GgaINT1016981 @ galGal4
Intron Retention
Gene
ENSGALG00000011558 | LRP6
Description
low density lipoprotein receptor-related protein 6 [Source:HGNC Symbol;Acc:HGNC:6698]
Coordinates
chr1:71845138-71846955:-
Coord C1 exon
chr1:71846746-71846955
Coord A exon
chr1:71845264-71846745
Coord C2 exon
chr1:71845138-71845263
Length
1482 bp
Sequences
Splice sites
5' ss Seq
ACAGTAAGT
5' ss Score
9.49
3' ss Seq
TCTTATTCTTAAAATCATAGGAC
3' ss Score
6.5
Exon sequences
Seq C1 exon
GTGCTAACCGAGTTGTTTTGGAAGATTCCAATATTTTGCAACCTGTGGGACTAACTGTATTTGAGAACTGGCTGTATTGGATTGACAGACAACAGCAGATGATTGAAAAGATTGATATGACTGGTCGAGAAGGACGTACAAAGGTCCAAGCTCGTATTGCACAACTCAGCGACATTCATGCTGTGAAAGAGCTTAACGTTCAGGAATACA
Seq A exon
GTAAGTGCACTTCCTTTGTGCAAGTGAAAACAGTGGCTGTGGGACTGGAGGCAGGTAATGACTAAGAGAGATGAAGCCTCCTTTTCCTTATCACTGATCAACATCAGTGTGAATCAAAGGGGCCAGAAGTATCATTTTGTCTGTTATATAGCTAGTATGGTATTGTTTGTCTCCTTAGTGCAGTTGGCAATGGACATGCAAACTATGCATGTCACAAACCCAGCATCATATTTTGTTGCTCTGACAACTTTGTTGTTACTCCTGTACAAGCACCTGGGATTTGAGTGTATATAGGCACAGTGGGAATATTCTGTTACCCCTAGTAGAGGATTTTCTGGATTATGGATGTGGCAGACTACTAATGCAGAGTATCAAAGCCGTCACTATTAGGACTTTACTCCTTCTGGAATTCTGAGGGCCCTTTACTAGCTGTAAATATTTCAGCAGACTAGCTACCTTGCCTGCACAGCCTTGGAAGAAAAGTGAAAGAAGTTTTGTTAGTGTCAATTCATATTGAAACTAAGTGGTGGACACTGCATTGCACAAAGGAAGTGTGTGGTAAATAACAATTTGTGCTTAATGTGCCTGCACTTCAAAAAGTTTTCTGCTTACCAGGATATAGCTTTCCCTGCACACACTCACTTGAAATGAAGGGAGCTAGATGGTTAAAGCAGTAGAGCTGCTGTTTTCATGGACAGAATAGGCCTGGTTAATAGGCTCTGGTGTATGCCTTCAAGAAATATGTAGAAAGATGTCTGGGGATGTTTAATTAAAGCATCAGTGCAGACTACTACTAGTTTTGTTTGCTATTAATCTCAGTAAATCTGTCAGGAGTTCCAAGGAAAGTATGTTGTCTTTATTAAACATTAAAATGAAGAGACATATTTATCTAGAGCATGCTCATTTGAGTTTTGGAAATCGTGTGAAAGCTTCAGAATTCATTAATTAGAAAAGTTTACTTTTTTTTTAATGATTTTTGATAGGAAAAGATTAAAGAAGTATAGAACCCAAGGCACCTTTTTATTACTAATGTTGCTCTTTTTGCTGAAGAACTTCTACCTCACACAAGAGCAAATGGTTTGAGTATTGTTTACTAGTTTAAAAGGCCGTATGGTGTGATTCTTGGTGTTTTAGATCACAGATAAATAATTATTTGTGTAAAGGAAAGTAGTACAATGAATCACAACTTTTTCAGAGTTGATTTTAGAAATGCCCTCCACACTGAGAAGGGGGTAATGGGGAGAGTCCTGAGAGGTCGCTGAAAGGTTTGAAAAGAGGTGGGGATTTCTTGTCACAGGACTTACCAAATTATTAGAAAGTAAATCTGAATTGGCTTTTTCCAGATTCCACCATTACTGTAGGGTACTTGAGGTAGAGGAAATTAAGAAGGAGCAGGGAATAAACCAACACTATCTCATGTACTTATCCTCGCAAGTGTGATTGCAGTTGTACTCCCTATTTGTCTTATTCTTAAAATCATAG
Seq C2 exon
GACAACACCCTTGTTCTCAAGATAATGGTGGTTGCTCACACATTTGCATTGTGAAGGGCGATGGCACCACACGCTGCTCTTGTCCAGTCCACCTTGTTTTGCTGCAGGATGAGCTGTCCTGTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011558:ENSGALT00000018841:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.056 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0005812=Ldl_recept_b=PD(51.2=29.6),PF0005812=Ldl_recept_b=WD(100=52.1)
A:
NA
C2:
PF146701=FXa_inhibition=WD(100=86.0)
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:
GTGCTAACCGAGTTGTTTTGGA
R:
CTCCACAGGACAGCTCATCC
Band lengths:
336-1818
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]