GgaINT0121421 @ galGal3
Intron Retention
Gene
ENSGALG00000011558 | LRP6
Description
NA
Coordinates
chr1:74002885-74004690:-
Coord C1 exon
chr1:74004474-74004690
Coord A exon
chr1:74003181-74004473
Coord C2 exon
chr1:74002885-74003180
Length
1293 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGT
5' ss Score
9.27
3' ss Seq
TGTTTTTCCTTGTGTTGCATGCT
3' ss Score
1.89
Exon sequences
Seq C1 exon
GTCATGAATGCTGATGGAACTGGAAGAAGAGTTCTTGTAGAGGACAAACTTCCTCACATCTTTGGATTCACATTATTGGGAGACTATGTTTATTGGACAGATTGGCAAAGACGCAGTATTGAACGTGTGCATAAGCGGACAGCAGAAAGAGAAATCATCATAGATCAACTGCCTGATCTAATGGGCCTCAAAGCTACAAATGTACACCAGATAATTG
Seq A exon
GTGAGTGACACTACAAATCATGCTAGTAAAATAAAATTGAAAATTTCACCAGTATTCTTTTGAAGGGATCGCTTTATACTAGGTCAGATTTTTAGAATGGGGCAGAATACAGTTTCTTGCCTGACAGCTGCAGGCTGCAATTTGAAAGAGTGTGGTAGGCCTTTTGTGTGGTGCTTCAGTTCTCTAACCTGGCCGAATAGTAAGACAAAAAATCAGACATTCCCAGCTTCCATGACACTCCCATCTATTCTCCTGCTCAGGTAATTGAAGCGCCTCATAGGCCTGAACAACCCTGGATCCAGTAAGGAGAGAAGGATCAGGGAAAATGAGAACAGCCGGCTGTTAGGTTAGCCCAGCTGTTTTTGGAGTTATAGCTGTAGCAGGTATTCATCCTGCAGTCTGAACATGTGTTCTTGGTGAGCAAGAGCTAAGAATGAGCCAGTTTTAGTCTGTTCAGTGTTTTTCAAATGAATACTGCAAAATCATGTTTAAAAACAACCAGAAGTATGTTACGCTCTGTGGTATTTATGGAATGAAAACACAGGATCTAGTTCCAAATTGGTTTTCAAAACACTGGTACACAGTTGAGCTGTGGCATCACAGAACTTGTCACGTTCCCTGAATATGTGGGCAGGGCTTTCAGTTTCTTGGTGCCAGGTCTAGATTGTACACCAGGGAATTAGTTAAATGTAGTTGAGGTGTATCTTTGCATCACTGCTACGTGAAGAGGCTTGACAGTACATGTGTTTGAAATACAGCCCTCTTTCCAGCTGCTTGGCTAATTGATCTTGGTAACGGTGGGTGAATTTCTAGCGTATGCAGGTACATGTGCTATTATTGCAAAGAGCTGCTTTACTAGCATACTGGAGAGAAGTGCCCATTAAGTGGATGTGAAAAGAATCTCAAAATTTTCCATCCCGAGGAATGCAAACAGGGTACATAATTGGACCAGTCCTATGAAAAGTGACAGGACTTGCACTTGCTTTCTTATGTATTTTCCTTCCCTTCCCTGCTTATGCTATGAATCAGTATCGTCGATGCTTGAGTCCTGATCTCATCCCCTATTGCTAGGTTTTTTTCACAGTGTCAGGAAAAGAAGTGCTGGCTTTCCAGCCATGTAGATTAATATCCCTCTAAAAGACTAGAAGAGACAAAAGCAAATTGATTCAGGACAAAAGGTGGAAAACTACTTATATTTCTTAAAGGGCTCATACTGTTGTTGATACATGTGAGGTCTGGCTTTGTCTTCCAAATGAAGACAATTTGTAATGATTGTTTTTCCTTGTGTTGCAT
Seq C2 exon
GCTTAGGTACAAACCCTTGTGCAGAGGATAATGGTGGTTGCAGCCATCTGTGTCTGTACAGACCGCAAGGCCTTCGCTGTGCTTGTCCCATAGGCTTGGAGCTCATCAATGACATGAAGACCTGCATTGTCCCAGAAGCTTTCCTTCTGTTTTCTCGGAGAGCAGATATTAGACGAATCTCTTTAGAAACAAACAACAACAACGTTGCTATTCCACTTACTGGAGTTAAGGAAGCTTCCGCTCTGGATTTTGATGTGACAGACAATCGAATTTACTGGACTGATATTTCATTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011558:ENSGALT00000018841:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0005812=Ldl_recept_b=PD(61.5=32.9)
A:
NA
C2:
PF146701=FXa_inhibition=WD(100=36.4),PF0005812=Ldl_recept_b=PU(24.4=10.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACGCAGTATTGAACGTGTGCA
R:
CGGAAGCTTCCTTAACTCCAGT
Band lengths:
347-1640
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]