DreINT0090465 @ danRer10
Intron Retention
Gene
ENSDARG00000029146 | lrp1ab
Description
low density lipoprotein receptor-related protein 1Ab [Source:ZFIN;Acc:ZDB-GENE-030131-7126]
Coordinates
chr23:25591360-25592128:-
Coord C1 exon
chr23:25591997-25592128
Coord A exon
chr23:25591495-25591996
Coord C2 exon
chr23:25591360-25591494
Length
502 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
3' ss Seq
GGGTGTTTTTTTTTCTGTAGACA
3' ss Score
8.25
Exon sequences
Seq C1 exon
GAATGGGCTCGTTTTTGCTCTACTCTGTGCATGAGGGCATCCGTGGCATTCCTTTGGACCCATCAGATAAATCTGATGCCCTGGTACCAGTATCTGGTACCTCTCTTGCTGTGGGCATTGACTTCCATGCCG
Seq A exon
GTGAGTGTACAGATATATTTGTGTACAAGTTTGTGTACAAATTAACATTTTCCAGACCTGCAAACTGTCTGTGAATTGAGAAAATTGATTATTATTATTATTGTTGTTATTTGTAGTCATCATTATCAATATTTTTATTTTATTATTAATTTTTTTATAAAAATATTTATTTATTTTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATGTTGTTATATTATTATATTATTTATTCAAATTATAAAAACAAAAATTAAGATTTATTTTATGATTACTATGATTACTATGGTTTTATGATTACTTATGATTAAATATAGCTGTAGTACTATTAAACTGTGAGGTATTTCATCATAATTTTAAAATATTTATGTAATAATGTAAATTGGTATAGGCTCACGTGACACTTTTTGCTTCTAGTGTTGAGTTTTAGGCCCTTTATGCAAGAATTCAGTCAAACTAAAACTAACTTGGGTGTTTTTTTTTCTGTAG
Seq C2 exon
ACAATGACACCATCTACTGGGTTGACATGGGCCTGAGCACCATTAGCCGAGCCAAGAGAGACCAGACGTGGAGGGAGGACATTGTGACCAATGGCATTGGACGTGTGGAAGGAATCACTGTGGACTGGATCGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000029146:ENSDART00000088208:35
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:
NO
A:
NA
C2:
PF0005812=Ldl_recept_b=WD(100=89.1),PF0005812=Ldl_recept_b=PU(0.1=0.0)
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:
TGGGCTCGTTTTTGCTCTACT
R:
TGCGATCCAGTCCACAGTGAT
Band lengths:
263-765
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]