GgaINT0048765 @ galGal3
Intron Retention
Gene
ENSGALG00000012407 | LRP1B
Description
NA
Coordinates
chr7:33731510-33732977:-
Coord C1 exon
chr7:33732858-33732977
Coord A exon
chr7:33731639-33732857
Coord C2 exon
chr7:33731510-33731638
Length
1219 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAC
5' ss Score
7.82
3' ss Seq
TTTCATTTACATCCCTTTAGATT
3' ss Score
9.12
Exon sequences
Seq C1 exon
AATTGCTACCCAGGTGCCAACAGATGAATTGCCAATATAAATGTGCCATTACCAGGAATGGCAGCAAGTGTTACTGTGGAGATGGCTATGAAACAAGCAATGATGGAAGAAGCTGCACAG
Seq A exon
GTAAACAAGGAAGATGCTGTAGGATTGACACAAAAATTTCTTAATGACTCCTTGATGGCTGTTAGATACAAAGAGCTGGTGGTGGGCTACCAGCTTTCATCTTGGAGCCACAAAGGGTGACCAACAGCAAGCTGATGAGCATGGATGAGCTTCCTTGCCCATATTCAGTGCTGTTTGCTCATCAGGAAATGAGCACAGGCTTGTGGAGTCAAGCAGGGGAAAGAGTCCTCCATAATCAGTCAAGACACGGTACAACTTACAGCATTTCACCTCGTGTCCATAAAGTCACATCTAGATCACAATTTGATAAACAAACACTTCCAAATCATACAACTTAGCTGGGAAAGTTATTCTGGCATAATTAAATGTGTATTGAAATTGGTGTTCTTTTCCATTTTTTAAATATATGATTTTTTAATTCAGTTATTTGATTCTTGTTTTATTTTTTTTCTCTTTTTGTAAGCAGATTGGAATTCTGTTGCTCAGTCCCAATCATTCCTCTCTTCAAGTAATAGTGCTAAGCCAGATTCTTCATAAATGCAATTTATTTTGAGTTCTTTTGCTCTATGGTTGTCATGTTCTGTGATTGAAAATATGGCTGAGGAAATAATTTCAGCAGCAGTTTTTAAAATGTCAATTTATTACTTAAACTCTCAACCACTGTTAAACAGCATGTCTTGATTTTATGGTATTATGTCTATATGCCCTACTTGAGGAAGCTGCTCTTCAGATTAAAGAAATATATAGTTTTTGATGCAGTGGATGATAGTTTAATCTAGAAATTGTGACAGTTCATTTAAGGAACTATAAGACATTTCCAGCACAAATAGGTTGAGAGGGATAATCAATTTCCTCCCTTGAAATGTTGTTTCATTCACAGTCCCTGATAATTTTTAATAGAAATGGTTTTCTAGTAGAACAGGGGTCTAGATGTCTCCCTAACATAGTGTGTACATTGGATGTTAATTGAACATATGAAGGTTTTAACTTTAAAAATAAATAGCAATTAAACTTGAGAACTCCTTGCCTTCTGTTTGGTTGCTGGAATAATTTCATCAGCCACCCCCTGTGATAAGGTCATGGCTTGAGAAGAGGAATATGTAAATGACCATTCTATAGTGTTTTAATGGATCACAATTTCCTCTTACAATTTCAATTCCTTTTTTTTTTTTTTTACTCCTTAAAAAAAAAATCATTAATTTCATTTACATCCCTTTAG
Seq C2 exon
ATTTGAATGAATGTAATACATATGGAAGCTGCAGCCAGATGTGTGTGAATACGGATGGATCTTACACCTGTAGCTGTGTAGAGGGTTACGTTCTTCAGCCTGATAACAAATCTTGCAAGGCCAAAAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012407:ENSGALT00000020272:3
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:
PF126622=cEGF=PU(83.3=48.8)
A:
NA
C2:
PF126622=cEGF=PD(12.5=6.8),PF146701=FXa_inhibition=WD(100=81.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AATTGCTACCCAGGTGCCAAC
R:
TTTTGGCCTTGCAAGATTTGT
Band lengths:
246-1465
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]