GgaINT0048778 @ galGal3
Intron Retention
Gene
ENSGALG00000012407 | LRP1B
Description
NA
Coordinates
chr7:33648597-33650305:-
Coord C1 exon
chr7:33650180-33650305
Coord A exon
chr7:33648714-33650179
Coord C2 exon
chr7:33648597-33648713
Length
1466 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAA
5' ss Score
8.59
3' ss Seq
GGAGTGTTTTGTCTTGACAGCAA
3' ss Score
5.33
Exon sequences
Seq C1 exon
TCAATCACAGTTGTCCTGAAAATCAGTTTAAGTGCCAAAATAATCGCTGCATTCCCAAGAGATGGCTTTGTGATGGAGCTAATGACTGTGGTAATAACGAAGATGAATCAAATAAAACCTGTGCAG
Seq A exon
GTAAAAACTTTACTTAATTCCAGCTCCATAAGCAATTCTGTGCTGAACTGAACCAGTCAGCTATTAGTAATCTGATTATTGTCATTTTAAATTAATTCAGATGTTGATGCCACTAAGATGGAATACAAATTGCATTTTACTTCATCTTTGTGCTTGATTGTGCTTTCCAAAGTAATTCAGCACTTAATCTGTCCATATGGGCTGACTGTCAAAGTACTACTTAGGTACAAACTTGTTCCTGCTAAATCTTTTTTGGCAGTTAGAATTGTTTGTTAACATGCTCTGATGAGTAAATTTTATTTTGTGCTGACAAAAGCATAATTTTTTACTTGGTTTCCCCTTGGTACCTTGAAAATTGTTTTCATTTGTAATTTATTTTCTGTATAATGAATTTTTAAGGAAATGTCGAGATGAAGATTGTTCACTGATTCTACTGCAATAAATCACGGAGTTCCAAATCCATGATGTTTACTTCTTGTCAGTAGAGTATGCTAAACGATCACTGAATATTTGCTGTACAAAATATTAGACATCAATGGCTGATTGCTGTTTAACTGAATAGCAGTGATAAACAGCATTGTCATAAATTCCCAGGAGTTATTTTGTTTGATTTAACTTTTCAGGTGTGGAATGATCTGTTCATGGGTTGGTATTTGTGCAATTTGGCTAAAAAAATCTCTAGCACAAATTCAGATCTATAGATTCCATGTCACCATTGCAGTTATTGCAATTGTAATACATATTGATGTCTTTCCATATTCAAGTTTGTAATCATAATCTACGTTTCTATTTCTGTTATTTTAGTCATGAGTTCACGTTTTGAATAAATACAGTTATAGGTTCAGCTTTATATGTTAGACTTTACTGATATTGTACTATTTATCAGATTTCAAAATCATGTATTTAATTGCATAGTATAATTTCTTTTGGTTATATTTGTTTCATCAGAGGAAAGGCATACATCATATACTTTAATGGATCATTATGGTTGCATATTTACAAATGGAAAGAGTTCAAGAAAAGTGAGGCCAGGCACGTTGCATGCATTATTGGTTTTATTTTGTGTGTGTAAATATGACTCTCAGTACATCATTGCTTATAGTAGGAAATACAGATTTTTTTTTTAAATAAGTAAAATTCCAATTGTAAGTTAGATGTTTTTATTCCCTGATTCGCTTCTGCTCTAGCACTAACATTACTTTATCAAGCATTACTGTTCTTCTACTGACTAAGACTGTGTATTCACACTAACAAGTGTATGATTCAAAGATAGATAGGACAGAGTCCTGCAGATTTCAATTTCCTCTGAAATCAAAGGAGGTGAATGATGTTTAGTTAAAGTGAAATGAGCAGCCAGGCCAGGAGATGCCATCTAGATTTGTGACTTCTACATACAGACTTGAACCAAAAGATCTAACAGATTTAGTCCATTTCCCTTGCATTTTTGGAGTGTTTTGTCTTGACAG
Seq C2 exon
CAAGAACATGTCAGTTCGACCAATTTTCTTGTGGGAATGGACGCTGTATTCCAACATCTTGGCTGTGTGACAGGGAGGATGATTGTGGAGATCAAACTGATGAAATGACATCCTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012407:ENSGALT00000020272:16
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=WD(100=90.7)
A:
NA
C2:
PF0005713=Ldl_recept_a=WD(100=95.0)
Main Inclusion Isoform:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCACAGTTGTCCTGAAAATCAGT
R:
CACAGGATGTCATTTCATCAGTT
Band lengths:
239-1705
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]