DreINT0090877 @ danRer10
Intron Retention
Gene
ENSDARG00000006921 | lrp5
Description
low density lipoprotein receptor-related protein 5 [Source:ZFIN;Acc:ZDB-GENE-050518-2]
Coordinates
chr25:10611986-10612651:-
Coord C1 exon
chr25:10612255-10612651
Coord A exon
chr25:10612158-10612254
Coord C2 exon
chr25:10611986-10612157
Length
97 bp
Sequences
Splice sites
5' ss Seq
TGGGTACGA
5' ss Score
5.84
3' ss Seq
TTTTATGTATATATGTACAGATA
3' ss Score
5.76
Exon sequences
Seq C1 exon
GAGCAGAACAGGTGCTTTTACTTGCTCGTCGCACTGATCTTCGGCGGATATCCTTGGACTTGCCTGACTTTACAGATATCGTCCTTCAAGTCAATGATATTCGTCATGCAATTGCCATCGATTATGACCCGGTGGAGGGATATGTCTACTGGACGGACGATGAGTTGAGGGCTATACGGCGTGCTCGAATTGATGGAAGCGATGCCCAGACTTTAATCACCAATGAGATCAATCATCCTGATGGAATTGCTGTGGATTGGGTGGCACGAAACCTCTACTGGACGGACACTGGCACAGATCGCATTGAGGTGACCAGACTCAATGGCACTTCTCGACGGGTCCTCATATCTGAGAACCTGGACGAACCACGAGCCATTGTATTGGATCCCATAAATGG
Seq A exon
GTACGAACTTCACATTAAGATCATTTCTGAGATTTCTTTCCTAAGAATTTTCATGTGATTTTTGCAGATTTTCATTTTTTTATGTATATATGTACAG
Seq C2 exon
ATACATGTATTGGACTGACTGGGGGGAATTGCCCAAAATTGAACGAGCAAACCTGGATGGCACGGACCGGGTCGTGCTTCTCAACACTTCTCTTGGCTGGCCGAACGGTTTGGCTATAGACTATATAGCCGGAAAGCTTTACTGGGGTGATGCCAAAACAGACAAAATTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000006921:ENSDART00000121724:7
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=0.000
Domain overlap (PFAM):
C1:
PF0005812=Ldl_recept_b=WD(100=30.8),PF0005812=Ldl_recept_b=WD(100=30.8),PF0005812=Ldl_recept_b=PU(0.1=0.0)
A:
NA
C2:
PF0005812=Ldl_recept_b=WD(100=72.4),PF0005812=Ldl_recept_b=PU(33.3=22.4)
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:
GGTGACCAGACTCAATGGCAC
R:
AAGTGTTGAGAAGCACGACCC
Band lengths:
179-276
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]