DreINT0090553 @ danRer10
Intron Retention
Gene
ENSDARG00000004789 | lrp1ba
Description
low density lipoprotein receptor-related protein 1Ba [Source:ZFIN;Acc:ZDB-GENE-050208-608]
Coordinates
chr22:14533752-14535949:-
Coord C1 exon
chr22:14535820-14535949
Coord A exon
chr22:14533879-14535819
Coord C2 exon
chr22:14533752-14533878
Length
1941 bp
Sequences
Splice sites
5' ss Seq
GGGGTATGT
5' ss Score
7.48
3' ss Seq
TTTCCTTTGAATACATGCAGGTT
3' ss Score
7.11
Exon sequences
Seq C1 exon
GTAATATTTACTGGGCGGACCATGGCTTAAATCTCATTGAGGTTGCGCGATTGAATGGTATGTACCGTGCAGTGGTCATATCGGAAGAACTCGATCAACCTAGAGCCATTGCGGTACACCCAGTGAAGGG
Seq A exon
GTATGTATCTGCCTTTAAAATTGCTCTGTGGGTTATTTGTTTCTAGTGCTTAGCTTCTGTTTCACCCAACTATAGCAACACCGCTTAAATGAACAACCTTTGATTGTCTAGAGAACCGTTAGTGTGTGCAATTAGCACCTCAAAGCTTGTTAACTGCAGATGTAAGTCCTCCTTAAAGCCCTATGATTTCTTTTGCATGCACGCTAATAGGAGAGGGCCATCATAATCTTGACCTTGTGTTTGTATTTAGTTACCTCATTATCTACAGCTCTGTATTGTAAAGGTGGAGTATAAACATTAAGCTTTAAAAACCTATTTCAAATCCCTATTGAGGTATTACGTTGTTTGTCTTACTAAGAATTTTAAGTCACTTTTTAAAATGGGATTAGCAATGAGCAACTTCATTCAGTAGATCACTGTTGCTGTTTTTTATAATCAATATGACGGGTGAACAAACCTGCTCCAGGAAGGCCATGGTTGTGCAGAGTTTAGCTCAGACCCTGATTAAAAACATCTAAACTATATAATCATGGTATTTTGACTCACTAGAGACTTTCAGGGAAGTGTATTGGAGCTAAACTGAGCAACATGTTGGCCTTTGATGAGCAAGATTGGACACCTTTGTGATATAATATTAGAGTAACTTTTTTTGCACATTTTTTTTGGTATTTTTGACTTATTTACTGTTGCATGCTATTCCGAAGAAAGGTTTGTCCTTATAGACTGTCTTCAAACAAACTATTTTCACTATTCTTTAGCAACTGAAATGACCAAGAGCTTAATGACGGGTAAACAAACGTGCTTTGGGAAGACCATGGTTGTGCAGAGTTTAGCTCGGACCCTGATTAAACACAACTGAAATAAATAATCATGGTCTTCAGACTCACTGGAAACTTCCAGGGAAGGGTTTTGGAGTTAAACTGAGCAACATGTTGGTCCCTGATAAGCAAGATTAGACACTTTTGTGATATGATATTGGAGTAACTTTTCTTACAAGTTACAAGTTTCTTTGCATGCTATTCCAAAGAAAGGTTTGTCCTTATAGACGGCCATTAAATAAGCCATTTTCACTATTCCTTGGCAACTGAAATGACCAAAGACTCACTGACGGGTGTACAAACCTGCTCTAGGAAGGCCATGGCTGTGCAGAGTTTAGCTCAGACCCCAATTAAACAAACCTGAACTATAAAATCATAGTCTTTTGACTGATTGTAAACATCCAGGAAAGGTTTTGGAGTTAAACGGAGCAAGATGTTGGCCCTCGATAAGTAAACTATTCTTACACATTTTTTGGTCTATTTGATTTATTTTTTGTCGCATACTATTTCAAAGAATGGTTTGTCCTTATAGTCTGTCATCAAATAAACTATTTTCACTATTCTTTGGCAACTGAATTTTTCACATTTTTAATTTTCAAAACTAAATTTTTTAAAGAGTTTGGATGACTTAAGTCAAGTCCTGTTCTACATTTTGTCTCGTTAAAACTTTCATAATATAATGTGCAAACATTGTAACTTTTAAAGGGACATCTTTCTACTTGTACCTAAAATGTTTGTAATGGTACCTTAAGGGTACATATTGTTACATTTAGATGACAGTGTACTTCTTTAATAGATAAATTAAGAAATAAGGTAAAGTGTTTAGAAAACACCTTTGTGTTTCAATTACAACGTGAGTGAAATGTTCTTGGACACAAAAATGGTACAAATTTTGCATATTTTTTCACTTAGTAATGGGCTGTGAATGATAGAGAAGTGTAAAAACTGAACCTAATTTGGATTTCTGAAATTCCCAGGAGGACTTGAACAGTTTAACCACAGCCAAATGAAGCCTGATAGCATTGCGCTTGTTTTCACTGTAACTGAAGATAAATCTTCGAGTGCAAAGGTCAGAAATCCTCAAGAAGGCTACTTAAATGAGTTTTCCTTTGAATACATGCAG
Seq C2 exon
GTTTCTTTTCTGGACAGAGTGGGGCCAAAGTCCTACCATCTCCAGGTCACGTCTTGATGGTTCAGAGCAATCTGTGCTTGTTAGCACCGGACTGGCACGGCCTAACGGCGTCTCCATAGACTACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000004789:ENSDART00000133385:36
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:
PF0005812=Ldl_recept_b=WD(100=93.2),PF0005812=Ldl_recept_b=PU(0.1=0.0)
A:
NA
C2:
PF0005812=Ldl_recept_b=WD(100=97.7)
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:
GGCGGACCATGGCTTAAATCT
R:
GTCTATGGAGACGCCGTTAGG
Band lengths:
238-2179
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]