BtaINT0073193 @ bosTau6
Intron Retention
Gene
ENSBTAG00000033330 | HOXD
Description
Bos taurus homeobox D11 (HOXD11), mRNA. [Source:RefSeq mRNA;Acc:NM_001206324]
Coordinates
chr2:20839236-20841537:-
Coord C1 exon
chr2:20840760-20841537
Coord A exon
chr2:20839996-20840759
Coord C2 exon
chr2:20839236-20839995
Length
764 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGC
5' ss Score
9.88
3' ss Seq
TTGGTCTCTTTAACTTGCAGTGG
3' ss Score
8.5
Exon sequences
Seq C1 exon
ATGAACGACTTTGACGAGTGCGGCCCGAGCGCAGCCAGCATGTACCTGCCCGGCTGCGCCTACTATGTGGCCCCGTCGGACTTCGCCAGCAAGCCGTCGTTCCTGTCTCAACCGTCGTCCTGCCAGATGACTTTCCCCTACTCTTCCAACCTGGCGCCGCACGTCCAACCCGTGCGCGAAGTGGCCTTCCGCGACTACGGCCTGGAGCGCGCCAAGTGGCCATACCGCGGCGGCGGCGGCAGCGGCGGCGCAGGGGGAGGCGGCGGCGGGGGCGGCCCCGGCGGGGGCGGCAGTGGCGGCGCCGGGGGCTACGCTCCCTACTACGCGGCTGCTGCTGCGGCGGCGGCGGCGGCGGCTGCGGCCGAGGAGGCGGCCATGCAGCGCGAGCTGCTCCCGCCCGCGGGCCGCCGGCCGGACGTGCTCTTCAAGGCGCCCGAGCCGGTATGCGCCGCGCCCGGGCCGCCGCACGGCCCTGCGGGCGCCGCCTCCAACTTCTACAGCGCCGTGGGCCGCAACGGCATCCTGCCTCAGGGCTTCGACCAGTTCTACGAGGCTGCGCCCGGGCCCCCGTTCGCCGGGCCGCAGCCCCCTCCGCCGCCCGCGCCGCCGCAGCCCGAGGGCGCAGCCGACAAGAGCGACCCCAAGACGGCGGCCAGTGGCGGCGGGGGAAGTCCCTGCGCCAAGACGACCCCCGGCTCGGAGCCCAAGGGGGCGGCAGAAGGCGGCGACGGCGAGGTGCCCCCGGGGGAGGCGGGGGCTGAGAAGAGTGGAGGCACAG
Seq A exon
GTAGGCACCGGACGCGGGGTGGGCGGCTGGGCTTGGGGGCCGTGGGCGCGGGGGGGCGGAGGGGGCCTCCCTCTGCTTGCGCCGTTTTATGTGCTACTTTATAAGCGTTCGAAGGGGTTTATACATCCTATAAGATTTCCCTGGCCGTTGTAAAGCGTGTTTACGATAGGAAACCAATTTAGGTGGGCTTAAGGTAGACTTCGAGGGGGACATTAATCGCTGCAGAGAGCTTTCCCCCAGTTTTGTGCGTGTGTGTGGGGGTGTCCTAGAGAGCGTGGAGGGAGGGAGGAAGGGAGGGGAGATTTCAAGCCAATTTGTGAGTGTGGACACTCGAGCCTCCTGCTTTTAAAGGAGTGGGGGGTTGGGGAGAGTTTGATCCTTGAACTGGACTTTATCCAAGCCTCTGCCTGACGCACGCTGCTGGCTGGAGTCGAGTAGATGCCCGGCACGCTCGTGTTTCTCTCCCTTCTGAGTCCAGCTCAGAGCCTGCCTCGCTCTCGCTCTCTGCTTCCCACCTCGATGCCAGGCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTCGGGGCGTGAACATAGGTCCACGCCCGCACTCTCTCCTGTGCCCGCCCATATATCATCCCCCACGACGCAGGCAGAGCCTTTCAGCCCTAGCAGGGACGTCCCCAACCGGCCGAGGCCTGGCCCTTGCGCGGCCCGAGCGGACAGCCAGGGGTGGGCAGGCAGTGGCCTCTCTTACCCCTTGGTCTCTTTAACTTGCAG
Seq C2 exon
TGGCCCCCCAGCGGTCTCGGAAAAAGCGCTGTCCCTACACCAAGTACCAGATCCGCGAACTGGAACGCGAGTTTTTCTTTAACGTGTACATAAACAAAGAGAAAAGACTCCAACTCTCTCGGATGCTCAACCTTACTGACCGGCAAGTCAAAATCTGGTTCCAGAATCGCAGGATGAAAGAAAAGAAACTGAACAGAGACCGTCTGCAGTATTTCACTGGAAACCCCTTATTTTGAGAGCTCCAGGAGCACCCCTCTCCCCTGAGCCCCACGCACCCACTCTCCTCCCCACCAGCCTGCCCTGAGCAGGCCCAATGTCCTTGGGTTTAATGACGCCTCTTCTCTGTGGAACTCCACGATTCCTTCCCACGGTCAACTCGGGACCTCCCAGCGACCACTGCAGCCTGCGGACGAGGTCGGGGACTTGGCCGAACGGATCCTAATAAGGGGAAAATGGTAAATGCAAACGTCCCTTTACAATTTTACCGCCAATGTGCTGTTGTTGTTCCCTCTCTCTGAGCTCCCGTGGGGACGCTGTGGGATCTGTAGAGAGTTAGGCCGAGGGGCTGGAAGGCACTTGTTTTTGTTCTGAGTTTAAGGGACTGCATCTTTTCCCCTTGGTGAATGCAGATAAAATAAACTCTGGGAAATGTACCTTTGGTCTATCCTATCAAGGCACGAGTCACTGTCTTTTGTGTGAATAAATGGTTTCTAGTAAAATGGAGGTTATAGCTTCAATACACTGTATGAATTTTCCTCTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000033330:ENSBTAT00000054133:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.588 A=NA C2=0.256
Domain overlap (PFAM):
C1:
PF120453=DUF3528=WD(100=71.5)
A:
NA
C2:
PF0004624=Homeobox=WD(100=72.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm10)
No conservation detected
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCCAACTTCTACAGCGCCG
R:
GTTCGCGGATCTGGTACTTGG
Band lengths:
353-1117
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]