GgaINT1016976 @ galGal4
Intron Retention
Gene
ENSGALG00000011558 | LRP6
Description
low density lipoprotein receptor-related protein 6 [Source:HGNC Symbol;Acc:HGNC:6698]
Coordinates
chr1:71857207-71859321:-
Coord C1 exon
chr1:71859137-71859321
Coord A exon
chr1:71857540-71859136
Coord C2 exon
chr1:71857207-71857539
Length
1597 bp
Sequences
Splice sites
5' ss Seq
TAGGTGAGC
5' ss Score
7.96
3' ss Seq
TTTTCTGCCTTCATTTTTGGAAA
3' ss Score
3.63
Exon sequences
Seq C1 exon
GTTTATGTACTGGACTGAATGGGGTGGTAAACCGAAGATTGATAGAGCTTCTATGGATGGCAGTGAGCGGACTACTCTGGTACCCAATGTGGGACGTGCCAACGGCCTAACAATTGATTATGCTAAAAGACGACTGTACTGGACTGACCTTGATACCAACCTGATAGAATCCTCCAACATGCTAG
Seq A exon
GTGAGCTCCAGAGTCCTGGACAGCCTCACAGGGATACTGTTGCTCTTTTACAGCTCCCCATGACAATTTGTTGCTTGATAAATGTCTTAAGATGAAAATAAATTTTCCCAAACCCACACATCTTCAATATTTGCTTCTAAAATTAATGTGTACACAATAAAATATTTAGTGGTGCCTCTTTTCTTGTAAATAATAGTTGCTCACAGCTTAAATTATACAAGCTATATGTGTTTTCAGTTATATGTAGGACGAAGCTGTCAACTTTGTGTTTTGGAGTCTTGTTTTTCTGCTCTGAAGAATGTTGTTGAATACATACCAAACACTTAATCATCTGTAGAAAGTCAGAGAAAAAGTTAAGATAACAACAGCTTATTGGTTAGTTTTCACAGTGTAATTTAATACATTTTGTTTTTTAATCTTTGTTGGTATCCCCAGGGTTCAGTAATTTTTTCCTAATATCTTGCATGCTGGAGAGTGTTCCTGGCTCATACAGGGGTGTTCTTTCTCATACAAGGGTCTGCGTAACCGTTTTATAAACTGTTTCTTGCAGCCAAAATGAGATGGAATATTTTATTCTTTCATTATCCCAGGGTAGTCTACTGTGGACCCACATCCTATCAACTTTGCCCATATCATGTTTTTAACACCTTTGCAACCATGGGAGCAGACTGCTTTGTGTATCAAATTATTCAGATTATTTTTATCACTAGCCATTACTTAAGGTTAAAGGAGCTTGTCTGCTTTAAATAGTATGTTACCAATAGTGGAACTAAGCTAGAGAAAAGTCAAAACATGGAAGTGCATTACTAGGAATTACACGTAATATAAATGCTTTCCCTTCAGCCTTTCATGAATTTTGGTGTGCTGTTGAGGCTGGGTTAGTGCTCCCCAATGTACAGTGGAACTGGACATAGAATTTCAGCTTTCCTGTGGCCATTAACAGCAAAGTGCAGGACTGTAGATCCTCCTTTGCGCAAGAGGGAATGACTTCCTCTTTTAATAGTCTCCCATTCGTTTTCTGTGACTAGACAACAAGAGATTCCATGGTAATAAAATGGTTGAAATCATTGTGGTGGAAATCCTTCCACCCAATACCCTGTTTCTTAAGGTCTCAATCTTCCCACAGTATACACTATTAACTGTTTGTTACCTTGAGTTCCTGAGTGTTCTTAATACAAAGTAGAATTGTACTAAGCTCATAACAGTTCTGTGTCTGTAAGCAGTGGGCAGAGATATCTGTGTGTGGTGCCAGAGACGCTGAAGTGGGAATACAGTGTCGCCTTCAGTGGGATGCTGTTCGTTTCAGGGAGGACAGAAAGGACAGAATCTTTCTGAGAACCCTGATAATTTTTAAGACTGAAACTTTTCTCTTGTGTTCAGTTCTGTGAGTTACAAGCAGGATTAGCACATTTCTGTGATAGGCTCTGAGACTTCAGAATGGCCCTTTGAGTATTGTATATTGCTTTATAATTTACTTTTGTAACAGTGAAATAGTAACTATGTTTTAACCTTTCTGTGCATATGGCACATCTAAAGCATTATCCAGCATCCATTTTGTTTGGAAATAGTAATGCTTTTTTTCTGCCTTCATTTTTGG
Seq C2 exon
AAACAGGCCTTGACCGTGAGATTATAGCTGATGACTTGCCTCACCCATTCGGCTTGACTCAGTATCAGGATTACATTTACTGGACAGACTGGAGCCGGCGCAGCATTGAACGAGCCAACAAGACGAGTGGCCAGAACAGAACTATCATCCAAGGGCATTTGGATTATGTTATGGACATCCTGGTCTTCCATTCCTCCAGGCAGGCAGGCTGGAACGAGTGTGCCTCTAGCAATGGCCATTGCTCTCATCTCTGCTTAGCAGTCCCTGTTGGTGGTTTTGTCTGCGGGTGCCCTGCTCACTACTCTCTGAACTCTGACAACAGGACTTGCAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011558:ENSGALT00000018841:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.079 A=NA C2=0.027
Domain overlap (PFAM):
C1:
PF0005812=Ldl_recept_b=WD(100=65.1),PF0005812=Ldl_recept_b=PU(48.7=30.2)
A:
NA
C2:
PF0005812=Ldl_recept_b=PD(48.7=17.0),PF0005812=Ldl_recept_b=WD(100=36.6),PF146701=FXa_inhibition=WD(100=33.0)
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:
GACGACTGTACTGGACTGACCT
R:
CGCAGACAAAACCACCAACAG
Band lengths:
342-1939
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]