GgaINT0046322 @ galGal3
Intron Retention
Gene
ENSGALG00000010858 | LRP2
Description
NA
Coordinates
chr7:20268938-20270675:+
Coord C1 exon
chr7:20268938-20269180
Coord A exon
chr7:20269181-20270549
Coord C2 exon
chr7:20270550-20270675
Length
1369 bp
Sequences
Splice sites
5' ss Seq
GCCGTAAGT
5' ss Score
10.11
3' ss Seq
TTTTTGCCGTCTCTTTAAAGCGG
3' ss Score
8.8
Exon sequences
Seq C1 exon
CTTTCCATACTTGTCAGCCAACAGCTTTTACCTGTGGTAATGGGCGATGTGTGCCCTATCATTACCGCTGTGATCACTACAACGACTGTGGAGACAATAGTGATGAGGCTGGCTGCTTATTCCGAACTTGTGACTCCCACACAGAATTTACTTGCAATAATGGAAGATGTATATCTCTTCAGTACGTCTGCAATGGAGTAAATAATTGTTACGATAATGGCACATCAGATGAGAGAAATTGCC
Seq A exon
GTAAGTCCTTCCAAATTACTAAGTGCATATTTGAGTCTGACTCTTTAGACCAAAGAAGAGGCAAATCTCTTTGAGTGTGAAGAATTATGACAAAGGCAGCAGAAAGGACAAAAGGTTTTTATATTTACATTACAGATGCTGGTTTGTGTTATTTTGAAGCAAACTGATCCTTGAAAGATATTCTTGAGTACCCTGAGATCTTTCTTAATAACTATTGCTTTAATCTGCCTTGACCCAGCAAATACTATTAGAGTGCTTAATGTTAGCTATTGTGAGTAATCCCATAGACTTGAAAAAGATTATTTGAGATAAATTGGATGCAGGACTTACATTTATGCAGAATTGACGTGGAATTTGGCAGCAGATTTTTGCTGTATGCTTTGCAGCATGCTATGTCAAGTATACAGGATTTAATCATTTGGAATGAATATGTGACTCTTATACAAGCATGATTTATATTTATTCTTTTTAAAATACTTTTCAAAAAGTTACCAGTTTTATTTGTTTTCCATAAAATACCAGTTGTGATCAGCTCAGTATTAACTCCTAATGCAGTTAATCAAACTAATCTTGCTTTTTTGCAGTAAGATTGTTAGATTATGTTAGAGAAGTATGTTGATTTAAAAACTAGAAAAAAAAAGATTGTTTTAACACTGTTTTCTTGAAATGTATTGCTTGTGACTTATTTTTTTAGTTCCAAGTGAAATCTGTACATTTGAAATTCCCAGTCTATTAGTCATTTGTAGTTGATGTGGTGATTCACACAGTACCAGCTGGTTGCAAATGCAAGCATTACAGTGTGAATGCTTGTCAGTTTACATTCCCTCACCTCTGAGTATTAGCATGTATTTATTTGATCATGTTTTTGATGCCACTTTTCCCAATAAAAGCAGTGGCCTCATCATTTCCATATAGAACGAGAGGTATGAGTGCACTTTAGCATTTGAGCTGAAATGAGAGGAAAATGGCTTGTGTTATTTACACATTTCTTTTGAATTTTCCTAGGAAAGCTGTTTTTATCCTCTATTGAAGAGGAAGATGGCAGTGAATATGTATAGCATATATTACTTTGCTTCTCATTTAGTATTGTTTTGAGTGGGTGGAGTATATCTACAGCTGTCTCAGCTCTGGGAATTTCTAAAACTATTTCAGCTTCTCCAAAGACTTTTGGCCACTTCTGGGTGAAAGTGATAATGAATCACTGACAATCTTATATCTGAAAAATATGTGACAAAATGCAATCTGGATTGATCAGATCAGTCCACTCTGGATTGGTCCCAGATCAGTCTATTAAAAAAACAAACAAACAAACAAAAAACAGTGTTATGTATGTATGTATCAATGAGATGTTTTTGCCGTCTCTTTAAAG
Seq C2 exon
CGGAGCGCACTTGCCAGTCTGGTTTTACCAAATGTCAAAGCACAAACATCTGCATTCCTCGAACATACTTGTGTGATGGTGACAATGACTGTGGAGATATGAGTGATGAGAGCCCTACTCACTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000010858:ENSGALT00000020276:43
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=45.1),PF0005713=Ldl_recept_a=WD(100=48.8)
A:
NA
C2:
PF0005713=Ldl_recept_a=WD(100=93.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCAACAGCTTTTACCTGTGG
R:
ACAGTGAGTAGGGCTCTCATCA
Band lengths:
352-1721
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]