GgaINT0048798 @ galGal3
Intron Retention
Gene
ENSGALG00000012407 | LRP1B
Description
NA
Coordinates
chr7:33592050-33595556:-
Coord C1 exon
chr7:33595427-33595556
Coord A exon
chr7:33592177-33595426
Coord C2 exon
chr7:33592050-33592176
Length
3250 bp
Sequences
Splice sites
5' ss Seq
AGGGTAATG
5' ss Score
5.98
3' ss Seq
TAATTTCTGTAACATTTCAGGTA
3' ss Score
7.33
Exon sequences
Seq C1 exon
GTAACATATATTGGACAGATCATGGTTTCAACTTAATTGAAGTTGCCAGGCTCAACGGCTCATTCCGATATGTAATCATATCCCAGGGTCTGGACCAGCCAAGATCTATTGCAGTACACCCCGAAAAAGG
Seq A exon
GTAATGTGACTATGGCTACATATTTTTTTTAACATCTGCATAATCGCAATGAAGCTTTTAGGAATCAAGGCCTTTTTTCTAATATATAACATTTAATAAAACTCAAAAGTACTGTAATGAGATGTATTTTGCTATAACTGGACCCAGGTGGAAGAAAATGTTCTTAGCCTATCCCGAGAATTTTCATGAGTCTCTATCTGCAGGAAGTACTATATTTTTCTTTGTCTTAGAAAATGAAAGCTTGCACAATCATTTTAGCTGAAGCATATCCATTGCATGGAAACTTGCTTAAATCTGTTAAGCACTTAAGCTTCCAGCATATCCAAGAAGTCACACTAGCTAATGAAGACCTCAGTGTGGTAGTGAAATAGTATAATGGCATATTCTCTGATAGTTATAAATACCAGTATCGTGTAATGTCACTCTGCATCAACCAAGGAGATTACCCAGGGTAGCTGAAAGCTATGTCAGATAAATATTTGGGTAACTCTTGTTTAAAAATTACATCAGTTTTCATCCAACTGTTTGATGAGACAACAATGCTTCTCTAACAGAAATGAGAAGTTTCTATCCCTTCAGGCTATAATGCTGATGTTAGGAGAGCTACAAGTAAAACAGAAGCAGTAAATTCTGCAAAGGATTTCCAACTTATTTTTTTTCCACTGGAATATAAAATATACTTTCTCAGCAGATTTAACTGCTACAGTTGCCTTCCTGAAGTGTAAACCGCATGGTGTGCATCGAAGTTGTAAAGAAGCATTTGAAAAGCTACCTCCTCCCAGAAACAGAGACAAAGCTGTGTCATTCATTTTCCCCAGGCTCAATTAAATGAATATCACAGTATGTTCAGAAATGCAGTTTCAGTATTCAGCCAGAGGAGTCTGCATCTCTAGTGATGAAGAATTCCAACTTCTCAACAAGAAGTGATGCAAAATGCTGTCTGGAACTTGCCACAGTTTCTTTTATGAGAAATATAGTTTTAGCGAACTTTGTATTTTGCAGATTAGAAGTGTATTTAAAAGTGAGGGTGAACATAAAAGTAGTTTTTATTTTCTGCATAATGCAATTGCTTATGTCACAAATCATTACAGTTGGGTTCATATGGCACCACTGGTTGCTTGACCATATTTGTTCACAGTTCAGGATTTATGTTGTTTTTCAGGATCTGGATAATTTTTTTACTTTGTGTTCAGTGTATTCATATGTTAAGAAAAAAAAAAAAACAACACAACCTTTGCAGAATATTGCATAAGAGTCCAATAAAATTCTTTTGACCAGAAGAGCACCCCAAACTTCTTCAAAACAGTAATTCATTTACAGTGTAGTTTTCCTCAACATGTATATAATATACTTAGATAAGTTCTGTGAACATGTAAAAGCTTGGACTGTTTAATACTGTGCCACAAAGTGCTCTGTTCAGATGACTCCAATCAAAGTTAATTCATGCAACAAGGATAGCAATGTTTTTCTAGTGAAGTAAATGTGTATCTTTATAGAGGAAGATAAAGGCCTGCTTATCCTCTGCATTATTGTCATCTCTTTCCCTTTGTCAGGCAAAACATTCAAAAGTGTTCCTCCCTTCTTGCCCTCTCCTTGCCCTGTGTTCACATTTTTCATTTCTCTTGAAGCTTGAGTTGACAGCTTTAAGAACGGAGAGGAAAATAGCAGTTATTTGATCTCATTGAATCTGCCCCTTATACCAAGATACGAAGCATCCAGCATTCAGCTGGTTGGTAGTATTATTTAAAGTTATGCATGTGTAGTTCTAGAAAGAAGTGTCTTTCTCCCTCATCAGGAATACTTATTCATTTAAAACACATTTGGTTTCCATTTTTCTTCTATGATTAAATAACTTTTCTGGCGAAGCTCAAAACTGTGCTTGAAATACAGAGTAAAGGTCATTCTGAAATATTTCTTAGATTTTGAATCTTCCTCCTTTGAAGACATTCGGGAAACTTCATTTGTGTTTGCACTGTTGAAGTTTAAACCCCAATTTTGTTTTCTTCACAGATGTTTTTTTTTAAAGTTAATTCTAGGACCACATCAAAATTTTGTCATTTACATCTATGTGTCAGCTACTTAACTTACATGTGGGATAGTTCCTAGAAAAGTTGTCATTCTTCTAGCATTGCAATATAAATGGCAAACAGCTAGGTAGCATAACACTGCAAAGGTCCAAGTGTTTTAGAGCTTCTGAGACATTTGGGAAGATCCATTTTTTTTCTATGCTATTTGATGATTTACTGATGTTAATATATCAATATATTTATAACCATCAATGCTCCAATAATGTCTTAAGCAATATGTGTTACCTTTTCAGGATTTTCTTTGGAGATTTCCAGATTTTTTTAAAATCTGATAGTTGTGTTTATTTAATGTTGGTTGGTTTGTTTAAACAACTAGGCTGAGAGAATATTGTGTGCATAACTGAATACCAAATGCTCACCTATCTGTAGTCAATAATCCTTAATGCAGAATATCAACTAATATTCACCTCTGAGCAAATCTGTGAATACAAGTTCAGTTATGTATAAAAGTGCTGTTGGCAATCTCAGTAAAGGAAGCACTGTCTGTAGATTTGTTAGCCTAATTCGGCTATATGTAAAGCAACAGATTGAGTAGTAGGAAGTCAAGGCAGAAATTTATCCTAGCATCTCACCTTAAAGCAGTGATGTGTCTGTGCCAGTAAGTATACAGCAGTGCATACATAGATAAGTGAGATGAAAATTTTTCCCATGAGCATAAGGGAGACAGGCAAAACAACTTTCCCCTACCAATTCCCTAACTGCTTTCCTATTTAATACATTTTTATTTAGACATACACGTCCTGTTATATCACAGTGTTTGTTAGTAGGTATTAGATTTGAGTTTATGTTCCAGTAATTTCTAATTTGGTTTTATTCTCCCAAGCACCAAACTATATTCTTTAAGCACAGAATTGCATATTGATGGATTAATTATGATTGTAATAATTACTTCATGTGTAGCAACTCTAAAAAAAAAAAAAAGTCTAAATAAAATAGTTTATCAAATGAGTACATTTATCCCCTGAAGGTTCAAAGATGTATTCAAAGATGTATAAGCATGATTATGTTTTGAAGTACCTATTTGTGATGGTAATGATGCATTCATTTTTTGCAATTTTGGACCGTTTGCAATTGGAGGACAGTATTACACATTTTCATCTTTGTTTTTATGCTAAATTTTAATTTAATTTAAATTTTAATAGGTAATTTCTGTAACATTTCAG
Seq C2 exon
GTATTTATTTTGGACAGAGTGGGGACAGATTCCTTGCATAGGAAAGGCATATTTAGATGGATCTGAGAAGGTTGTTCTTGTGAGCCTGGGGATTGTGTGGCCTAATGGGATTTCCATTGACTATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012407:ENSGALT00000020272:36
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:
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]