DreINT0090421 @ danRer10
Intron Retention
Gene
ENSDARG00000023479 | lrp13
Description
low-density lipoprotein receptor related-protein 13 [Source:ZFIN;Acc:ZDB-GENE-130729-1]
Coordinates
chr5:8691497-8693013:-
Coord C1 exon
chr5:8692812-8693013
Coord A exon
chr5:8691662-8692811
Coord C2 exon
chr5:8691497-8691661
Length
1150 bp
Sequences
Splice sites
5' ss Seq
AAGGTATCG
5' ss Score
8.7
3' ss Seq
AATTTTTCATGATTTCATAGCTC
3' ss Score
6.42
Exon sequences
Seq C1 exon
AATAATGTTCTGGTCAGAAACTGGGGACGAGGCTCAGATTGAAAGAGCAGGAATGGACGGTTCAGACAGACGTGTGCTGGTCAGTAAATCTCTGCGGTGGCCGGTCAGTCTGACCGTCGACTCCCTGCATCAAAGGATCTACTGGACTGATGAGAAACTCAAGTGCATCGGTTCAGCTAACATTGACGGAGGAGATGTAAAG
Seq A exon
GTATCGGATGCAAGTTACTGATGCAACTTACAGATGAGGCTGTCATTCAAATAATATTAATACACAATAATTGTGGGTAACACTTTAGAACAATGGTCCATTAGTTAATGTATTTACTAACATAACCTATGTATGAATAATATTGTAAGTCATTTATTAATCATTGTTCAACATTAACCAATGCATTATTACAATCCAAAGTTGTGCTTGTTAACATTAGTTGATGAACAGTGTGGTGACAAGAACTAACGTTCTATAATATTAACAAAGTTGAATAAATACAGTAATTATTAATAAATGCATTAACTAATGGACCATTATTTTTAAGTGTTACCTAATGTTGTATTAATGTTAATGTATTTGTCGACAAACCACGAACAATACATTTATTACAATGTTTAAATGTTAATTAATGTTCATTAATAGTTTAACTTTGTGCATTAATGTTAATAAGCATGAATTTGGATTTTAGTAAATGTTGATCTGATTATTAAATGCTGTTCAAGTGTTGTTCATACTTGGTTCATGTTAGTAAATGAGCATTAACTAATGAAACCTATTGTAAAGTGTGACCAATTATTGACATGATGCTTAGATACTATTAATCACAAATTCAAATTCACTGACAAATTCCCCCAAAAAGCATGAGGAAAATCTTTCCTCAAAAGAAATGTATTTAAAATTATTAATTAGATTTTAATGTAATATATTACACAAATATTTAGGCTAATAACTATTAGGCTAGGCAATTTGTTTTTGTGTTAAGCTAGATTCATATTTGGATCTATATATAACATTTACTGCTCAAATCATTTGTTTACCAGCATTTTTTTTATGGTTTTACAAAAGTTCCAACAGGTTTGCAATAAGACAGAAATGTCATTTTTGGTAAATTATCACTTCATTTTTATTTTATTAAATTGTTTTATTAATATGAAAATATGAAATTGTTAAATGATCTGCTAAAAAAAGAAACTACAACTGGCAATAGATGGCAGTAAAAGTCATTGCTTCATTTATTCAGTCGATTCTTTCCCAAGTTTCTTTGATACTTTAAGCAATGAAACAGAGTAACTAATTAATAATGCAGTGTTTAAAAAAATTATAACCTTCAATCTTTTTAATCTCTTAATTTTTCATGATTTCATAG
Seq C2 exon
CTCTTGCAGCTCATGGAAACCCCCAGTCCATTCTCAGTCTCAGTCTTCAATGATCAGGTCTACTGGTCTGATACCAAAAGAGGAACCATTCAGAGAGCTCACAAAACCACAGGAAAACAGCGCCAAGTCCTGCTCAAACGTCCCGGACAGCCATTCGGATTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000023479:ENSDART00000134896:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.044 A=NA C2=0.073
Domain overlap (PFAM):
C1:
PF0005812=Ldl_recept_b=WD(100=61.8),PF0061417=PLDc=WD(100=39.7),PF0005812=Ldl_recept_b=PU(82.1=33.8)
A:
NA
C2:
PF0005812=Ldl_recept_b=PD(10.7=5.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGTCAGAAACTGGGGACGAG
R:
TTCAATCCGAATGGCTGTCCG
Band lengths:
356-1506
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]