DreINT0090484 @ danRer10
Intron Retention
Gene
ENSDARG00000029146 | lrp1ab
Description
low density lipoprotein receptor-related protein 1Ab [Source:ZFIN;Acc:ZDB-GENE-030131-7126]
Coordinates
chr23:25568784-25570089:-
Coord C1 exon
chr23:25569961-25570089
Coord A exon
chr23:25568907-25569960
Coord C2 exon
chr23:25568784-25568906
Length
1054 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
TCTTTGTTTTCTCTCCCAAGTGT
3' ss Score
8.13
Exon sequences
Seq C1 exon
AGGCAAAGACTTGCGGTCCAGACTCTTTCCAGTGTCCGGGTTCCCATGTGTGTATTCTTCAGCGCTGGGTATGTGATGGGGATAAAGACTGCCCTGATGGAGGAGATGAGGGACTTAAGGCTGGCTGTG
Seq A exon
GTGAGTTACATAAGAAATCTCTTATTCTGGAACATGTTTTGTGGCAAAACAAGAAACACGAGCACTGAGAAAAGTTGTGTTGTCACATTTCACTTGCTTAATCTGCGCCAAAAAGCCACACTTGAACTTTTTGCTGAAGAATTGCAGGTGTCTGTTGACTAGCATGTCTACAGTATATCAACAGTTAACATACCTCATTCAAAATGGATTACCAAAATCCGGACTTACTGTCTAGACTTAAAAGACACAATTGACTTTAGGCTAGAAAATGTAAACTTATGTTTGTGTATATGAAAGCATATAAAGTAATATAAATGCTATTTATAAAATTGTATTCTTTTCATGTAATCATACGTTTTACTTTTTTGTTAAGAGGTACTTAGAAGGTTTCTTACCTTTACTGTTTTTTTGTGTTTTATATATGAATTTTTCAAAGATGTTTAAACAAGGTCAAACGAGCTTTACCAAATAGATGCAAAGATAAAATTAAAATTTTGTCTGGAAAAACTGAAAACAAAATGAACTAAAATTGAACTAAATTCAAAAAGTAGTTTTACAAGTAATGTAATGTGTATTTATATAGCGCGTTTATCATATATGGCCATAAAGCGCTTCAAAATTATGAGGGCGGCCTCTCCACACCACCACTAGTGTGCAGCATCCACTTGGATAATGCAACGGAAGCCACAGGACAACGGCGCCAGTGTGCTCACCACACACCAGCTCTAGGTGGAGTGGAGAAACAGCAATAGAGTCAATTCAGTGGATAGGGATGATTAGGAGACCATAAGGGCCGATGGAGGGAAATTGGCCAGGACACCGGGATTACACCCTAACTCTTTTACGAGAAGTGCCATGGGATTTTTTAATGACCACAGAGAATCAGGACCTCTGTTAAACGTCTCTTCTGAAAGATAGCGCTCACTGACAGTATAGTGTCCCCTTCATTTTACTGCACCAGACCATCAGCTTAGTGTGTCGCAGACTTAACATTCTATGTTTCCTTTGCAAATTCTTTAGTACATTTTTGCTAATCTTTGTTTTCTCTCCCAAG
Seq C2 exon
TGTTTAACAAGACCTGTGATGACACTGAGTTCCAGTGTCAGAATTCTCAGTGTATTCCCAAAAACTTCATGTGTGATCATGACATTGACTGTCGCGATGGCTCTGACGAGTCGCCAGAGTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000029146:ENSDART00000088208:52
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:
PF0005713=Ldl_recept_a=WD(100=93.2)
A:
NA
C2:
PF0005713=Ldl_recept_a=WD(100=90.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGACTTGCGGTCCAGACTCT
R:
ACACTCTGGCGACTCGTCA
Band lengths:
246-1300
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]