-1493
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]