GgaINT1016982 @ galGal4
Intron Retention
Gene
ENSGALG00000011558 | LRP6
Description
low density lipoprotein receptor-related protein 6 [Source:HGNC Symbol;Acc:HGNC:6698]
Coordinates
chr1:71843514-71845263:-
Coord C1 exon
chr1:71845138-71845263
Coord A exon
chr1:71843751-71845137
Coord C2 exon
chr1:71843514-71843750
Length
1387 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGT
5' ss Score
11.08
3' ss Seq
TATTTGCTTGATTTTTAAAGAAC
3' ss Score
3.25
Exon sequences
Seq C1 exon
GACAACACCCTTGTTCTCAAGATAATGGTGGTTGCTCACACATTTGCATTGTGAAGGGCGATGGCACCACACGCTGCTCTTGTCCAGTCCACCTTGTTTTGCTGCAGGATGAGCTGTCCTGTGGAG
Seq A exon
GTAAGTCCTTCCCATGCTCTGGGTTGCTGAGCTTACAGCTTCTGGGTGGGGAGGTCTCCGGCTTTAGTATCAGCTTCTGAGCAGAAAGAATATGAGAGTGTACCAGGTGTTGTAACATGTTTTTACTTGTTCACCTCTCTGCCTCAGTCCAGTGAGCTAAATCTGCAAGTTTGGAGGAGTAAAAGAATAGGATAATTTCATTAGCTGACTGTAGAATAAGGATTTCTGTTCACGCTTTCTACTTAAGTCAATTGAATTATTTCAATTCGATTTCTTTTTATTGTATGATTTTTTATTACTTTTTGTATCGCTCTGTGTGTTCTTGTTTATCAGCTAATGGTAGGTTCCCACGTTCTGCCATATTCCGCCCCATCTACTGTCTGTGCCATTTAATTCTTCCCTTCTTTCCTCCTGAAACTCACCCTATGTTTGGCTTTCTGAACTGCAGCCTCAGAAGGACAAGTTGCCTCGTCCATGGTGGCATGACCACAGCAGCTTACATGCTGGTGCCTCCAAGGTTGTGGTTGAAATGGGGGAGAGGAAAGGCACTGTGGTACTTCAGTCCCTTTGTGCCAATATACTGAATGGGTTTATTATGCAATCTTCTTGGCATCAAGGCAACGTGTGGTCTCACAATGGAACAAGAACTAACATAACCCAGATATTTTCTCAAGTTTAATAAAATAGCAAGTTTAATACCAGGCCAAAAAGGAGAGAGGAAGAAAGGGGGAATAAAAAAAAAAAAAAGGGTGGAGGGGAGGAATACATGCTTACTTACTGCTTGAGATTAACAGTTACAGTAGTGAATGTTAAATAACAGCTAACAGCTGTGTTGATAGTGAGACAACTAGATGGAGCAGTTTTTTGTCATTTTAGAGGAATTTTGACTCAACAGAACTGTCAAGGGCGCATAACTAGACACTGAGTCACTGCACATCCATCTGCAGCACATTACATCCTCCTAATGTTTTCTATACAATGACTGTTGAGCATTAAGAAAGTGGACAATCAACTGTGTGTGCAGTGGTGCTGCAGGAAAGGGGGAGTAAAGGAAAAGTATGTAGATTTTAAAAAAAGACTTTTGAGGGTCTATGCTGAAGGATCTAAGAGGCTGAGGTGGGAAGAAAAGAATCGTGTTTTGAGTGTTCATGTTTCCTCTTCTTTGTCTAATGAGACTCCATTGACATCAACTTGCATCTGTCATGTGAGGCTCAAGACCTGCTCAAGTGATTATAGAGGCAGAGGGGGTGGAAATTACCTTATGATGCTGCATGTTTACCAGCTTCTTGATATGAAAGGAGCTGAGTTAGTCTTGTCCTTAACTGTTGTGATCTGCTGATTGTTCACCTGAATTTTTACTTTTTGTTTATTTGCTTGATTTTTAAAG
Seq C2 exon
AACCTCCAACATGCTCCCCTCAGCAATTCACCTGTTTCACAGGTGAGATTGACTGCATCCCGGTGGCCTGGCGCTGTGATGGTTTCACTGAATGTGAAGACCACAGTGATGAAAAAAACTGCCCAGTGTGCTCTGACACCCAGTTTCAGTGTGAAAGTGGACAGTGCATAGACAGTGCCCTCCGGTGCAATGGAGAAGCAAATTGCCAGGACAACTCAGATGAGAAGAACTGTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011558:ENSGALT00000018841:19
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:
PF146701=FXa_inhibition=WD(100=86.0)
A:
NA
C2:
PF0005713=Ldl_recept_a=WD(100=48.8),PF0005713=Ldl_recept_a=WD(100=46.2),PF0005713=Ldl_recept_a=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACAACACCCTTGTTCTCAAG
R:
TGAGTTGTCCTGGCAATTTGCT
Band lengths:
344-1731
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]