RnoINT0086711 @ rn6
Intron Retention
Gene
ENSRNOG00000006338 | Lrp6
Description
LDL receptor related protein 6 [Source:RGD Symbol;Acc:1304749]
Coordinates
chr4:168213382-168215266:-
Coord C1 exon
chr4:168215057-168215266
Coord A exon
chr4:168213508-168215056
Coord C2 exon
chr4:168213382-168213507
Length
1549 bp
Sequences
Splice sites
5' ss Seq
ACAGTGAGT
5' ss Score
8.34
3' ss Seq
GTGATAATCAACTCTTCCAGGAC
3' ss Score
6.64
Exon sequences
Seq C1 exon
GTGCCAACAGGATCGTGCTAGAGGACTCTAATATATTGCAGCCTGTGGGTCTGACCGTGTTTGAGAACTGGCTCTACTGGATTGATAAGCAGCAACAGATGATTGAAAAAATTGACATGACTGGTCGCGAAGGCAGAACCAAGGTCCAGGCTCGGATTGCTCAGCTCAGTGACATCCATGCAGTGAAGGAGCTGAACCTTCAGGAATACA
Seq A exon
GTGAGTGAGGCGAACAGTGCCAAGGGCGTTGCTGTGCTGTACGAATCAAGACATGGTCTCGTGGCTTCTTGACTTTTTTCTTCTTTATTTTGTTTTTATATTTAAAAAAACACTTTGTTGTAGTTTCTAAAAACTTAAATAGTGTGTGATTTGGGTTTATCAAAATCATAATGAAGCTAGGTAAAGAAGTATAGTCCTATAATCAGCACTCGGTGTGAAGGCAGGAAGATTGCGAATTTGAAACTAGTTTGAATTATGTATTTAGACCGAGTCTCGGTAAAACCAAGACCTGGGTATGGCTCAGTGGTGGAGGACTGACTGCATCCACGGGGCCTGGGCTTGGTCTTTAGACTAAGTAGATAAATGAACAGTCTTGTATGCGCGACAGACTGAGAACCACCTCTGCTGATAAATAGTCAAATACAGTAAGTGTTTTCTGTTTTGCGCAATCCACTCCTTTGTAGATACTTGATCAACAAGGTCAATGTAGCACCCATCTTATGATAGAAAAGAGATCATAGTTGATGGCTACATTGCATGATGGTAATGATACTGATGCTGTAATAGCAAAGATCAGATTGTTTATAACAAGAGCTAAATAGCAAACTCGGGGCAGAAAGTTCAAGTTCTAAGCTAGACGTTGAAGAGTTGCAGACTGGCTCGCCTCTGACACGTCACCAGTAAGAGCCACTCGGATCTTTGTGATGCTTCGTTGCAGTTGAGCAAGCAGGTGGTTTTGTCTCAGTTCCATAGTACCATAAAGTTCTTTCTTCTGTTACCTTAATTTTCTATAAATTCTTTATTAAAACATACCTTTTAACATGAAATAATTTATGCTTTAGGAAAGTAAACGTTCATTCAGAGTTAAAATACTTAGAGGAGAATTCTCAATTTTAAAAATAAAACTATGTAAGTGTCAGCAGTCTCTGTAGCAACTTTTCTAGTTCTATAAGTCATTTTTTATTTATCTGGCCTTTTTGAAATAAGGTCTTGTTGTGTTGTCCTTACTGGCCCAGAACTTGCGATGTGACTAGTTCTGGCCTCTCCTATGGTGAGCCTTTACCTCTGCTTCCTAGGATAGGAATATAGGTATGCCCCATCATGCCCATGTTTGTAATTCATATCGTAATTACAAAATTAACATCATAACATATCATAGTTATTTATTATCTTGTTTAGGTTTGTTGTTGTTTGTATGGTGCTGGGGATTGAACCCAGGACATCACTCACGGCACGCACTCTTAAACAGAGTAGTTTTTCCCAGCCCTTACCAACAATAGTTGAAAGTGATGTAATGTGCTAGGTCTAACGTGCCTGTAATCTGGGTAGCTTTGGAGTCTGCGATAGGAGGATCAGTGGAACCTGAGAGTTTACGACTAGCTTGGACATAGCAGACTCCCATCTCATTCGTGCAGTGGTCATGTGTAATGCTGTGGTAGAGCTCATACAGGGATAGTGTAGAATTGTGCTGTGTAGTCGTAAAGTCAGAGCTTTTTTATATTTGGTATTGTTTGTGGAGATCATTGATTGTGATAATCAACTCTTCCAG
Seq C2 exon
GACAGCACCCGTGTGCCCAGGATAATGGTGGCTGTTCACATATTTGCCTTGTAAAAGGAGATGGTACCACAAGATGCTCCTGTCCCATGCATTTAGTTCTGCTTCAGGATGAGCTGTCCTGTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000006338:ENSRNOT00000066575:15
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
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCAACAGGATCGTGCTAGAG
R:
CTCCACAGGACAGCTCATCC
Band lengths:
334-1883
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]