RnoINT0086571 @ rn6
Intron Retention
Gene
ENSRNOG00000056184 | Lrp2
Description
LDL receptor related protein 2 [Source:RGD Symbol;Acc:68407]
Coordinates
chr3:55741433-55743101:-
Coord C1 exon
chr3:55742724-55743101
Coord A exon
chr3:55741682-55742723
Coord C2 exon
chr3:55741433-55741681
Length
1042 bp
Sequences
Splice sites
5' ss Seq
GCAGTAAGT
5' ss Score
9.07
3' ss Seq
CCCGTGACTCTTTCTTCTAGATC
3' ss Score
10.62
Exon sequences
Seq C1 exon
CCACCAGGCCTCCCGGCATGTGCCACCTGGATGAGTTCCAGTGCCAAGGAGACGGTACATGCATCCCTAACACCTGGGAGTGTGACGGGCATCCAGACTGTATCCACGGGTCCGACGAGCACACTGGCTGTGTTCCTAAGACCTGCTCGCCGACTCATTTCCTCTGTGACAATGGAAACTGCATCTACAAAGCGTGGATCTGTGATGGGGACAATGATTGTAGGGATATGAGTGATGAGAAGGACTGTCCTACCCAGCCTTTTCACTGTCCTAGCACGCAGTGGCAGTGCCCGGGCTACAGCACCTGTATCAATCTGAGTGCCCTGTGTGACGGCGTCTTTGACTGTCCGAATGGGACTGACGAGTCCCCACTTTGCA
Seq A exon
GTAAGTTCCCCGATCACAGTTTGCTGGACACAAATTTATTCTGAACAGTAGATAGCTGTTCCCCACCACTGTCACAGCTCCCGTGTAGTATATTGGGAAGGGGATCCTCTTGTCACTTTACATCCCCGTAGGAGTAACAATAAATTCCAATAAATGGTGACTGCATAACACTTCTCATTAATTTCTTTTTTACTTGTGTCTGGTGTCTCTTCTCTTTATGTCACTATCCAGGACATCACGCCATCAAATTAAATGTAGCTCTCTCCAGGAGTAACATGTCCATAAACTTTCCTAACTTGAAGATTTTCTAATTTTAACCGGAACTTGTTATCAAACCAATGAAGCCTGGGGGGGTTGTGTTTGCAGTGATTAAAATGCTCTGATTGGCATGTAATCCTAATTACTGTCCTTTCTCTCTTCCCTCTTTAATTAACGCTCTCTCTCAGATGAACCACAGCAAGGTATGACTGTGAACATCCTAGACCTTTATGATTTCACGTGACACGTGTATGTCGACACTGTACTAATTACTGTGACTTCCCCTTCTAGTGCATGTCCCCTGTGTGACTCTTTATCCATAAGTTACTGTGCTCCTGGGAATGGGAAGTATTTTTAGACCCAGTATATGATGTGGCTCTGGGCTGCTCCAGCCGTTGCCACACTGACCCTAAGAGTAAGGTGTGTTAGCAAATTGTGTCCTCTCCACTCGGTCGCTTACAGCTTTTTCTGCGAAACATCTCTACTTAGGCTGGAGAATTCCAGAGGGAGCATGTTAAATTTCTCTGCTCCATCAGTGACAGTTAGGTTTCTGGATGCCAGCGTTATTTTTTTCAAGGTTCTCTCACAGCCATAAACGGAACTATACTGGAGGGTGGCTCTAAGGCATACTATAGCCTCAAGCAAGTCAGAGAAGACACTATGTAGATCACCGAAGAGATTGGGGCTCTTGATTAACTCTCTTTAAAGTTGGCATGAAACTACATTGGAGTGAGTCGAAAAATCAAGGATGTCTGACTTTCCTCCCCGTGACTCTTTCTTCTAG
Seq C2 exon
ATCAAGACAGCTGCTCCCATTTTAATGGTGGCTGTACTCATCAGTGCATGCAAGGGCCCTTCGGAGCCACATGCCTATGCCCATTAGGATACCAACTTGCCAATGATACCAAGACCTGTGAAGATATCAATGAGTGCGATATTCCAGGCTTCTGCAGCCAGCACTGCGTCAACATGAGAGGTTCCTTCCGGTGCGCTTGTGATCCAGAATATACGCTGGAAAGTGATGGGCGGACTTGCAAAGTCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000056184:ENSRNOT00000082624:25
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=30.7),PF0005713=Ldl_recept_a=WD(100=29.1),PF0005713=Ldl_recept_a=PU(88.4=29.9)
A:
NA
C2:
PF0005713=Ldl_recept_a=PD(9.3=4.8),PF146701=FXa_inhibition=WD(100=42.9),PF146701=FXa_inhibition=WD(100=41.7)
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:
TCCAGACTGTATCCACGGGTC
R:
CCCTTGCATGCACTGATGAGT
Band lengths:
343-1385
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]