HsaINT0096400 @ hg38
Intron Retention
Gene
ENSG00000081479 | LRP2
Description
LDL receptor related protein 2 [Source:HGNC Symbol;Acc:HGNC:6694]
Coordinates
chr2:169238091-169239775:-
Coord C1 exon
chr2:169239527-169239775
Coord A exon
chr2:169238303-169239526
Coord C2 exon
chr2:169238091-169238302
Length
1224 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATT
5' ss Score
8.55
3' ss Seq
TGCATTTTTTTCTTGAACAGCAT
3' ss Score
8.17
Exon sequences
Seq C1 exon
ATGGGAACAGCTGCTCAGATTTCAATGGTGGTTGTACTCACGAGTGTGTTCAAGAGCCCTTTGGGGCTAAATGCCTATGTCCATTGGGATTCTTACTTGCCAATGATTCTAAGACCTGTGAAGACATAGATGAATGTGATATTCTAGGCTCTTGTAGCCAGCACTGTTACAATATGAGAGGTTCTTTCCGGTGCTCGTGTGATACAGGCTACATGTTAGAAAGTGATGGGAGGACTTGCAAAGTTACAG
Seq A exon
GTAATTGCTGAACTAACCCGAGCCAGTTTATCAGCACATCCCAGAGCTTAAAATCAAATGGCACATGTAGGTATTTGACAATGTTGATTAGGAGTTAGATCGACTTGAATCCTGGAAAGATTATGCAATCTCTTTAAACCTCAATTTTTTGTGAGGATTAAATGGGGTAATACACATTAAAATCCTGGTGTATTTTGGAAAATAGAGGTTAAAACATATACAAGTCAATGATTTTTAAAGTATTTAAAATAATACCAAATGGCTTTTATATAATTTAAAATGAGTTCTATACTATATTTAAGCATCTTTATATAATGCTTAATTGAATTCAACCAGTATTAATTCAATTTCTGCTATAAGAAAGTGCTTTTTACTATGTATTAGGATATTGATTTGACCACTTTCAAAGTGACCAAATAGAGGAAGCTAAAACAAAAACAGAAAGTTTCTTTCTTTTACATGTAGTAGGAGTCTGGATGTCAGAGAGTCCAGGGCATGGGGTCTGCTCTGTTATCCTCATCATGTGGCTTACATCAAGGGTTCCAATGCTCCAGGTTTTAGCTTCTCTTAGAAAGTAGGAAGGGGAAAGAGAAAGTGGAGGGCAAGCAGCTTCCTTTTTAGAATGTGACCTGAGATTTGATTCGTAATTTCTACTCACATCCTATTGGTCAGAACTTAGTCATGTGGTCACTCCAAACTTCAGTGGAGGGAGAGAAATGTCTCTGGCTGGAGAGTCTGTGCCAAGCTAAAACTTGGCATGCTTTATTACTAAAAAGAAAAAGAAGAGAGGGGGTGTTGGGAGAATTAGAACTCTCTACCATAGCTGAGGGCCTCAGAAAACAGAAATATTTAAGACATGATTCCTGCTGTCCAGAAGCCTACAACCTATTAAATAGTAAGGAAGATAACCAAAGTACAAAAATAAATACAGTAAAAGGAAGAATGTAAGCATAGTTTACTCTAGACTAGTATTTAGAAACACAGTTAAATATAACCCAAGAAAGAGTCTATTTTAAGTACTCATGAAAACCAGCTAACTATTAAGGTTAAGAATGAAGTGATTAAAATCATTCATATGGGGCTTCCTCCCCTCCCCACCAACTTACTATAGTTTGGAATTACACCTTCTTTCTGTTACCAAAAGTATTGAATCAAAAGTTTTAAAGAGTTGTTTTGTGTTTTCTCCCAGTATCATTGACATTTTTGCATTTTTTTCTTGAACAG
Seq C2 exon
CATCTGAGAGTCTGCTGTTACTTGTGGCAAGTCAGAACAAAATTATTGCCGACAGTGTCACCTCCCAGGTCCACAATATCTATTCATTGGTCGAGAATGGTTCTTACATTGTAGCTGTTGATTTTGATTCAATTAGTGGTCGTATCTTTTGGTCTGATGCAACTCAGGGTAAAACCTGGAGTGCGTTTCAAAATGGAACGGACAGAAGAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000081479:ENST00000263816:26
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(9.1=4.8),PF146701=FXa_inhibition=WD(100=42.9),PF146701=FXa_inhibition=WD(100=40.5)
A:
NA
C2:
PF0005812=Ldl_recept_b=PU(58.5=33.8)
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:
TCCATTGGGATTCTTACTTGCCA
R:
AACGCACTCCAGGTTTTACCC
Band lengths:
357-1581
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