DreINT0090760 @ danRer10
Intron Retention
Gene
ENSDARG00000102506 | lrp2a
Description
low density lipoprotein receptor-related protein 2a [Source:ZFIN;Acc:ZDB-GENE-050119-2]
Coordinates
chr9:48775456-48777594:+
Coord C1 exon
chr9:48775456-48775599
Coord A exon
chr9:48775600-48777474
Coord C2 exon
chr9:48777475-48777594
Length
1875 bp
Sequences
Splice sites
5' ss Seq
GCAGTCAGT
5' ss Score
-1.2
3' ss Seq
GTGTCTGTGTTTTGTGTCAGGTA
3' ss Score
10.22
Exon sequences
Seq C1 exon
ATAATGTCCAGCGGGAGTGTTATCCAGGCGAATGGCCGTGTCCTTCTTCTGGTGTCTGCATCCCTTTTGACCACCTCTGTGACGGGACAGTTCACTGTCCTGATGGAGAAGATGAGACCAACATCACCGCCGGACGCAACTGCA
Seq A exon
GTCAGTTAAAATCTAATAATCATTCAACCGCCTGTCACACTTGCTGATTGGTGTTTTTTGTTTGAGGTTTTATGTTTTAAAGATTTTATTTCAGTTTTGTTTCTATAACTGAAGATGATTTTAAAGACATAAAATAATCATAGAAACAACATTATTAACAAAATAATCAGTATTAAATGGATTAAGGTTTTCATCGAGAATATATTATTTCTTTCAGTTTCATTTATTAATTTTCCTTCGGCTCAGTCCCTTTATTAATCAGGGGTCGCCACAGCGGTATGAACCGCCAACTTATCCAGCATATGATTTACACAGCGGATGCCCTTTCAGCTGAAACCCCCTCACTGGGAAACATCTATACACACTCATTGACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACGTTAGGGACAATTTTAGCTTACCCAACTCACCTGTACCATATGTCTTTGGACTTATGGGGGAAACCGGAGCTGCCGGAGGAAACCTACACCAACACGGGGAGAGTATGCATAAAGAACTCCATAAAGAAATGCCATCTGATCAAGTCGGGACTCAAACCAGTGACCTTCTTGCTGTAAGGTGACAGTGCAAACCGTTGAGCCACCTTGACTCCATTATTTCACTTTTATTTCTATAAAAAAATTTAAAAAATAAAGAAAAATCTTCAAATAATTCTAGTTTTTTTGTTTAACACGTAAATTATTTTATTTTAGCATTATTTCTATAATTCAAATGATCAAATAAATTAGATTTTTAATACAATAATATGGTGGTGCAATTAAAATAATTTTAAAGACAAAAATTATAAAAAAAACAACAACTGGCTAGTAACATATTGAAATTAAATGCGAAGTTTTTAAATAAAAAAAAATTATTAAGGGGGTGGCATGGTGGCTCAGTGGTTAGCACTGTCTCTTCACAGCAAGAAGGTCGCTGGTTCGAGTCCCAGCTGGGTCAGTTGGTATTTCTGTGTGTAGTTTGCATTTTCTCCTCCTTGAAAAAAACTAGCCCAGCCGGGACTCAAACCAGTGACCTTCTTTAACTTACAAAATAGATTTTAGAAAAATGTTGTTTTCTATATTACCATTCTGTTTAGCATTTGCTTACTGTCAAGGTATTTAAGGGTATCATTAGCTGTGTTTCCATCCACCTATTTTTATGAGTATTTTGGATATGCACATAAAAAAAGGTTGATGGAAGCGTCAAAATGTGCATAGATTTTGAAAATGCGCATAAAAAACGTCATAACTGAGTAGGATAAACTTTTTATCCAATAAGAAAAGATGCGCATAAACTATGATGGAAATACTTTTACCGAACAAATTCCAGTATGTGCATTAAACAAGGTCATGTGATTTTGTTATAAGAGATCATGTGATGATAAAAATGTGTGTGACTGGACAAACCAGCAGGCTGAGCACACTGTAAAACATCTGAAATGTTCTGGTCAATCTAAAACACCAGAACCGTTTCAGTATTAGTGTTATTTTATTATTAATGACCTCCAGAATCAAGAACGCCACCGCACGTTCACTGCATGTCAGGATTGCCTTCTGAGGTGTAAGTAATTTATCAAATATAGAAAATATTCATGCACTTTTTACAGTTGATATTTGGCGCCAGTTAATCAGGAAGTGTGGATTTTGTTCTCTTTGACTCATTGGATGGAAACACTGCTGTATTCGCACGTCTTTTATGCAGTAATTTAGTTTTGCGCATCAAGTCAATTCACATTTTTGGATGGAAACATAGCTATTGACTTTGATCCTAAACTACCAGAATCGTTGTATATGTTTTCCTTGTATATGGATTTTGCTGATGTGTGTCTGTGTTTTGTGTCAG
Seq C2 exon
GTATCTGGCGCTGTGCTTCGCTGAGCTGTGAACATCACTGTCACGCGTCTCCGGATGGAGGAACCTGTGCTTGTCCACCTGGATATGTGATCAACACAAACGACAGCCGCTCCTGCATGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000102506:ENSDART00000167243:7
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:
PF0005713=Ldl_recept_a=WD(100=89.8)
A:
NA
C2:
PF146701=FXa_inhibition=WD(100=85.4)
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATAATGTCCAGCGGGAGTGTT
R:
CATGCAGGAGCGGCTGTC
Band lengths:
263-2138
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]