GgaINT1014991 @ galGal4
Intron Retention
Gene
ENSGALG00000028726 | HOXB6
Description
homeobox B6 [Source:HGNC Symbol;Acc:HGNC:5117]
Coordinates
chr27:3598947-3600970:+
Coord C1 exon
chr27:3598947-3599088
Coord A exon
chr27:3599089-3600710
Coord C2 exon
chr27:3600711-3600970
Length
1622 bp
Sequences
Splice sites
5' ss Seq
ATAGTGAGT
5' ss Score
6.97
3' ss Seq
TTATTTTGCGGGTGTCACAGGTT
3' ss Score
5.96
Exon sequences
Seq C1 exon
CCCAACCTGGACGAGGTCCCCTTCGCCCCCGAGCCGCGCAAGTCGGACTGCGCGCAGAGCAAAACTGTGTTCGGAGAGAGCGAGGAGCAAAAGTGTTCCGCCCCGGTTTACCCCTGGATGCAGCGGATGAACTCTTGCAATA
Seq A exon
GTGAGTTTACTCTTTTACAGAAATAAATACATCAATCTCCTCCCCCCCTTTCTTATTTGTTACCGCCAGAGTGAGAGAGCGAGAGAGAGCGAGGGAAGCAGGAATAAGGTTCACTTTAGAGCCCAAACTTCCAGCGGGGAACTTAGGCAACGTGAAAGGCTCCAAGTTCTCCTGACACGCACCAAAACTTCACGCCGTGAGGCTCTGCTCCTCTCGCCCAGCTCCCCAAATAGAACAGCAGCAAACAACTTTGCTCCGTATTTAATCCCCACTTACAGTATTTCTGCCCCCCTCCCTCCCCCCCCTCCTCCTATATTTTTTTTTATTTCACATTCCTGTTTGCGTGTCACGCAGTTCCAGCGATTTATCTCTGTCTTTCCCCGAACGGACGGGGAGATCTCCCCCAGTTCAGAGCTGGAGGACTCCGCACCCGCACGGACCCGCACCCCCACGCACCCCCCGTAGCCGAGCTGCAGTTAAATAATATAGAAGTGTTTAAATATTTGAAAGGAGGGAGAGCTTACATTTTTAATGAAACTCACACATAATGAAAAGTCTGCCCGGGGAGAATTTTTTTCCCCTTGGTGATATATGACTTCTTTAAGTGCTGTTTCCTCAATCAGGAGAAGGGAAAGAAAAAAAGGAAGGGGGGTGGGGTGGGAGGGGGATAAAAATAATAGAGGCTCACCACCCTCATCCCCGTGTTTAGATGCATTTGTTGCCTTTTAAAGTTCCGAATTGATGTCCATTAGCGCAGGGACATAAAGTGTTGTGTCCTCTTTAATGCAGAGTTTGGGCAGATCGATTCACTTCATTATTGCTTAAATGCTCAACTCCATTACAGCTGCCGGTAGGGTGGAAAACAGCGGCGGGGGGCGCGGGGAGGGGGGGTTCGGGGGTGGGGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAACAAGCGCGGGGCGGGGGGGCCGAGCTGTTCGGAACCTCCACCGCACCTCGGGGTTTTTCCCTTCATCTCCCCCCAACCTTTTTTCTTTTTCCTCTCTATTTAAAATATATATATATACATATCATCATCATCATCATTTATTTATTATTATTTTGCGGGTGTCACAG
Seq C2 exon
GTTCCTCCTTCGGGCCCAGCGGCCGCAGAGGCCGTCAGACGTACACCCGTTACCAAACCCTGGAGCTGGAGAAGGAATTCCACTTCAACCGCTACCTGACCCGGCGCCGGCGGATCGAGATCGCCCACTCGCTCTGTCTGACGGAACGGCAGATCAAGATCTGGTTCCAGAACCGTCGGATGAAGTGGAAAAAAGAGAACAAACTGCTCAGCTCCTCGCAGCTGAGCGCGGAGGAGGAGGAGGAGAAAACGGCGGAGTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000028726:ENSGALT00000043387:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.229 A=NA C2=0.267
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=65.5)
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:
CGCAGAGCAAAACTGTGTTCG
R:
CCGTTTTCTCCTCCTCCTCCT
Band lengths:
342-1964
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]