GgaINT0143070 @ galGal4
Intron Retention
Gene
ENSGALG00000001276 | HOXB9
Description
homeobox B9 [Source:HGNC Symbol;Acc:HGNC:5120]
Coordinates
chr27:3568746-3572701:+
Coord C1 exon
chr27:3568746-3569253
Coord A exon
chr27:3569254-3572504
Coord C2 exon
chr27:3572505-3572701
Length
3251 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
TCTTGGTGCTTTTCTTTCAGCCA
3' ss Score
7.89
Exon sequences
Seq C1 exon
ATGTCCATTTCTGGGACTCTTAGCAATTACTATGTCGACTCTATTATAAGTCATGAAAGTGAAGACTCGCCTTCAGCTAAATTTTCATCTGGGCAATATACAAGTTCCAGGCAAGCTGGGCACAATGAACATCTAGAATTCCCCTCTTGTAGTTTTCAGCCAAAACCTCCAGTTTTCAGCGCCTCCTGGACTCCTTTGAATCCACATTCTTCTGGTACCCTTCCTGCCGTCTACCATCCATATATTCAACATCAAAGCGTCCCATCTGATAGCAGGTATCTACGGAGCTGGCTGGATCCAGTGCCCAGAGCAGAGACCCTCCCCGGGCAGGGATCTGTTAAGGCAGAGCCGCTGCTGGGCCGTCCCGGGGATGTCCATAAACAGGGAACACAGGAGTACAATTTAGAAACTTCTGCTGCAAGGGAAGGGATCGTTTCCAATCAAAGGCCCAGCTTCGAGGACAATAAAGTTTGTGAAGGAAGCGAAGACAAAGACAGAACAGATCAAA
Seq A exon
GTAAGTTATAAAAGTGAGGAAGTAAACAGTATAAAAGCTGGAGGAGGTGCAATAAAAGGGGACAATGCTGCGTAAAGTTTAAAATCAGGGCTTAAAGAAAACTCTCAGATGGCTGATGCCAACCTAAGGGGAGAGGTGGGGAGGGGAGAGGGGTGGCATTGTTTCTGCGGGGAAATACAAATAAAAATTAAAACGAGCGTCGTCTCCGACCAAAACAGAGTCCAGAGCGGACAAAAGCTGGATCGAGCCGTCCTCTTTCCTACAGAGCGCTGACTCCGGCAGCGGAGATCATTGCTGTAAGCGGGAGTGAGAGCGTGAGGGGCTGCGGGCGGAGGGAACGGAGGGACGGGGCGGGGGGGGAGAGAACGGGGAAACGTCGGGAGAAGGGCCGGGAGAGGAGAGCGGAGGTCGGGGGAGAGAGGAGAAGGGGAAAATCGCGGAGGAAAAGTTCACGTGGGGGGGAAGTAAACAGCGGCAGGGGCTTTTCCGTGCCCGCTGAGCTGCGCTGCGCCGGCAGATTGCGGGCTCGGGGCTCCCCTTCACCTCGGGGTTGGTTTGTTTGTTTTTTTTTGCTGCCGAGTTTTGGTCGTGGGTGTATTTGTTGTGCGTAGTTTGCTTGGTTTCTTTTTTCCCCTTCCCTCCCTTTCTATTCCTTTTATTATTGTTGTTGTTATTGTTGTTGCTATTATTATTATTATTGCACGCGTTCGCTTATTTCTGTTTCGAATTGCTAGCATATTAATGCCTCAGTTCAGGGTCTGACTATTTCAAAGCCGAAATATCACTATTTCCAATTTCCCTCCGAGTTGAGTTGAAAAGAGAGAGAGGAGAGCGCTTCCAGCTTAATTAGCTCTTTATTTGTAATATAGCCAGATTGGAGAACAGCTAAACTTCAGCGTGTGCCTTTTTAGTGACCTGGTTTCTCTTTTATTCACCCTGAAACGCAGAAAGAAAAATCGTTTTGATGTATTTAATAAGGTTATAGTTCATTCTGCTTTGCAATATGCGTTGTTGTTATTACTAAAATGACGCAAGAGCGTTTGAGTGAGAAAGAATGGGTGCCTTCACCCCGTGCCGGTTCGGTTCGTACCCGGGGTCCATCTGGAAGGTGGAAGGGCTGTGCGGGAGGAGAGGGAGAAATTTGGCTCCGGCACAGCGGTGAACGTTTGCGCAGTGAAAGGCGAAGTTGTGCGGAGTGTTGGGTTGGGAAGGGCAGAGAAAGCCCCCGCCAAAGGCACAGCGTGCGGAGCGTGTGCAGGACACCCTGGCACAGTCACTCCGTGAATTAACTTCATTTTGGTTTTTCCACCCCCTCTCAATCCTCCCCCCTTAACCCCTCACCAAAGTGTAAGAGCAACAGTATTGAAAACGCGGTGCATTCCCCTCTCCGTGCGGTACGATGGTGCGGGGGCAGGTTTTTTTTCCCCTATCGTTTGGCTTGCACCGTGCACACGCACTCCACACACACACACACACACACACACACAAAAAGAAAGTCCTGTTCTATTGTGCTGGGCAGAGATCCAGAACAAACTGCAAGCGGGAGGTGAATGGTCGGAGAGAATGAAATATCCAGGTTCTGTGCTCAATGTCCCTGAAATTCAATATAGAAAAACCTCGTCCAAGAAAATGTTATTAAGTCCTAAGTAAGCGCGGGGACCCGCGCTAAGAGGATGCAGTGCGGTTTCTCTATGGCGTGTGGTTACGACGCATATTTTGTTTTAAATAATAGTTTAATTTGGGCTAATGTTGAGAGGCTGCCAGGGCTGGGAGACGGAGCTGTTTTGCAGAAAACGCTCCCACCCATTTCCCTGACTCTTTCAATTTTTGAAAGTATTTCACAATAATGAATCTCTGCGCCGGGTATGGCACCGGGATCTGTTAATTTATTTGCTAGGTTTGCAGGAAGCCATGTGCCAGAGCCTCCCCTCATTTGCTCGCCCGTTCAGGAGGGTGTATACAGCCAGTAAATAAAATATCCGCGTTTAAAATGCCTCAGATTTTAACGATCCGAGATACGACCAAAAAAATAAAATAAAATAAAACCCAACCAAATAAAAATCCGTTATGAAGCAGAGCCCTCCGTTGCCATTAAAGGATGGGTAGCAGGATTAACAGTATCAATTATTAACAGCTTTCTTCCTCTTTAATATTTAATTCTGCATATTAGATCGAGTCAATTACATTAAGGAAATAGCAGCGCAGATTTGGAGGAGGCAGGACTTACAGGGAAAGATTAGGTGGATTATTTGTAAATATATTCGATATATTTTCGTTTTACGTGGAGGGAACGTTGCGATGGGGCGCGTGTGCGTATGTATATATTTATAATGGTCCGTTTAATTGGTGTAAAGGTTTATGGCTTCGGCCATCATTTCAGAGGACGAAAGGGAAATAAAATAGAAATACGTGGTCTGTCCTTTTCCTTTTCCTTTCCCGCCTCTCCCCTACCCAACACTCCTCCGATATTTGCATGTGATTAACGAACGCTCTATTATTCGCCCCCGAAGCGCTTCACCTTTGGGTGCGACCTCAGCCAGCACTGCGTCTGCGGGGCTCATTTCTAAAATGGTGTTTTGATCCCTCATCCCCCCCCCCCCTTCCTCCCCCTCCCAAATCCCCATCCCAGCATTGGGTTTAAGCCCGAAATGTGCTTTTTGCAAAAGGTTCCCACGTAACTTCTCCCACACGAGAGTTATGGGGGGGAAAGGGGGGAGTTATATTGTTGGGGCCGCTGTTCTCCCTTCGCATCGGCCCTACAAACGTCCATGGTTCGGCATAACACTGTCCAGACCTCCTGCAGCAGAGTCCAGCCAGCCCTGAGGATGTTTATGACATCGAGTCCGTTTCTTGCCACGTAGCAAAAATAAGCAAGATTTATTCAACGGGCCTTTTTTTTTCGCCCCCCCCTCCCCTCTCTGTCCCCTTTACCCGCAACACTGTGCCTACGGGAGTGCACCCGCAGACACGTGGGGAAAAGCATCTGAAATAGATGCAGGATTTTGGCTTTGCTTTCTCCCAACGCAGGGAGAGAACATCAAGGCTGTACCTTGGGGATGGAGTGGGGGGGGGAGGATTCGGGCCCCCACGTGTGGGCAGGGCTCGCCTTGCCGAGGCCGGGCTGCTTTCAATCCGGCTCCCATCTCGGGTTCGCATATGCGTGTGTATAATCTTCATATTTGATGGCATGATGAAAACCTTCTGAGAAACACTCAGGCTGCATCGTATTGATCTTGGTGCTTTTCTTTCAG
Seq C2 exon
CCAACCCAGCTGCCAGCTGGCTGCACGCCCGCTCCTCCAGGAAAAAGCGATGCCCTTACACGAAATACCAGACCCTGGAACTAGAGAAGGAGTTTTTATTCAATATGTACCTGACGAGGGACCGTAGACACGAAGTGGCCAGACTCCTCAACCTGAGTGAGAGACAAGTCAAAATCTGGTTTCAGAACCGAAGGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001276:ENSGALT00000001947:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.688 A=NA C2=0.393
Domain overlap (PFAM):
C1:
PF046178=Hox9_act=WD(100=99.4)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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]