BtaINT0073170 @ bosTau6
Intron Retention
Gene
ENSBTAG00000014738 | HOXA11
Description
homeobox A11 [Source:HGNC Symbol;Acc:HGNC:5101]
Coordinates
chr4:69311987-69314613:+
Coord C1 exon
chr4:69311987-69312701
Coord A exon
chr4:69312702-69314117
Coord C2 exon
chr4:69314118-69314613
Length
1416 bp
Sequences
Splice sites
5' ss Seq
CCAGTACGT
5' ss Score
7.19
3' ss Seq
GCCTCTTTCGGCCTTCACAGGTG
3' ss Score
10.45
Exon sequences
Seq C1 exon
ATGGATTTTGATGAGCGTGGTCCCTGCTCCTCTAACATGTATTTGCCAAGTTGTACTTACTACGTCTCGGGTCCAGATTTCTCCAGCCTCCCTTCTTTTCTACCCCAGACCCCGTCTTCGCGCCCAATGACATACTCCTACTCTTCCAACCTGCCCCAGGTCCAACCCGTGCGCGAAGTGACCTTCAGAGAATACGCCATTGAGCCCGCCACTAAATGGCACCCCCGCGGCAATCTGGCCCACTGCTACTCCGCGGAGGAGCTCGTGCACAGAGACTGCCTGCAGGCGCCCAGCGCGGCCGGCGTGCCTGGCGACGTTCTGGCCAAGAGCTCGGCCAACGTCTACCACCACCCCACCCCCGCCGTCTCGTCCAATTTCTATAGCACCGTGGGCAGGAACGGCGTCCTGCCGCAGGCTTTCGACCAGTTTTTCGAGACGGCCTACGGCACCCCGGAAAACCTCGCCTCCTCCGACTACCCCGGGGACAAGAGCGCCGAGAAGGGGCCCCCGGCGGCCGCGGCGACCTCCGCGGCGGCGGCGGCGGCGGCGGCAGCGGCCACGGGCACGCCGGCAACTTCAAGTTCGGACAGCGGCGCCGGCGGCTGCCGGGAGGCGGCGGCGGCGGCGGAGGAAAAGGAGCGGCGGCGGCGCCCCGAGAGCAGCAGCAGCCCCGAGTCGTCTTCCGGCCACACTGAGGACAAGGCCGGCGGCTCCA
Seq A exon
GTACGTATAAAAGGCAGCGCGCCCTGCGCTTTATGAAAGGGGAGTTGGAAATCTAGCGCAGCACCGCTGTTAAATTTTTATATGCTGTTTTATAAGCATATAAGGTTTATGAAGGGCCTTTAGGTTTCCCCCCAACAAAACTTTGTTATAAAAGGCGGGATCACGTGGCGAGTGCTGAAATTGGCCGTGAAATACCCACCGGCCAAGGCATGCCTACAAAAAAAAACCCAAAAAAACAAAAAACCTCCCTTTTCCCCTTTTTTTCCCTTCTCGGCTCCCAAGCCCAGCAGCTCGACCCCGCTCGGGGCCAGCTTGGGGCTGGGGAGCCGGAGGTGGGCGCCTGTAAATTCTCCCTGCAAGGGTTCGGGAGCCTTTGATAGCGAGGTAATCCGGAGATTTTTATAAAAGCCATGTGTTGCGCCGGGACTCCAGTCCCGGCCGGGATTCAAAGGCATTGCTGTTTAACGATGGCTCTAGGAGCGTGTTTAACAGATAAAATAGCCCGCTTAGCTCGAGCAATATATTAAAAGAAACAAATTAACCCAAAGTTGGCCTTTTTGTCCAAAGGAAGCCATTTTCCTTGGGCGCAGTGGCAATTACGTGTGCTGCCTTCTGTCCGACTGCATGTTACAATTGTTATTCAATCTGTCAAAAGCGGGTTTTTTCTTTACTTCTGGTGGCGTTTTATTGAAAGGGGTGCAAATCGAGCCTGCCCGCAGCTCTGGGAAACCCCTCTGTCCTCCAGCCTATCGGGGACAGCACCCCAGCCCTGCCAGAGCACCAGGATGGCTGGGTGGCCTTGGTCCTTAGGGAAGGCCCGGGGTAGGGGGCTTCCGCCACCCGCTCCCCACCCCGCGGAAGCCAGGGGGCTGGCCGGGGAGGCAGGAGCTGATGACCAGGACTTAGGCTGACAAAGACCCGGCAGCTGCCCCCAGATGTTAACGAGGGCCGAGTCCCGCCGAAGCCGGTAAAGTCTGGGGCTGGGGCCGCCTTTACTGCCTCGGGACTCGGCCGCCCAGGTGCTGGAAGGTGAAATGGTCGCGGGCGGCTGTTTGTTTAGTCTGGCCGGGCTGGAGGCAGCCAGCAACCCCCACTCGCTGCTTTGAAAGCGGTTTCCGCGGCACTAACTCGCCTGTTGCAGTGAGGAACCCTCCTTTCTGCTCCGGAGCAGAGTAAGCAGCTTCCCTGGGGGCCTATCTAGGGAGCTGGCTTTTATCCGGAGCTGAGCCTCCTCCCGCAGCCTCTCCCCCAGCCGGCAGTAAGAGCCTGAAGGCAGGGACCTAGTCGGGGGACCTTGCTTGGGCTTGAGGCAGGGCTTCCATTCCCTGAGGCCAGCCCTTTCCCTTCACTTGGGGCTCTGGGATGGATTGCAACCGTCACACCTGGCTCACTCCCTGCCTCTTTCGGCCTTCACAG
Seq C2 exon
GTGGCCAACGAACCCGAAAGAAGCGCTGCCCCTACACCAAGTACCAGATCCGGGAGCTAGAGCGCGAGTTCTTCTTCAGTGTGTACATCAACAAAGAGAAACGCCTGCAACTATCCCGCATGCTCAACCTCACCGACCGTCAGGTCAAAATCTGGTTTCAGAACAGAAGAATGAAGGAAAAAAAAATTAACAGAGACCGTTTACAGTACTACTCGGCCAATCCGCTTCTCTAAAGGCTCCAGCCAGCAGGACCTGGGTGGGGGGCTTCATACACAGGAGATTATATGCAGATTTTGCCCTTGACAAGGTCAAGGCACATGGTGACTTTTCAAGAAAGGAGATGTGCAAGAGAGGAAAGGCAATACATGGAGACAGCCTGGAAGGAGGCTGCCCGGTGGTGGTTAAGATTTCTAATGATTCAGAGAGTTGTGCATCAACGAGAATGAATGGTTTAGGGCCTCTGGTGGTTCACCTTTGAAGACTGCTAGAGCTATGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000014738:ENSBTAT00000019611:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.448 A=NA C2=0.234
Domain overlap (PFAM):
C1:
PF120453=DUF3528=WD(100=62.8)
A:
NA
C2:
PF0004624=Homeobox=WD(100=73.1)
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:
TCGACCAGTTTTTCGAGACGG
R:
CTCCCGGATCTGGTACTTGGT
Band lengths:
353-1769
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]