GgaINT0048814 @ galGal3
Intron Retention
Gene
ENSGALG00000012407 | LRP1B
Description
NA
Coordinates
chr7:33558232-33559118:-
Coord C1 exon
chr7:33558996-33559118
Coord A exon
chr7:33558373-33558995
Coord C2 exon
chr7:33558232-33558372
Length
623 bp
Sequences
Splice sites
5' ss Seq
GTGGCAAGT
5' ss Score
2.6
3' ss Seq
TGAAATCACTGTACTTCTAGGAT
3' ss Score
6.57
Exon sequences
Seq C1 exon
CCCCTAATAACACTTGTGATGAGAATGCTTTCATGTGCCGTAATAACATCTGCATTCCAAAACAGTTTGTATGTGACCATGATGATGACTGTGGAGATGGATCAGATGAATCACTGGAATGTG
Seq A exon
GCAAGTATAATAAAAGTAGAGAAAACAGAAAAATTCCAAACTGTTCAATATAGGGCCTTCTGCAAGGTCTGTTGCTTTAAAGTCACTATTGCAAAAGAAAGATCCTTGCTTTCATGCGCTAATAGATTCAAGTCAATGTTACTATTTTAACTTTGAAATTTATAAATTTTATAGCTATTTCTTCTTTTTTTGTGTGTGTAAGTCTTAGAGAATACATGCTTAGAATGGTTAAAATGATTTCACATGTTTAAAAGAGAAAGCTTGTGTGGTGTAAGAGTTCTGTAAAACTACTTGCTGGGTATAGTAATTTCTAAAATAGCTGTTGGAAAACTATTTCCTAATAATTAGGATAAAGTTCCATTACTTATGGAAATTACTTAGGAAAATGTATTTAGGTTTATGTGAGAGCTGCATAACTACACTTCGCATTGGTGAGAATTGTTACAGGACTATACTGTGCTGCATAACACACATTTGATTTTTTTTTCTTTCTTGGAAGACACTTGTGTGTAAGCATATATTGCTTAGTATCTATTAGTGGAACAAAAGACAGTCTTTATTTTGTACATGCAACGTTCTACGTCAAAAGTGTTGAGCAAAGGATGAAATCACTGTACTTCTAG
Seq C2 exon
GATATCGTCGCTGTCATCCTGGAGAGTTCACTTGTGCTGATGGAAGATGCCTGTTAAATTCCCAGTGGCAATGTGATGGGGATTTTGACTGCCCGGACCATTCTGATGAAGCACCTATAAACAAAAAATGCAAAAGTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012407:ENSGALT00000020272:52
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=90.5)
A:
NA
C2:
PF0005713=Ldl_recept_a=WD(100=87.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCCTAATAACACTTGTGATGAGA
R:
TGTTTATAGGTGCTTCATCAGAATGG
Band lengths:
246-869
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]