GgaINT0126113 @ galGal3
Intron Retention
Gene
ENSGALG00000003928 | LHX3_CHICK
Description
NA
Coordinates
chr17:8735542-8738099:+
Coord C1 exon
chr17:8735542-8735611
Coord A exon
chr17:8735612-8737927
Coord C2 exon
chr17:8737928-8738099
Length
2316 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
TGGGGGGCTGCTTCCCGCAGAGA
3' ss Score
6.7
Exon sequences
Seq C1 exon
ATGCTGCTGGAGAGGGTCCGCGCCGGCTCGGAGAAGGCAGCGGAGCTCTGCCCCTTCCCTCGGAGCCCAG
Seq A exon
GTGAGAGGGCGCAGAGCTCCGCGTCCCCCAGCGGAGGCACCGCCGACGGCTCCGGGCGCCCCGCGGCACCGCGCTCGGGGTCGGCCGAGGGAAAGGCGGGCGGCCCGACGGCCTCTGCCTCCGTTCTCCGCCGTCCGACGTGTCCCGATCCCGGCGGCGCCCCGTGCCCGCTCCCGGTGCCCGTTTCGGTCCGTCCGTGCCGTCGGTGTAGCCGGGAGCCCTCCGCCCGCTGCCGAGGGAGAAACGCCGCGGCTGTGCCGGGCTGAGTGCGCGGCCCGGACCCGGGGGGCTCTGCTCGGCCCCGCGGAGCGGCGGATTCTGTCCCGTGGCGGCCGCCGCTCCGCGCGCAACGACGGCGGAGTGAGATGGGGAGCTGCTGCCCGGCGGCGGGCACCCCCTGTGCGACCCCCGTTGGCTCCGACGCTTTCCGTTCCCCCTCTGGAAAATTTCCGCGCAATTCCTCTTTTTTGTTGTTGTTTTTTCTTCCCAATTTAAAGAACGGCGAAAACGTCGGCGTTGTCGGTGCGGGCGAGAACCGTCGGTGCGGGGGTTTTAAACGAAAGCGAGGAGGGGACGAGACGGAGGGGGACGGCGTCGCGGTGCAGGCGCTGCCGGAGCTCCCCGCCGTCGGTTCGCTGCCCCTCGTCCCGCTCCGCTCCCCGCGTGTCTCTGCACCTCTCCCCGGCGGCTCTCCGCGCTGCGCTCACCGCGGGAGTTGCGCGGTTGGCCCCCAACATCGGGAGGCGGTTCCTCTTAGCGGCGGGGAAGGGACCGAAACAGCCCGGAGCGAATTCCTGGTGGGAGGAACGGGACCAAAACGCCGATTCCCCGCAGGACGCGACGCCCGCAAATAGCCCCGCGGCCCGGGGGAGAGAGGGGGACAGGGAGGCGGTGCGGGGCGCTGCGGGGCTGAGTTCGTCTTGCTTTTATTATTGAATAATTGTTTTCGTTTTCGTTGTCTTTCATTTTTTTATCCTGTGGTCATTCCCTTTTCTCAGCAGCTCGCGGCCGTTTGCAGCGCACAACGAATTCCGGGCACCGACCGCCGCTTTCCCCCCCGCTCCGTTCCTCCCCCGGCGCGGCCCCCGGGCCCAGCGCGGTCTCTGCCATCCCTCAGCCCCGTCGGGGCGGCTCCGCCCGGATTTCGTTTCCGGGCACCGCGGAGCCGTCTCCCTCCCGCAGAGCGCAGCCGAGAAGGGGATTAAATACAGCGCCCCGCGAAGCGCTGCACGGGAACGGCCGAGGGCTGCAAATAACCATCCCGGGGGGGTTCAATCGGATAACGGAGGGCTGAGGGAGCGGGGAGGGACGGCGGAGGGACGCCCCGATTGAGCCCCGGAGTGCTGTCCCGCCTGAGCGAGCGGAGCGCGATGCAGCGTAAGAGCCGCCGGGCTCAGACAGCCCCGTGTGCGCCTCCGCAGTGCCGCTGCCGCTGCTCGGCTCTCCGGGCAGTTCGGGGTCGGCTGTCGCCGTTGCCGTTATCGCTACCGCCGCGGGTGTCGTTTGTTCGGACGCGGATAAGTGTAGAGACGATTATAGCGATAACGATATCACCTGAACCTCTGCTCCTACCCGCAGCCGTACATCTCTGTATGTCTCCACACGGTTACCTTTGCATACAGATACCCGTACGTCTGTGTTTATCTGCATCCACGCAGCTGCGTCTGTATATCTGATAAACCCGTATTTCTGTGTCTGTGCAGCTACATTTCTCTCTCTCTCTCCATACTTGCTGATATCTGTATATTTATGTCCATATATCTGTAGGTTTTCACTTTCTAACCTACTTGCCTGTTCATTTTTTGTTCCTCTGTTTCCATATCTCTGTATCATCTCATTCCAGAGATCACCTCTTCTGATACCTGCAAGGTGACTGAGCACTCCTGCTATGTTTTGTTTTCAGTAGAATTTTCACTATTTGGGGCAGTTTGTTCCCCCCCGTCCCCAAGCCGTTATTTGCTGATGAATATTTGAAATGTCGGAAAAGCAAAGAGATGGAATAACTGTGAGGCAGTGTGGGCAGCTCAGCTGGGGCTGAAGTCCCTTCCCATCGCTTCCCTTCGTGTTTTCCCATGCTGTGCGCGGCTCGGGGTGGGGGGGGTGGGGTCTTTGCGCTCCGTGCCGCGGGGAGAGGCTCTCACAACGCCGCACCAACGAATCTGAATGAAAAAGAATGTTTTTCACGCCGTTCCCGGGGCCAATCCCGGGATTTCAGACGGGGGCAGCTCCGGGAATGCCGGGCCGGGGGGGATCGGGCGGAGATGGGAGGCAGTTGGGCGGTCGGAGCGGCAGCTGATGGGGGGCTGCTTCCCGCAG
Seq C2 exon
AGATCCCGCTGTGCGCCGGCTGCAATCAGCACATCGTGGACAGGTTCATCCTCAAGGTCCTGGACCGGCATTGGCACAGCAAGTGCTTGAAATGTTCCGACTGCCAGACGCAGCTGGCCGAGAAGTGCTTCAGCCGAGGGGACGGCGTGTACTGCAAGGAGGATTTCTTCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003928:ENSGALT00000002663:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0041217=LIM=PU(94.6=91.4),PF036609=PHF5=PU(12.7=15.5)
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:
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]