HsaINT0096319 @ hg19
Intron Retention
Gene
ENSG00000168702 | LRP1B
Description
low density lipoprotein receptor-related protein 1B [Source:HGNC Symbol;Acc:6693]
Coordinates
chr2:141526782-141528575:-
Coord C1 exon
chr2:141528450-141528575
Coord A exon
chr2:141526914-141528449
Coord C2 exon
chr2:141526782-141526913
Length
1536 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGA
5' ss Score
9.11
3' ss Seq
ATCTCCGGCCCTGCATTTAGGTA
3' ss Score
8.82
Exon sequences
Seq C1 exon
GCAGCAATTCCTGCCAACTAAACAATGGTGGATGCTCTCAACTTTGTTTACCAACATCTGAAACTACAAGGACTTGTATGTGTACAGTGGGATATTATCTCCAAAAGAACCGTATGTCATGTCAAG
Seq A exon
GTATGAGTTCATGAAAAACCTTACCTCTGGTTCATTTACTTCACTAATCATTACATACCATGCAGATGTTAGGCAACCAAAGTCAGTTAAACATTAGAAAAAAATTAACTAGTTATTAGGAAATGGTATACTGTTTAGTCTCATATGTGTAAGATTTTAATATTTGAAATATTTAAAATATCATTGTTCTGCCTTATAAGACATTCTAATTTTTTAGTCATTTTAGCAACTGCTGTATATTATCAAACCTTTAACCAAATCTAGTAAAAGCTACCTTCGACCTGAATAGGCAAAAATTATAGTAAAAAGCAGTACTTGATTGGCTGGAATTAATGTAGAATTTGAACTAAGTAATGTTTACTTTAGACTATATTAGAGGAAGCACTAGAGAGAATGTGAGGTCTCAGGTTTGCATAACTGAGGGAGAAAAGCACTGTAAGAGAACTGGTACCTAAGAAATCTTCCTGTTTTGCAGTCTCTAGTTCTATTAGTCCCAAATAACTTTGGTTCTAGAATGATCTTTTATATCTAATGATCATAGGTTAATTTTTATCGTTAAAAATGTTCCAATCTTATTTGAGAAATATCTATATATCTATATATGTATTATCATTTATTTTATTTTAAATCCAATATTTATATGATACTTATGTGCATGGCACTGTTCTAAGCACCTTAAACGTATTAATTCACTTAATCCTCATAACCTCATGAGGTAGTTCTCTTATTATCCCCATTTAAGAAATGAGGAAACTGAGGCACAGAGAAATTAAGCAACTTAGGTTACATGGATAGGAAATAGTGGAAACAGATTTAATTCTAGGCATTCTAGTTTTAATAAGAAAAAAATATAAATATTTTCTAATATATTGGCAAAATGCATAAGCATTAGAGTGTGTACTTCTGGTAGTTAGCTTAATATTTATGTGCCTATTTGGGGACAGGCTTTTGATGCCAGAGAAGTGTGATATTAATAGCTAATTAAGCTATTGATGTATTCTTAGTATGACAAAGATTTATGAAGACTAACTTCAAAAATTTCTTAAGAAATCTAAATGTCTATTAAAAGTATCAGTGATACAGTTATCTTAAATCAGGTTTATTATCATATATAAGTAAAGAGATGTTTGGATTTTAAAGAAGAGGGAATAAATTTTGGTTGAGAGATGAGGTAGGCTTCCACAAATCATCTAACTCAGTGCTTATGAAAGTGTGGGGCCCGTACCAGCATCATCATCACCAATTGGGAGATTTTTAGATATTTAAATGATCAGGCTTCTGGGATGGGGCCCACTAATTCATTTTAATAAATTCCTATTTTAACAAATCATATGCATAATCAAGTTTGAGAACTACAAATCTACCTACCTTTCGTTAGTCAGGAAGTGTAGTACACAATAATTTTTTTAAAAGGCCAGGAAATACATTTGTTAACATAAATTAAGATTGTTAAAAATAATACAAATGAAATTATTTGTATTTTAAATATTCATTCTGGGCTTCCCTTCCCCCCCTTATCTCCGGCCCTGCATTTAG
Seq C2 exon
GTATAGAATCATTTCTTATGTACTCTGTTCATGAAGGAATCAGGGGAATACCTCTTGAACCAAGTGACAAAATGGATGCTTTGATGCCTATATCAGGAACTTCATTTGCCGTGGGAATAGATTTCCATGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000168702-LRP1B:NM_018557:34
Average complexity
IR-S
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:
PF146701=FXa_inhibition=WD(100=86.0)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCAATTCCTGCCAACTAAACA
R:
AATCTATTCCCACGGCAAATGA
Band lengths:
246-1782
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)