GgaINT0048795 @ galGal4
Intron Retention
Gene
ENSGALG00000012407 | LRP1B
Description
low density lipoprotein receptor-related protein 1B [Source:HGNC Symbol;Acc:HGNC:6693]
Coordinates
chr7:31482888-31484781:-
Coord C1 exon
chr7:31484656-31484781
Coord A exon
chr7:31483020-31484655
Coord C2 exon
chr7:31482888-31483019
Length
1636 bp
Sequences
Splice sites
5' ss Seq
AAGGTTAGA
5' ss Score
6.12
3' ss Seq
CTATTTGATTTTTCCCTTAGGTA
3' ss Score
10.42
Exon sequences
Seq C1 exon
GTAGCAATTCCTGTCAATTCAATAATGGTGGATGTTCCCAGCTCTGTTTACCAACATCAGAAAGTACAAGAACCTGTGTTTGTACAGTAGGCTACAACCTCCAAAAAAACCGCATGGCATGCAAAG
Seq A exon
GTTAGAAATGCTTTCAGTATTTATTTTTAGCTAACTTCAGTTTTATGGGAACTCTGTAAGTAATTTATAAAGAAACTTCAATTATTTATTTGGGTGATTAAAACAGAAGAGTTTACTGTGGTGAAGAGATAAATTTAGCATTTCATTTGTTTATTTAGCTATGCATTGCTTTTTGTGGAAAACCCTAAGGTGTATTTTTCACTTTTTTTAAATATTCAGACCATCTGACCCATCATTTGAGTGACACATATTTGTCATTCACCTTATCTTAAAACTTAATTACAAACTACAGTCTGAAAGGTTGGGTATCTACTGCTATTACATTACACTTAGCAAAAACTAAATCCTTATTGTATGAAACAGCGAAAGGCACTTTATTTTTGAGGTGCCATGGTAGTTATGAATTTTTTTAATTATTCCTATTGGATATTGCTGTATGTTCATAGCAGACTATACTTGGAAACAAGCAGTTAAGCAACATAAACATGGCTTTCTACTTAGATCTTGCCGTATGTAACTTAGCAATGTTTTTTTTTTCCTTCTAGTATATTCTTTTGCACTTCTTCAGATAGTTATAACTTTTAGTTGTGGGTAAAACTGGTGGATGTTGTGTTTTTTAATAGTTTTCTAGATAATAACAGATTTGATTATTTAATTTTCCTTTAATTTAAAACAGGTATTTTTATTTTCTTTTTTTTTTTTTTCATGAAAACTTGTGGAAAAAGCTAACAGGTAGCATCCCATGCATACAGACTTGTTTAGTATTGTTCATTTCATTTACTAGATAAATGTCGTCTTGTTTGGAAGAAATTTTGTACTATTTTATCTGTAACATTTTAGTTCACATTCTTAAGGTATTTCTACTAGCTGTCTTTTTGCAAAGAAAAAGGTTTTTAAACAAATGATGTGAAGAAAAAGACACCTGCTTGTGTATAATACCTGATCTTCAAGATTTTGAGTTGCATATCATCACACTATGTCATTTCCCTTAAACCTGGGAGAGTTTTATTACAAGGACTTGGAGATAAATGCAACAAAATACTTGTTATAACTTTGTTTATCAAAAGGTGTGATTCATTTCAACTGTTTCTTCCTACTTAATAGAAATCAATGCTTCTGTTGTGTTATTAATGTAACACAAATGTAGACTTTTAAAGTGTATCTAAAGCATGATTTTCTTAAACTGTGTACCTCTCTATTGTTTCTAAAGGATAGGTGCATGATTGAATGAGGTAAGATGAATCTCATGCCTCAGAAGTCAATTTATACAGTCTCGGGTTGTGCTTTTATTGAGTTATCTGTAACTGTCTCTTGCTAAATACCTAAAATGTGGATAAGCACTGAAAATATTCTTAAATGTCTCGTAATTCAAAATAGTTTCTTCTTAGTTTAAATTTTCATTAGGATTAATTGTAAGATTGTGCTTGAATGAACAATAATTCACTTCTTTTTGTAAAACTGTATTAATAATTTAATTAGAAATAAGCTATAATAATTCATGGATTTTTTTTAAGAGTTGGATTTATCATTCTGGACAACTATGGAACAGTATAGGAAAACTCTGTTAATTCCTCAAGTGTTGCTAATAGGGAAAGTCTCCATTTTGCTCCCCTTAACTATTTGATTTTTCCCTTAG
Seq C2 exon
GTATAGAATCATTTATTATGTATTCTGTTCATGAAGGGATTAGAGGAATTTCTCTTGATCCAAATGATAAAATGGAAGCTTTAATGCCTGTATCTGGAACCTCATTTGCAGTGGGCATAGACTTCCATGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012407:ENSGALT00000020272:35
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:
PF146701=FXa_inhibition=WD(100=86.0)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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:
TCCTGTCAATTCAATAATGGTGGA
R:
ATGGAAGTCTATGCCCACTGC
Band lengths:
246-1882
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]