DreINT0090629 @ danRer10
Intron Retention
Gene
ENSDARG00000061517 | lrp1bb
Description
low density lipoprotein receptor-related protein 1Bb [Source:ZFIN;Acc:ZDB-GENE-070912-401]
Coordinates
chr9:36697597-36699090:+
Coord C1 exon
chr9:36697597-36697691
Coord A exon
chr9:36697692-36698940
Coord C2 exon
chr9:36698941-36699090
Length
1249 bp
Sequences
Splice sites
5' ss Seq
TTGGTATGT
5' ss Score
7.12
3' ss Seq
TTTCTCATTTCCCCCTGTAGGAC
3' ss Score
12.24
Exon sequences
Seq C1 exon
AAAAATCTACTGGACCGATGGCAATACAATAAACGTAGCCAACATGGATGGAAGCAACAGGAAGGTTCTTCATCAGAACCAGAAGGAACCAGTTG
Seq A exon
GTATGTTTAATTTGAATATAAGTACAATATTTCAATAGCATTGCATTTTTACAGTCAATAAAGGTTTAAAAGGCAAGTAATATAAAAAGTATTGCACTAAAAAGAAACAGTGCAATGAAGAGATCACATTGATGTCAGAACTTTCAATGCCAAAAAGAACCTTATTTTTTTTCATTGATAGTGATTTACAGATGATGCAGTATATACGACTTAAATCGCAGATAATTGTGCTTTCCTGCTGTACCTAATTATATTTACAAGGACAATAGTATTTTTATAAAGCATGTTTTCTTGCGCACAGTCTTTCCTTAAGAGCTTTAATGTGCCATTTTGCATGTTATGTATTATTTCTACTCGCAAAGATAAATAAAAAGCTTTTCAAACCATTTACTCAAAATGACCACGAAATCCATTTCAGTCCACAGTGTAACTGACCTCAAGGATGGCCATTTGTCCTTGTGGAAAAAAGCCCTGTGATACAGTACAGCAATTGCTCTAAATTAATTTTAAATATAACCATTGCGAACTTGAACTTAAGTCAACTGTCTCTATAAACTTCTGCTGGAATTAGCTTTCAGGAAGTTTCATATATATTAAATTTCATGCCCACATCCTTACAAAGCCAAGACCCTGAGAAAATTGCATTTTAACAGACTGCTTTACAGAGTTTGTGCAGTAAATTGCTTTAATAAAAAAAATCTCCCCAGCCTCTTGATTTCATCAGTCTGTTTCTGAAAAAATGTTTATTTTTTAATGCACAGCAAAATAATAGTTTTTTTTTGGTAGTAAAGAACATTACTCAAGTCCTCTCCTCCAGCTTAAATATCATTCATCTATACATATACGTTCATTGATAGTCAAAGCTCATGCTCCTTTTTTGTATTGGACGAGGTGTCTGAGAGTTAAAAGTCTTGTCTATTGTTGTTTGGAGTATATCATGCACTCGCCCCGCTCAGTCAAAGCTGTCCTGACACTCGATTGAAATATCCTTCACTTGTCACAATCAATTTTCCATCTCTGTCAAACTCTCACCATTTCCACTTTTGAATCAGGTTTCAGACAGAGATGAATTTTATTGAAGTGATTTAAAGTGTCACGAAGCGATTGCAACTGTATATCCAGCTATATAAATGTATATAATAAAACACTTCAAACGCACACTAGTATGCATTTACTGTAGAGCATATGCAAAGTAATAACCAGAACTCTAAACAACAATTTCTACAAGGTTTCTCATTTCCCCCTGTAG
Seq C2 exon
GACTTTCGATTGACTTTCCAGCTGGGAAAATGTATTGGATCAGTTCCGCTAATGGCACTATCAACAGGTGCAATCTGGACGGCAGTGGCTTTGAGGTCATTGAAAGCATGAAGAGGGACTTAACTAAAGCCACGGCTCTTGCAGTCATGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000061517:ENSDART00000139033:28
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.188 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0005812=Ldl_recept_b=PU(79.5=96.9)
A:
NA
C2:
PF0005812=Ldl_recept_b=PD(15.4=12.0)
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:
AATCTACTGGACCGATGGCAA
R:
CATGACTGCAAGAGCCGTGG
Band lengths:
241-1490
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]