GgaINT0126117 @ galGal3
Intron Retention
Gene
ENSGALG00000003928 | LHX3_CHICK
Description
NA
Coordinates
chr17:8738872-8741059:+
Coord C1 exon
chr17:8738872-8739043
Coord A exon
chr17:8739044-8740634
Coord C2 exon
chr17:8740635-8741059
Length
1591 bp
Sequences
Splice sites
5' ss Seq
CAGGTCGGT
5' ss Score
7.53
3' ss Seq
CCAGTCCGTTTCCATTTCAGACG
3' ss Score
8.85
Exon sequences
Seq C1 exon
GTCTGGTTCCAGAACCGCCGGGCCAAGGAGAAGCGGCTGAAGAAGGACGCGGGGAGGCAGCGCTGGGGGCAGTACTTCAGGAACATGAAGAGGTCCCGGGGGACCTCCAAGTCCGACAAGGACAGCATCCAGGAGGAGGGGCCCGACAGCGACGCCGAGGTCTCCTTCACAG
Seq A exon
GTCGGTGCGCGGAGCTCTGCTCCCGGCGGGGCTGTGCCGAACGCTGCCGGCTGAGCAGCGGCCCGGGCTGGGCTCGCTTCACCCCACATTAATAATTTTTAGCTGTAATATAATGAGGGAAAACAAATGCGGAAGGAGGAAGGCGGAGTGCGGGGACCGCCCTGGCACAGCCAGAGCCGCTGCGGCCGGAGACAGCCGTGAGCTGAGAAATGGCACGGGAAAACCCTGTGCCAGATCCCAGACGGAGCAGGGAGAGCTCCCCGGGCAGCGCTGGGCTGTTGGAGCAGTCCCTGCATGCAGACTTCTGAAGGGACTGTGAGAAATACAAAACTCAGAGTTCAGAATTACTGAACTAAGCTATGAGGAGAAGCGCGTAGGTTCCTCTTAGTTTGGCTGCTGTTGTATTATCCTATTTAGAATCGTTTTATTCGTGTGTTTCCTACTTAATTACTTCCCAGTCGTGTGGGAGCTGTTACCTCCGTGCTGTAAAAAAAAAACTGCTCCGTGTTGGGATATTTCTGCACTACATTGTCCCGTTTTTGGGGCGGCCGTCTCTGCAGATAAACCCCGGAGCTCACAGCTCTGTGCTCCTCACGCAGCCCTGCGCTGGGGTGGGTGCACGGCGACGGCAGTGCCAAACCACCCCCGCTGACAGCGCCTGCAATGCATCCCCGCGGGGCTCAGCTGTGTGCATGGACGCCGTTTGTAGGGGTACGGGAGAGAAGCTGAAATGCAAAGCTGTGCAGGAGCTGAAATACAGAACTGTGCTGACAACGACATACGCCCGCAGTGCACGGATGTTTATACGCACACAGCTTTGTGGTTCTGCTCTCTCCCGCGTTCCTAAAAGCTGTTTGACTTTCCAGTCTGTGTATACACGCTGTGCCTCAGCGTCATTAAATATGAATGTACTATAAATAATAACTAAAAATTGTTGAACAATTACTGATAGCTCCGTGCCAAAGCAGATTTGTATCCAAGGCAACAGAATAGCTCTCACTGTCCATAAAGCCCCAAATGAAAGCAAACAATTTTTGCTGGTAATTTACAAAATATTTTCATTTTTCAGAAGTGTTTTTAAGCCTTCCGTCTCCTTATCCCAATCCCGAGAAAACAAACACTGCTGAGATTTAATACATCTTCTCTGAGCAAGGCAGTTTTTCTTGGGCTGAATGCTCAGGTAGCTCCTAAAGAGGAGTCCGAAATTCAAAATAAACCTCAAAGCCAAATAGAAATGAGAGACTAAAAAAACAAAAAAGGATGGAAAGATCTTGAACTCACGTTCCTCTTTAAAGGATTACTTTAAAACCACGGTCCTATATTTTAAGGTGTGCTTTTCATGCCTGTTTTTTTAGATCCAAAATGTGTTAGACGTTTGTACTCGGAAAAAATAATCCCGTGGCTTTCTTTGGAGACTCATCAACGAGGGCAGGAATAATAAGGAATAATAAGGAATTACAAGTAGGAAGTGCACGACTGCTCAATTCCCACCCATCTCATCTGTTCGTACCCAGGGCTCAGGGGAGCTCCTGTGTGTGCTGCCGGCCGTGGCCATCGCTCTCCCAGTAAAACCAGTCCGTTTCCATTTCAG
Seq C2 exon
ACGAGCCCTCCATGTCCGAGATGAGCCACTCCAATGGCATTTACAGCAATCTCAGCGAGGCGTCCCCGGCCCTGGGGAGGCAGGCTGGGACCAACGGGGGCTTCTCTCTGGATCACAGTGGCATCCCAGCTCAGGACCAGTACCACGACCTGCGATCCAACAGCCCCTATGGGATTCCCCAGTCACCGGCTTCATTGCAAGCGCTGCCGGGCCACCAGCCTTTAATCTCCAGCTTGGTTTACCCTGACAGCGGTTTGGGCATCATGGGACAAGGTGGACAGGGGGTGCCCCAGTCCATGCGGGTCCTGGCCGGGAATGGGCCCAGCTCCGACCTCTCCACCGGCAGCAGTGGGGGATACCCGGATTTCCCTGCCAGCCCGGCCTCCTGGCTGGATGAAGTCGATCACGCTCAGTTTTGATAGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003928:ENSGALT00000002663:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.746 A=NA C2=0.871
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PD(19.3=19.0)
A:
NA
C2:
NO
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:
GAGAAGCGGCTGAAGAAGGAC
R:
CTTGCAATGAAGCCGGTGACT
Band lengths:
346-1937
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]