DreINT0090427 @ danRer10
Intron Retention
Gene
ENSDARG00000023479 | lrp13
Description
low-density lipoprotein receptor related-protein 13 [Source:ZFIN;Acc:ZDB-GENE-130729-1]
Coordinates
chr5:8680464-8682428:-
Coord C1 exon
chr5:8682195-8682428
Coord A exon
chr5:8680783-8682194
Coord C2 exon
chr5:8680464-8680782
Length
1412 bp
Sequences
Splice sites
5' ss Seq
ACTGTGAGA
5' ss Score
2.78
3' ss Seq
TCATTATTTTTGTTTTTCAGGTC
3' ss Score
12.68
Exon sequences
Seq C1 exon
GCACTAATCTCTGCTCTAATGGTAATGGTGGCTGCAATCAGCTCTGTCTGGCGTTCCCGGGAGGAAAGACGTGTCGTTGTGCTCATGATCATCGTCTGCTCGATGACGGAGACTGTAGACTTGAGTCCCACTGTCCTGAAAACAGCAAACCATGTCTGAGCGAAGACATGTGCCTTCCTCTGGAGCAGTTCTGCAATGGCGTCGCAGATTGTCCAGATCATTCTGACGAGAACT
Seq A exon
GTGAGAAATTGATCATTGTTTTTTATTGTTTTACTTTAAACAATTGTTTTACTGATGCATATTAGTCAGAGTTACAATATTAAATATAAAGAATCAGCAAGACGTCAATTGTTACAATCTATCAGTAGAAAACTAAAGGAGTTCACGTTTCTTCCTCTGAATCAAACAGTACAATTATATATTCTTGCATCAAAAACAAGGCAAAACACAAATAAAAAAAATCTATAATAACATTATAAAAAAGCCAACACATGTTGGGCTATATAGTAATACAAAAACATATATAAAAATATAAATTTGCAAAAGGTACAGCAGTAAAAAAAAGAAATGTAAATTCAAAAATATTTCCTGCTTGCTTTTTTTGCAAAATTGATACAAGTATGGTCTAAAATTTCATTCTTTGTGGTATTAAAAAGGTCTTAATGTCTTAAATATAACTCAAATTAAACCTGCAGATTGCCTGACTTGCACAGATGTCAAACCTGAAGCTACATACATTTTCAAAAACGGTATTTACATAAATCGTTTAATGTGACGTAGCAGCTTTACACTAAACTCTGAAAATCCTGCAGTCTGAACTCCGCATAAAGCGGGTCTGTGTCTGCTCTAAGTAGTCGTGGCACAGATGTTTTCCCACTGCATGACTATCTGGAGCAGCATTTCATCACTGCTGTTTACACTGCAGGATGGACTGGCGTTAGGGAGTTAGGCGTTAGGGACCCAAACTACATCTCACAACCAAACACGCGCGAGAAGTGACATGGAAACAACACAATGTCACGTAGTATTTCTTGTTATGGATTACATAATGAGAAAGAAGCCTTTAATGGAGTAGAAAATGGACTTATTTTGCTCACCTGGCTTTAGAAGGGAATTGGCAATTTCTCTCAAACGTTTTTGACCCAGTTTTGCTCAGATGATACGTCAAACAGACACGGGTGCTAAATTTACACTGGCTTTTCCTGGGTCTAAAAGCCCAGAGAAGTCATTTTAACTTCTCCCCTAACCTCCCGCTGGCCTGCAACTACCCATACTAGTGGATGCTGCTCTCTCATTGGCTGTAGGTAATCGCAGATGTTATTTTCAATCAGAACACATTTAACACAACATGATTTTGAATCACTGACAGCTCCAGATTTTTAGCATGCTGAATGGGTATCAGCGACTCATCTGCAATTCTTTCAGATCATGTCTTTGGGGGTTCACAATGTTTTATTGTTACTCGCGTGAACGAGCACTTATTTACCTGTGATTTCAGACATTTGTCGGCGAGTAAAAATCAGGGCTAAAATCATGCAGTCTGAACTTGGCATTAGGAGCATCTTAAATGATTTGAATGTCTTTTTAAAAATTATCTAGTCTGCTCTGCAGTCTGTAAAATTAATTCTATTCTCATTATTTTTGTTTTTCAG
Seq C2 exon
GTCTTGATGATAAACAGTATAAAACGATTGGGATCAATCCTAAATCGTTTGCTCCAGGTTTGAGTGAGAACATCGTCCCGGCGAATGTGGAGTCAGAGATGTGTGACATTAAGCTGTGTAAAGGGAACGGCAAGTGTGTGAGCCGGAACGGCAAGACTGTGTGTGACTGTCATCCAGAATTTAGCGGTGAAAACTGTGAGAATCGTTCAGGTCTCTTGCAGGGACCCGTCCTGTATGGAGTGATTGGACTGTGTGCTGGTGTGGTGGTCCTGGCAGTCACTGTCGGCATCATTCAGAGGAAGAAAGCCACAAATCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000023479:ENSDART00000134896:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.019
Domain overlap (PFAM):
C1:
PF146701=FXa_inhibition=WD(100=44.3),PF0005713=Ldl_recept_a=WD(100=46.8)
A:
NA
C2:
PF0005713=Ldl_recept_a=PD(0.1=0.0),PF0000822=EGF=WD(100=29.0),PF108123=DUF2561=PU(44.3=32.7)
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:
CTGAGCGAAGACATGTGCCTT
R:
CACACCAGCACACAGTCCAAT
Band lengths:
342-1754
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]