DreINT0090481 @ danRer10
Intron Retention
Gene
ENSDARG00000029146 | lrp1ab
Description
low density lipoprotein receptor-related protein 1Ab [Source:ZFIN;Acc:ZDB-GENE-030131-7126]
Coordinates
chr23:25665430-25666225:-
Coord C1 exon
chr23:25666097-25666225
Coord A exon
chr23:25665685-25666096
Coord C2 exon
chr23:25665430-25665684
Length
412 bp
Sequences
Splice sites
5' ss Seq
ATGGTAGGA
5' ss Score
6.66
3' ss Seq
TATCCTTATCTATGTTTAAGACC
3' ss Score
5.97
Exon sequences
Seq C1 exon
ACTTTAACGAATGTGCCGTGTACGGGACTTGCAGTCAGACCTGCACAAACTCAGAGGGCTCCTACACCTGCAGCTGTGTGGAGGGTTACCTGCCGCAACTGGACAACCGCTCATGCAAGGCCAAGAATG
Seq A exon
GTAGGACACATTTCTTTCTGCTGGTTCATCTTGCTCTCTGTCTGCTCTTGCTCTAAAATTGTCCCCTATGACTGGTTTTGGGGTCTAAGGTCACATATTTGTAATCTATGTACATCTCTATGTATGTGTATGTCTATGTACTGTATGTTCAAAGTCTCTTGACTTCAAAAAATGTATCATATTATGACTGCTGATTTCATTCATCTGAAATGCAGAGGTGGGTTCTCACGCCCTTACTGATCATATTCAGAAATATCAGTAGATGTATTTGTATTGATTCTTTATTCAGACTATCAACAGTAGAATCAGATAAAGTGTTTGTTAATTGTAGTCAAATTAAATTTAAAAATCTGCTTCAACTTCCATCCCTATAATCCAAAATAATGATTATTTATCCTTATCTATGTTTAAG
Seq C2 exon
ACCCAGTGGATCGGCTCCCGTTCCTCCTTATAGCCAACTCCCAAAACATCCAAGCCACCTCTCTGAGTGGAGCAAACCCTATTACCATCAACGACAAACAGACCACCACAATGGACTTCATCTACGCCCAGGAGACCGTGTGCTGGATCCACATGGGCGACTCTCCCACTGCCTCGCAACTCAAGTGTGCCAAGTTTCCCAATGCCAAGAGCTTTACGGAGGAGAAGACCATTAACATCTCCCTCAGCCTGCACC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000029146:ENSDART00000088208:5
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:
PF126622=cEGF=PD(12.5=6.8),PF146701=FXa_inhibition=WD(100=79.5)
A:
NA
C2:
NO
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:
GACCTGCACAAACTCAGAGGG
R:
TGCAGGCTGAGGGAGATGTTA
Band lengths:
345-757
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]