GgaINT0048775 @ galGal3
Intron Retention
Gene
ENSGALG00000012407 | LRP1B
Description
NA
Coordinates
chr7:33655765-33657767:-
Coord C1 exon
chr7:33657578-33657767
Coord A exon
chr7:33655888-33657577
Coord C2 exon
chr7:33655765-33655887
Length
1690 bp
Sequences
Splice sites
5' ss Seq
AAGGTATTA
5' ss Score
7.04
3' ss Seq
GTTTTATGTTGCTTTTACAGGTA
3' ss Score
11.4
Exon sequences
Seq C1 exon
GTAATCTACAGCGGAAAAGATTTGAATCATCCTTTTGGATTATCACATCACGGAAATCATATTTACTGGACAGACTATATGAATGGATCTATTTTCCAGCTGGATCTGATCACAAGGAATGTGACACTATTAAGAAGTGAGAGACCACCTTTGTTTGGGCTTCAGATATATGACCCGCGTAAACAGCAAG
Seq A exon
GTATTAATATGATATGATTTCTCAGAGATCTACTACAAAAGGACATTTTCCCTCCTAACCTTGCAATACTTTGAAAATACTAGTTGAACAATGATAGGAAAAGGAATATGCTGATTGTGGCATGGCAAAGACACTTCTTAATATTTCAATCTTGTAGTTACTGAAAGCAGTGAGACAAAATAGTATTTATAACTGTATTTCTTTGTATTTATTGGCATTTTCCTTGTTTGTGAAAGAGGAAAAGCTGTGAAAATATAAAATAGAATAGATAATATGTATGCAGTGGCTCATGCACGTAAAATACATTATTGTATTTACCTTTTCTCAGGGAAAGTTCATAGCTTCTTTGTGTCTTTTTTTCCTTTCTATAACTTCCTTCTTCTCCTTGGTCTCCATCAGTACCATATGACTTAGCCTGCTGAAAGTACATGGTAACATGATCTAGAATCCAAATCAGTGGCCTTTGTTAGTAGTGGAAAAGTGGGTTCTTGATATTGCTTGTTTCATTAGAGAAATAAGATATAAGGCCATAGAGTAGCATGGATAGTGCTTACAAAATGAACACACTTTAATTTACAGATTTAGTTTTAAGGAGGAAATTTTGGAAGCCATTTTTTATATACGGCATTTTAGATGAGTGGTGAATATTTGCTTTCTTTAGTGAAAACATAGTTCTGGTTATAGTCTGCCACCTCAGATGGAAAGCATGAAAGTAAGCATCAGGACTTAATATAAACAAAATACTGTTCTAAAAGCTGACAGTGTTTAATATTAATACCTCTACAGATCTCAAAAAGAAGAATGTCTAGCTTATTGGGCTATCATTTTTGACATGTACTGGTAAAAGAGTGTTTCTATTTACATAGTTCCTATAGAAAACCTTAAGTGTTTTTTCCTGAAACTTTTGATTCTGTGAACAAAATAGAAACAAAATGGAAATTTCCATATTTATCACATTGCTACTTAGTACATATACAACTTTAAAATGTACTTTGCTCAACTGTAATAACCAATATGCTAAAACTGTTTTATTAGGTGCCTCACAGGTACCTTGTTCCCAGGCTTCAAGCTCAGTTATGTTTTTACAGTATCATCACTAGTGTGCAGCAGTTCTTGTTAGGTGATTGGAACACCTGACAGCTGTCGCTATCCTCATGTGAACAGCATATGGCATTTGGGGAGAAACAACAACAGGGGAACAGAAAGTGGAGAAATAGCAGATGTGTTCAGAAAAAGTGCCATAATATTTGCCTAAAACTCTGCCTTCCATAGATGTTGTTATACTTCTGATTTCTGTTTTCTTTCTCTTTTAAGTCTACATTTGTAGCTACGTTGTTTTAACGTGTGCAGCTGCCAGTATACTTCAGATCATTTCTATATATACTGCTAAATGTCTTTAAACTACTACATGCATGGCAATCTGTCAGCATTTGTATCTGTGACATATTTAAATCTTTAATACTTGTTCATCTTCTGAAAGAAGTTGCACAGAATCCTGTGAACCGATGGCATCTGTTTTTATTCTTTCAGGTTATTGCAACCTGTTTTAATATTATAACTAATAGTAACCAAACTAGGAGAATGAGTCCCTAATAGAGAAGAAAATAAATGTAAAAAGGTATTCATGTGCTTACAGCTCCTTACTTTAGCATGGCTGTTGGTTTTAAAGTGTTTTATGTTGCTTTTACAG
Seq C2 exon
GTAACAATGCATGTCGCGTTAACAATGGAGGCTGCAGTACTCTCTGTTTAGCCATTCCTGGAGGCAGAGTTTGTGCCTGTGCTGATAATCAGTTTTTGGAGGAAAACAGTACAACCTGCATGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012407:ENSGALT00000020272:13
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:
PF0005812=Ldl_recept_b=PD(34.2=20.3)
A:
NA
C2:
PF146701=FXa_inhibition=WD(100=85.7)
Main Inclusion Isoform:
NA
Other Inclusion 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:
GTAATCTACAGCGGAAAAGATTTGA
R:
TGCAGGTTGTACTGTTTTCCTCC
Band lengths:
310-2000
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]