DreINT0090722 @ danRer10
Intron Retention
Gene
ENSDARG00000102506 | lrp2a
Description
low density lipoprotein receptor-related protein 2a [Source:ZFIN;Acc:ZDB-GENE-050119-2]
Coordinates
chr9:48861793-48862276:+
Coord C1 exon
chr9:48861793-48861902
Coord A exon
chr9:48861903-48862098
Coord C2 exon
chr9:48862099-48862276
Length
196 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGA
5' ss Score
8.91
3' ss Seq
ATATTCTGTTTGTGTTTTAGAAA
3' ss Score
11.07
Exon sequences
Seq C1 exon
GTTCTAAGGCTTAAAGGAGAAATTCAGTACAGAAAAACCCTCATCACGAACAACGGCTCACCTACAGGCGCAGGAGCTCCCGTTGGCATTGCGGTGGATCCGGCACGTGG
Seq A exon
GTAAGAGCAGATCAGCAGATCTCTGCCCTTAACCCTGATCTCTGAATTCAATGTCATCTGCCAGGATTAAACTGCCTGAGCACATTAAACATGAGTCAACACATACAAAGTATTAGGATGCTCATGCTAATGTAGTACTAATGCAAATGCAAATAAGCTGTGGTTACTCTTTGCTCATATTCTGTTTGTGTTTTAG
Seq C2 exon
AAAGATGTACTGGACTGATCATGGAACAGAGAGCGGGATCCCGGCTAAGGTGGCATCAGCAGATATGGACGGCTCCAACGCGGCCATCCTCTTCACACATAATCTAGAACATGTGGAGTTTATAACCATAGACATCACAGAGAACAAACTTTACTGGGCCGTCACAGGGACTGGTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000102506:ENSDART00000167243:34
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.161 A=NA C2=0.067
Domain overlap (PFAM):
C1:
PF0005812=Ldl_recept_b=PU(0.1=0.0)
A:
NA
C2:
PF0005812=Ldl_recept_b=WD(100=76.7),PF0005812=Ldl_recept_b=PU(28.2=18.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACAGAAAAACCCTCATCACGAACA
R:
CTGTGACGGCCCAGTAAAGTT
Band lengths:
249-445
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]