GgaINT0059804 @ galGal3
Intron Retention
Gene
ENSGALG00000006998 | Q5ZKF9_CHICK
Description
NA
Coordinates
chr5:17639682-17640916:+
Coord C1 exon
chr5:17639682-17640078
Coord A exon
chr5:17640079-17640744
Coord C2 exon
chr5:17640745-17640916
Length
666 bp
Sequences
Splice sites
5' ss Seq
GGGGTAAGT
5' ss Score
9.65
3' ss Seq
TTCTGCTGTTTTCTTTACAGCTA
3' ss Score
11.62
Exon sequences
Seq C1 exon
GTGCTGAAGAAGTGTTGCTGCTTGCTAGGAGGACTGACTTGAGAAGGATTTCCTTGGACATGCCAGATTTCACTGACATTATTCTGCAGATAGACAATATCAGGCATGCAATTGCCATAGACTATGATCCTGTGGAAGGCTACATCTACTGGACTGATGATGATGTTCGGGCAATTCGTCGGGCGTACCTTGATGGCTCTGGAGCACAGACTCTGGTAACCACAGAAATCAACCATCCAGATGGTATTGCTGTGGACTGGGTGGCAAGGAACCTGTACTGGACTGATACTGGAACAGACCGCATTGAAGTGACCCGTTTGAATGGAACATCAAGAAAGATCCTTATATCAGAAAATCTGGATGAACCTCGTGCAATTGTGCTCAATCCTGTGATGGG
Seq A exon
GTAAGTTTTATTTTCATTGGTGGCCCTGCAGTAGTAGGCTTTGGGGTCCAGTTTTGCCCTCTTCAAACTGAAAATCTGCAAATTACAAATGATGTGTATATTATTTGTCAAATATTCATTTTGTTCTAGACATGACAAGCTCTCCCTTGCTTCATCCAACACGTACATAGGCATGTAGAAGGTGACTGTTAAATAGTATTCTTAAATGAAAATGTGTTGTATGTTTGGTTGAATTTTATTTTCTCTGTATCTTCAACATAATAGCTATTAAGGAATCAGGCCACTGCACACTTTCAGTACTTTGATTTAGTTAACAGTTAAACTGTAGATTATCATTACTGGTTGCAGAATTTACAGGATGGCTGAGGTGGGTAGGGGTTAGAACTGGATGACCCATCATGTTCCTTTCAATCCAAGCTATATTCTATAATCTAGTCCAACTCCACCCAAGCAGGGACATCCGGAGCAGGGTGCCCAGGGCTGTGTCCAGGCAGAGGAGGCTCCACAGCCTCCCTGTGCAGAAAGGTTACAGTTAAAGTTGGTTGGTTTATTTGCTACAGTTTGGAAAGCAGGAAGTTAGCAAGTTCTTTCCAAAACAGAACAGATCTTAATACTTTCTGTATTGCAGGTTATGTGCATTGATTGTTTCTGCTGTTTTCTTTACAG
Seq C2 exon
CTACATGTATTGGACAGACTGGGGTGAAAGTCCAAAGATAGAATGTGCTTATTTGGATGGATCAGAGAGGAGAGTTCTGGTGAATACGTCCTTGGGTTGGCCTAACGGCTTGGCACTGGATCTTGAAGAGGACAAACTTTACTGGGGAGATGCCAAAACAGATAAAATTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006998:ENSGALT00000011330:5
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=30.8),PF0005812=Ldl_recept_b=WD(100=30.8),PF0005812=Ldl_recept_b=PU(0.1=0.0)
A:
NA
C2:
PF0005812=Ldl_recept_b=WD(100=72.4),PF0005812=Ldl_recept_b=PU(33.3=22.4)
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:
TGATGTTCGGGCAATTCGTCG
R:
TTAGGCCAACCCAAGGACGTA
Band lengths:
342-1008
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]