GgaINT0097591 @ galGal3
Intron Retention
Gene
ENSGALG00000011061 | HOXA7
Description
NA
Coordinates
chr2:32570286-32571988:-
Coord C1 exon
chr2:32571709-32571988
Coord A exon
chr2:32570607-32571708
Coord C2 exon
chr2:32570286-32570606
Length
1102 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGG
5' ss Score
9.46
3' ss Seq
GTGTGCCTGCCTGCCTTCAGGTC
3' ss Score
11.53
Exon sequences
Seq C1 exon
NGCAACTCCCAGAGAAGCGGCTATGGACCAGGCGCGGGTGCCTTCGCCTCCTCCATGCCCGGCTTGTACAATGTGAACAGTACCATATATCAAAGCCCGTTCTCTTCCGGATACAGCCTGGGCTCTGATGCCTACAACCTGCATTGTTCCTCTTTTGATCAGAACATTCCCGTCCTCTGCAATGACCTAACCAAACCCAGCTGTGAGAAAGCGGAGGAAAGCAACCTGCACAACCAGGCTGAGGCTAATTTCCGGATATACCCCTGGATGAGGTCTTCAG
Seq A exon
GTAGGGGCGAGCGGGGCTGGAGCTGTGGCAGCCAGGCAAAGCGTGTCGCCAAAATTACTGTCAGCACAGCCTCGATGGTTTTAATTATAGCCGAGGCGCCATTGCGTAGAAAGCCCGTGGCATTGTATGTAAATGAGTATCATAAAACTTTTTATTGCCCAATTAATGGGTTCTAGCCTCGTAAATTTATTTAACTCCATTTGCTATGGAATTTTAGCGTCGAGTTTATTTGCGCTTTTTGCTGCAGAAACGCGGAGAGTTGGCTGCGTGCTCGCAGAGCCCCCTCGGGTGAGGGTCCCCACTGCCCTCCGCCGAAGTCGGGCAGAAAAGCTCCGCCCGGGGGGGGAAGGGGAGCCCGGGAGCGGGGACGGCTGTGCCGGGGCTCCGCCGGGCCGCGCTGAGCCGCGTTCGCCCCCTGCCCCCTCCGCGGAGATAAGAATCTATAGAAACGGACTGAACAGGAAAGCGGAGGGAGGGGGGGAGCCGGGGGGGGCCGGGGGCGAGAGTGTGTGAAAAGCGAGAGCTCGCTTCTGGGGCTGAACGCGGGGTATTGTTTACGATCCGGGCGGGGTAGGGGAGCGGTGTGTGTGCGTGTGTGTGCGTGCCTGTGTGTGTGTGTGTGTGTGTGTGCGGAGGGAGCCCCCGACACCAAAATAAAATAAATACGGCCCGGCCTTCTAGATTTTTATTTCCCCTTACGAACCGTAAAAGCCTGGAAGGTTTTAGGGAAATATATCGCCCCGGGGAAAGTTCCTCCTCCCAAAAGCAATTTCCTCCCCCACCTCCTCTCCTGAATGCTTTCTCTCCACCTTTTCTATGTCTCGAGGAACTTAATTTTTGCTTTGCCCGAGCAGGACAGGTCGTGTCGCTGAAATGTCTTTGTTAGGACAAAGTGTGTGTGTAGGGGGGGGGGGGGGAGGAGGCCGTGTTGGGNNNNNNNNNNGGGGAGAAGGGGATTATTCACTCTCGCTTGGGCCGGTTTTGTTAAGGTGTTTGTTTCTTCGCGTTGGAAAAAAAAAAAATGGTGAAAAAATAGAACAGATAAAACTTTCCTCTTCTCTTCCTGCCTAATCGCTGGGCGTGTGTGCCTGCCTGCCTTCAG
Seq C2 exon
GTCCCGATAGGAAGCGAGGGCGCCAGACCTACACCCGCTACCAGACCCTGGAGCTGGAGAAGGAATTCCACTTCAATCGCTATCTGACTCGGCGGCGGCGGATAGAGATCGCCCATGCCCTCTGCCTGACGGAGCGGCAGATCAAGATCTGGTTCCAGAACCGGCGGATGAAGTGGAAGAAGGAGCACAAGGAGGAGAGTTCCAGCACTCCGGCTCCCAACGAGCCCACGTCAGCAGCAGCGTCTGTGGAGAAAGTGGAAGAAGATGAGGAAGAGGAGGACTAGGGAGTCCCAGTCGAGGAAGCAATCTCTTAGAATAACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011061:ENSGALT00000018013:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.170 A=NA C2=0.468
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=60.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGGCTGAGGCTAATTTCCGG
R:
AGATTGCTTCCTCGACTGGGA
Band lengths:
355-1457
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]