HsaINT0096537 @ hg19
Intron Retention
Gene
ENSG00000070018 | LRP6
Description
low density lipoprotein receptor-related protein 6 [Source:HGNC Symbol;Acc:6698]
Coordinates
chr12:12311763-12312898:-
Coord C1 exon
chr12:12312714-12312898
Coord A exon
chr12:12312090-12312713
Coord C2 exon
chr12:12311763-12312089
Length
624 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGC
5' ss Score
8.72
3' ss Seq
TACTGCCTTTCTGAAAATAGGGC
3' ss Score
5.89
Exon sequences
Seq C1 exon
ATTTATGTATTGGACTGAATGGGGTGGAAAACCTAAGATAGACAGAGCTGCAATGGATGGAAGTGAACGTACTACCTTAGTTCCAAATGTGGGGCGGGCAAACGGCCTAACTATTGATTATGCTAAAAGGAGGCTTTATTGGACAGACCTGGACACCAACTTAATAGAATCTTCAAATATGCTTG
Seq A exon
GTAAGCTTTACTACTTTTTACTCAAACAGTATATTCTTTCCATGCAAATATCAGTGGCTGCTATTTATCATTGGTTAGATACTTTTAATACAACTTCATATGAATGTGTCCATTCTTCTTCTGTTCTGGAATTGTATCCTGTTTGTTATTAATAGTGATCCAGGTACTTGGATTCATCTTTTTATTATGTGAAAGTTTCATTATTATTGGACTTGTAATGAAATTTATAACTCCCTAGATACTCCTGAAATGACTTTTGTACCAGTAAAATATATATATTTCCATCTTTTCCTTCTATAGTTCAAGAAGAAAAAGTGAACTGTAGACCCTTATATAGAGAAAATAAAACCACATTTAAAGTAGACCATTTGCAAGAATTTTAGGAAACTGAGTGATTTGTAGCAGGAATATAAGTTTGAAGCATGGGGTCAGAAGATAGATTGATTTCAGAGAATTGGTCTCGTTTTAGAATTGCTTTTAAATGAATTTTTCTATTTTAAATTGCTTACAATGTAATGTTTTATATGTTAGGGCTTTTTTTTTTCTTTTTGCCAGCAAGACACTTGTATTCTCACATATTTCATCACTCTGCTTCTCCCCTGTCTACTGCCTTTCTGAAAATAG
Seq C2 exon
GGCTCAACCGTGAAGTTATAGCAGATGACTTGCCTCATCCTTTTGGCTTAACTCAGTACCAAGATTATATCTACTGGACGGACTGGAGCCGACGCAGCATTGAGCGTGCCAACAAAACCAGTGGCCAAAACCGCACCATCATTCAGGGCCATTTGGATTATGTGATGGACATCCTCGTCTTTCACTCATCTCGACAGTCAGGGTGGAATGAATGTGCTTCCAGCAATGGGCACTGCTCCCACCTCTGCTTGGCTGTGCCAGTTGGGGGTTTTGTTTGTGGATGCCCTGCCCACTACTCTCTTAATGCTGACAACAGGACTTGTAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000070018-LRP6:NM_002336:11
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.063 A=NA C2=0.027
Domain overlap (PFAM):
C1:
PF0005812=Ldl_recept_b=WD(100=65.1),PF0005812=Ldl_recept_b=PU(51.4=30.2)
A:
NA
C2:
PF0005812=Ldl_recept_b=PD(45.9=15.5),PF0005812=Ldl_recept_b=WD(100=37.3),PF146701=FXa_inhibition=WD(100=33.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATTGGACAGACCTGGACACCA
R:
TAAGAGAGTAGTGGGCAGGGC
Band lengths:
351-975
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)