DreINT0090556 @ danRer10
Intron Retention
Gene
ENSDARG00000004789 | lrp1ba
Description
low density lipoprotein receptor-related protein 1Ba [Source:ZFIN;Acc:ZDB-GENE-050208-608]
Coordinates
chr22:14531837-14533167:-
Coord C1 exon
chr22:14533043-14533167
Coord A exon
chr22:14532209-14533042
Coord C2 exon
chr22:14531837-14532208
Length
834 bp
Sequences
Splice sites
5' ss Seq
AAGGTTGAG
5' ss Score
1.33
3' ss Seq
TTTCCGACTTCTTTACCCAGGTA
3' ss Score
8.34
Exon sequences
Seq C1 exon
AGCCTACGCCAACGGATCCATCCGACGTGCTTCCAAAAAAGACGCTGTGGATGTAGTGACCATCAGGAGTGGCTTGAGTGTCAGCCTGAAAGATGTGAAGGTCTTTAACCAGGATCGGGAGAAAG
Seq A exon
GTTGAGGTTTCACTTAATGGCAGTTTTCCTGTTTTTTTGAACATCACACCAACGCACACAAGTCTATGCCAGCTAAAGCAGGAGTGTTCAGACCAGCTCCTGGAAAACCACATTTATCCAGAATTTAGCTCCGACATAGATTCCTTTATGTTTGTTGTAACCCTAAAGACCTTAATTAGCTAGTTTATGGGTAGTTAATTAGGGATGCAGGATTAGAGCCAAATTCAAATGGGAAATGGCCATCCAGGAGAAGGATTTGGACACTTTTGCTGATAACAGAACACTTTCTGTTTTTGCACAAATCCACAGAAGATCAATTAGACTTGGTATCTCAAGCAGTTAATGTATGATGTATGAAACATTCTTTTTATTTATTTATTTTTTTTTAAGTATTACACTTGTGTAGTTCACCCAAACATGAGATCCACATAATGAACTAGAACTGTATTAGGGAGTACTTTAAAAAGTTTTGCATGCTAAACAATGAAAGAGCTACAGTAATGTTATGCTGGTTTTACACCAAACTGCATCACTGACTCTAGTTTACTCGTGGAATGTTTTCCCCAAGCATGGATGTTCACTCTACTTGAAATATTTGAAAGTGTGCATTACACATTATTGAAGCAAATTCCACTTTCACATTAAACGCATTGGATTCCGCTTCATTTGTACAGCATGATGATAATTTGCCTATGTTTCTTCATTTGAGTTGTATGTAATTTCTCACAAATACCTCATTCCAATAGTTTGATGTGCATCCAGCATTAGGTGATATCCTTTGATTAGACACTTTGTAGGAAACCTGATCTCTGATTTTCCGACTTCTTTACCCAG
Seq C2 exon
GTACAAACGCTTGCAGCAAATCAAACGGAGGATGCCAGCAACTTTGCTTTTACTTGGGGAATAACCGGAAAACATGCGCATGTGCTCATGGATATCTTGCTCAGGATGGACTCAGGTGTATCCGGTATGAGGGATACCTGCTTTACTCTGAGAGGACCGTCTTAAGGACTATTCATCTATCAGACGAGAATGACCTCAACTCGCCTATTAGGGCATACGAGAACCCAGTTTATTTTAAAAACATCATCGCTTTGGCCTTTGATCATCGACAGAACGCACATGGAACTAATCGGATTTTCTTTAGCGACGTTCACTATGGGAATATACAAGTCATCAATGACGACTGGACTGGAAGGCGCATCATTGCCGAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000004789:ENSDART00000133385:39
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:
PF146701=FXa_inhibition=WD(100=29.0)
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:
TCAGGAGTGGCTTGAGTGTCA
R:
CCATGTGCGTTCTGTCGATGA
Band lengths:
346-1180
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]