HsaINT0096326 @ hg19
Intron Retention
Gene
ENSG00000168702 | LRP1B
Description
low density lipoprotein receptor-related protein 1B [Source:HGNC Symbol;Acc:6693]
Coordinates
chr2:141457819-141459414:-
Coord C1 exon
chr2:141459290-141459414
Coord A exon
chr2:141458191-141459289
Coord C2 exon
chr2:141457819-141458190
Length
1099 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGC
5' ss Score
7.09
3' ss Seq
GTATCATTTTTCTTCATTAGGGA
3' ss Score
8.45
Exon sequences
Seq C1 exon
AGCACATGCAAACGGGTCTGTCAGAAGGGGCCACAAGAATGATGCCACAGAAACGATAACCATGAGAACCGGCCTTGGAGTCAACCTGAAGGAGGTTAAAATATTTAACCGAGTAAGAGAGAAAG
Seq A exon
GTCAGCACTCTTGAAAGAATACATAATATGTATATTTTATGTGATTTCTCTCCAATTTTTAAAAACATTGTCAAACTTAGAAATTCTTCTATAAGTCTAAAACCTCAAAACATTATCTTTACATCTAATTTCCTGCAAGTATCATATAGTAGCCTAATACAATAAATATGTCATATTTCATACAAAAGCGTATTTGCCCAGGACAGCACAGGTACATGGACATGTTACATACCTGGCATGTCTTGATTATAGGTTTTGGCTAAGGAATATAGAAAAACTTGAAACATGTATTGATTGGATAAAAAATTAAAAGCATAAGTAGGATATTAATAAAAGGCAGTTGAAATTTTTATACATAATATGAATCATATTATATAATAAGTGGTTATGATCCCAAAGGTGATGCTGTTAATGTAAAATATTTCCAAAGTCATTACTTCCTTAAAATATTTATTCTAAACTTACAGGACAATGATTTGGGTATTTAAAATTTGTTTACCTCCATTAAAATAAATTGTAACTAACTTTTTTGTATCAAAGGAAGTTATAATAATGTTGGAGATAATAATAATGAATTCACAAAGGAGAATTAGACTGGTGAAGAAATTTTAAGTGCATTTTTTATCTTCACTTAAAATTGGAGTAAGAACTTATGCTCAGCATATTTAGGAGGTTAGGCACATTGTAGCTATAGATTTCTTTGATGCTTTCCATATCTCAAAGATAGAGTTTAAAGCAGTGCATTATTTCTGGTGAGATCAATTCATGTTTTAAATGAACAATATATGAAACACTATAAGTATCAAGTTTCAAAAAAGATTTATATACTTAACTGGTTCATTAAGGGAAAAATTTAATGCTTAACTTGGATGGTGAATGAAACAGACTATGATTTTCCAAATAAAGAAACCCAAGATTTAAACTGCTGTGATTTTTTAAAAAACAATACTTTTTTAATTTTTTATTGACCAGCTTAAAATTAAGAGCAAAAAGAGAATATTCAACATCAAAGTTTTAATATTTCTTTATGGAGAATTTTGTTTCAAAAACAAAAGAAAAACATAAACATGTGCATGTGTGTATCATTTTTCTTCATTAG
Seq C2 exon
GGACCAATGTTTGTGCCAGGGACAATGGTGGCTGTAAGCAACTCTGTCTTTATCGAGGAAATTCCCGGAGAACTTGTGCTTGTGCCCATGGATATTTGGCAGAAGATGGAGTTACTTGCCTGAGGCATGAAGGCTATTTACTGTATTCAGGAAGAACAATATTAAAAAGTATACATCTTTCTGATGAAACCAATTTAAATTCCCCAATAAGGCCATATGAGAATCCACGTTATTTCAAGAATGTCATAGCCTTGGCTTTTGACTATAATCAAAGAAGAAAAGGTACCAACCGAATCTTTTACAGTGATGCACACTTTGGAAATATACAGCTTATTAAAGACAACTGGGAAGACAGACAAGTAATTGTTGAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000168702-LRP1B:NM_018557:40
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.163 A=NA C2=0.016
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF146701=FXa_inhibition=WD(100=28.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAAACGGGTCTGTCAGAAGGG
R:
ACGTGGATTCTCATATGGCCT
Band lengths:
347-1446
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)