GgaINT0126114 @ galGal3
Intron Retention
Gene
ENSGALG00000003928 | LHX3_CHICK
Description
NA
Coordinates
chr17:8737928-8738479:+
Coord C1 exon
chr17:8737928-8738099
Coord A exon
chr17:8738100-8738276
Coord C2 exon
chr17:8738277-8738479
Length
177 bp
Sequences
Splice sites
5' ss Seq
CAAGTGCGT
5' ss Score
6.68
3' ss Seq
CCGTCTGTCGCCCCACTCAGACG
3' ss Score
6.46
Exon sequences
Seq C1 exon
AGATCCCGCTGTGCGCCGGCTGCAATCAGCACATCGTGGACAGGTTCATCCTCAAGGTCCTGGACCGGCATTGGCACAGCAAGTGCTTGAAATGTTCCGACTGCCAGACGCAGCTGGCCGAGAAGTGCTTCAGCCGAGGGGACGGCGTGTACTGCAAGGAGGATTTCTTCAA
Seq A exon
GTGCGTGGGCCGGGGGGCGGCGGAGGGGAACCGGGGGGGCGGAGGGGAACCGGGGGGCGCTCAGCCCCGTGGACGGTGGCTCCGTCCCGGGGTTCAGCACCGCGGACAGCGGCCGCTCTCGGGCTCAGCCCGCGCGGCTCTCCGCGCTCAGCGGCCGCCGTCTGTCGCCCCACTCAG
Seq C2 exon
ACGCTTCGGGACGAAGTGCGCCGCCTGCCAGCAGGGCATCCCCCCGACCCAGGTGGTGCGCCGGGCCCAGGACTTCGTGTACCACCTGCACTGCTTCGCCTGCATCGTCTGCAAGCGGCAGCTGGCCACCGGAGATGAGTTCTACCTGATGGAGGACAGCAGGCTGGTGTGCAAGGCTGACTACGAGACGGCCAAGCAGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003928:ENSGALT00000002663:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.014
Domain overlap (PFAM):
C1:
PF0041217=LIM=PU(94.6=91.4),PF036609=PHF5=PU(12.7=15.5)
A:
NA
C2:
PF0041217=LIM=PD(3.6=2.9),PF036609=PHF5=PD(85.9=88.4),PF0041217=LIM=WD(100=87.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGGCCGAGAAGTGCTTCAG
R:
GTCTCGTAGTCAGCCTTGCAC
Band lengths:
248-425
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]