RnoINT0086706 @ rn6
Intron Retention
Gene
ENSRNOG00000006338 | Lrp6
Description
LDL receptor related protein 6 [Source:RGD Symbol;Acc:1304749]
Coordinates
chr4:168230117-168231198:-
Coord C1 exon
chr4:168231014-168231198
Coord A exon
chr4:168230444-168231013
Coord C2 exon
chr4:168230117-168230443
Length
570 bp
Sequences
Splice sites
5' ss Seq
TCGGTAAAC
5' ss Score
4.93
3' ss Seq
TACTGACTTTCCCAAAATAGGAC
3' ss Score
7.52
Exon sequences
Seq C1 exon
ATTTATGTATTGGACTGAGTGGGGAGGGAAGCCTAAGATTGACAGAGCGGCTATGGATGGAAGTGAACGCACTACATTAGTTCCAAATGTGGGTCGAGCAAATGGCCTTACCATCGACTATGCTAAGAGGCGGCTTTACTGGACAGACCTGGACACTAACTTAATAGAATCTTCAAATATGCTCG
Seq A exon
GTAAACGTCACTAGATTTTTTTTTCTAGGTGATTTATGTAAAGTCAGTGGCTGCCACTCATCCTTGTTTCGATGCTGTGGCTGACACTTTGTGTTGGCAGCTATTCTAGAATTGCACCTTTTTATTATTATTAATAGTCGCCTGGTGACTTAGAGTTATTTATTTATATAGTATGCAGTTTTATTACTATTGGATCTGTACTGATATTTATGAAGAGGATACTCATGTGCACATGTATTCCCCCCCCCCCCATCTTTTTGTGGAAGGGAGAATGAAATACTGAATTGTAAGTCCTCATGCAGAGGAAATAAAACCAAAATCAAAATAGATCATAGGAGTTTAAAGAAACCTAGTGATGTATAAAGAAAGATGAGTTTTAGGCATGGAGCAGATTAAGATGGACTAGTTTCAGAGGTCTTATCTGGTTTTAGAATTGCTTTTAAATAAAGTGTTCTATTTTAAATTGCTTACAAATTTAATGTTTCTTATGCCACCTTTTTTTCCCCCAAAAAGATACTTGTTCCTCACACGCTTACGCCTCTCCCTTGTCTACTGACTTTCCCAAAATAG
Seq C2 exon
GACTCAACCGTGAAGTTATAGCAGATGACTTGCCTCATCCTTTTGGCTTAACTCAGTACCAAGATTACATCTACTGGACAGACTGGAGCCGACGCAGCATTGAACGTGCCAACAAAACCAGTGGCCAAAACCGCACCATCATCCAGGGCCATTTGGATTATGTGATGGACATCCTAGTCTTTCACTCTTCCCGGCAGGCAGGGTGGAATGAATGTGCCTCCAGCAACGGGCACTGCTCCCACCTTTGCTTGGCTGTGCCTGTTGGAGGTTTTGTGTGTGGATGCCCTGCCCACTACTCCCTGAATGCTGACAACAGGACCTGTAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000006338:ENSRNOT00000066575:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.063 A=NA C2=0.027
Domain overlap (PFAM):
C1:
PF0005812=Ldl_recept_b=WD(100=65.1),PF0005812=Ldl_recept_b=PU(51.4=30.2)
A:
NA
C2:
PF0005812=Ldl_recept_b=PD(45.9=15.5),PF0005812=Ldl_recept_b=WD(100=37.3),PF146701=FXa_inhibition=WD(100=33.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGAGCGGCTATGGATGGAAGT
R:
ACATTCATTCCACCCTGCCTG
Band lengths:
357-927
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]