DreINT0090662 @ danRer10
Intron Retention
Gene
ENSDARG00000061517 | lrp1bb
Description
low density lipoprotein receptor-related protein 1Bb [Source:ZFIN;Acc:ZDB-GENE-070912-401]
Coordinates
chr9:36801558-36803476:+
Coord C1 exon
chr9:36801558-36801746
Coord A exon
chr9:36801747-36803327
Coord C2 exon
chr9:36803328-36803476
Length
1581 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGAG
5' ss Score
6.38
3' ss Seq
TGTCTACCCTTATTTGACAGTTC
3' ss Score
7.97
Exon sequences
Seq C1 exon
TTCCTCATGACCACATCCAGGGTGTGATGGGGCTCACGCTGTTCGAGGACTTCATTTATTGGACTGACGGGAAGTCTAAATCTCTCCGCCGAGCTCATAAGACCACTGGTGCTAATGCTGTGGAACTCCTAAATTCATGGCAAGCCATTAAGTCTGTCATTGTCTACCACCCACTGCGCCAACCTGAAG
Seq A exon
GTAGAGACTGTTTCAAATCAATATTATATTAATTTAACACTTGATTTGCCCCAAAATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTTCATTACATTATATTATATTATTTTGTATTGTATTATATTATACATATGTAGTTATTATTTTTTTATCATTTTATTAGAATTGACAAGTTTTGGGGTCAGTAAGATTGTATTAAATATTTTGACAAAACCGTAATATTTTAAAATATTGTCAAAATGTTGTAGTGTTTTGGAAACATTACACTTGTTTAAGAATCGAAGGATCAAGTAAACACTAATGATGATAATAAATTGAAAATAAGGCTTTTTTAAAGCTTAATAAATGTCTTTACTTTGTATTTTGATTAATGTAATAGGTCAGACATAACCCTTTTTTCTAGTTTCCCAAAGAACATTTTAGTGATGGGGTCTTCGAATATTATTCATGGTGCTAATAATATTGTAATGGCATTTTTGATAAATAATATTTGTAATAGACTGCACTTTAATTTAAGGTGACATAACTACTTGTATTTTACCATTCATTTTGGCTTTAACAGTTTATTGATAACTAGCCTAATTAAAAAACCTTTAACTAAGCTCTGTGAAAATTTTTGCATGTTGGCATACAGTCAAAATTTTAATATTAGAGCCATGGCTGTAGCGAGTCGACAATACTTTGTCTGAAATTAAACTATTTATCTTATTAGAAAATGATAAACAGTTATCCCAGGTGCAGCATTGTATTAGATATTAGCAAATAGGAACAAAACATGGAGAAAACACCTTCACCTTTCACGGAGAAACCTTGGCATCGAGTCATCCACCTTCAGAATTTGCCACTACTGAGAAGGAAGCTCAGCTGCCCCCTAATGGTAATGTAATTCCTGAGTCAGAGAATTTCCCTGAGTACTGCGATGAACCATGGTTAGTCATGGCATTCTGTTTTCTGAGACGTGCATTTCTTAAGACCCTTTCTGTATTGACTTATCTACTAAGTAATACTAATTAAATGCACGTAATTGCATTTAATTGTTATATGGTTGGGGTTAGAATATTAGAAAATGTGTGTTAGGTTTAAGGTTAGTTTTTTGTATGTACACTCTCAGAAATAAAGATACAAGAGCTGTCACTGTGACAGTACCTTTTCAAAAGGTACATAATTGTACAAAAAAGTCCTTAGTGGTGCCTTAAAGGTATATATCTGTACCCAAATGCACCTAAAATGTACCTTTGAGGTACCAATATGGACTCTACAGGTACAAATATGTACCTTCTAAAAAGGTAATGCCCCAGTGACAGCTCCTGTACCTTTATTTCTGAGACTGTATGTATGCATAATTCATTTAATTACTATAGTAAGTGCATGAAACATGTAACTATGTCACCTTAAATGTAAGTTTCATATTATGTTTTGTTTTATTACATTACAATATAGAATGGCATAACAATACTTGTTTTATAAATAACCCTGTAATATAACCCATGTCTACCCTTATTTGACAG
Seq C2 exon
TTCCCAAACACCAGTGTCAAGTGGCTAATGGAGGCTGTAGCCACCTATGTTTGCTCTCACCTGGAGGAGGTCACAAATGCGCCTGTCCAACTAACTTCTACTTGGCCGCCGATAACAAGACATGCCTATCCAACTGCACAGCCAGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000061517:ENSDART00000139033:58
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.032 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF146701=FXa_inhibition=WD(100=74.0),PF0005713=Ldl_recept_a=PU(15.8=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:
TCCTCATGACCACATCCAGGG
R:
GCTGGCTGTGCAGTTGGATAG
Band lengths:
334-1915
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]