RnoINT0086572 @ rn6
Intron Retention
Gene
ENSRNOG00000056184 | Lrp2
Description
LDL receptor related protein 2 [Source:RGD Symbol;Acc:68407]
Coordinates
chr3:55740131-55741681:-
Coord C1 exon
chr3:55741433-55741681
Coord A exon
chr3:55740343-55741432
Coord C2 exon
chr3:55740131-55740342
Length
1090 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATA
5' ss Score
8.55
3' ss Seq
TTTTTCCATTTCCAACACAGGAT
3' ss Score
8.12
Exon sequences
Seq C1 exon
ATCAAGACAGCTGCTCCCATTTTAATGGTGGCTGTACTCATCAGTGCATGCAAGGGCCCTTCGGAGCCACATGCCTATGCCCATTAGGATACCAACTTGCCAATGATACCAAGACCTGTGAAGATATCAATGAGTGCGATATTCCAGGCTTCTGCAGCCAGCACTGCGTCAACATGAGAGGTTCCTTCCGGTGCGCTTGTGATCCAGAATATACGCTGGAAAGTGATGGGCGGACTTGCAAAGTCACAG
Seq A exon
GTAATAATTGAGCTTAATGGGGAACTAACTCCAGAAAATTTAATAGGCTCTATCAGAGTGTAAGCCTTTGGTAAGATCGATTATTCGTCAGCCCGACTAGAGAGCTGATTTAATGCCTTTTGACCCATATGAAAGTGAATATACCGGATATCAGAATATTGACTCAGCTGCTTTCAAAGTGATTCAACAGCAGAGGACTTAAAAGTTCCTTTATTGCAGGATGCAGTGGCATATGCCTGCTATCCCAGCATTTGGGAGGTAGGATCAGGTCAGCATGGGCTTCATAGTGAGTTCGAGGCCAACCTGGACTACACGAGGCTTTGCTTCAAAAATACCAATGTCAAACAAGGAACCTTTCTTTTCAAGAAGGCTGGGTGAAAACAGTCTAAGGACAGACTGATTCTTACTATCTGAAGTTCTCATTCAAGGTCTAACAAATTTGCTTTAGTCTTTTCTTTCCCTTAGAAAGTAGGCTAGGGAAAGAAACTTCCTTTTGAGGAAGGAGATCCATCACTTCTGCGGATACACAATTGGTCAGAACTCAGTCATTTGATTACAGCAGCTTCAGTGAAGGCAGAGACTGGTCTCTATCTGAGTAGCCTTAGGCCAACCTAAATGTAGTGTGGCTTAATACTAAACCGACAAGGGGGAAAGGAATATTAGTAGACAGAACTCTTCTGCTACACCTAATGGTTTGAAACTTGAAACCAAGCCTACGGTCTGCTAAGATAGAAAGCAAGTTGAGACAATAAAAGCAGCTCAAGGATCAGTGTGTGAACAGCTCACTCCAGACTGGAACATAGATGCCCACTGCAATAATCTGAGAAAGAGAGCTTTTCCAGAACATAACTATTTTACATGCTATTATCAATGAACAAACAAGGTTCTCCTGATCCTGCTTAGCGTCTGATGAGATCAGGGATGTTCAGGATGATATGGCTGTAGACAAAGTAATTCTTGTGGTCTTACTCTCCCATTTCTCTAGTTTGGTACCACGCACTGGATGCTGATGAGACTCTTTAATTGTATTTTTTTCTTTCAGATTCATTGACAGTTTCTTTTTCTTTTTCTTTTTCCATTTCCAACACAG
Seq C2 exon
GATCTGAAAATCCGTTGTTAGTTGTAGCAAGTCGTGACAAAATCATTGTGGACAACATCACTGCCCACACGCACAATCTCTACTCGTTGGTCCAGGATGTTTCTTTTGTGGTTGCTCTTGATTTTGATTCAGTCACTGGTCGTGTCTTCTGGAGTGACTTACTGCAGGGTAAAACCTGGAGTGTCTTTCAAAACGGAACAGACAAGAGAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000056184:ENSRNOT00000082624:26
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=PD(9.3=4.8),PF146701=FXa_inhibition=WD(100=42.9),PF146701=FXa_inhibition=WD(100=41.7)
A:
NA
C2:
NO
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:
CTTCGGAGCCACATGCCTATG
R:
ACTCCAGAAGACACGACCAGT
Band lengths:
346-1436
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]