BtaINT0073201 @ bosTau6
Intron Retention
Gene
ENSBTAG00000016033 | HOXD9
Description
homeobox D9 [Source:HGNC Symbol;Acc:HGNC:5140]
Coordinates
chr2:20824235-20825910:-
Coord C1 exon
chr2:20825088-20825910
Coord A exon
chr2:20824736-20825087
Coord C2 exon
chr2:20824235-20824735
Length
352 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
TCAAACCCCCCTCTTCATAGACA
3' ss Score
7.2
Exon sequences
Seq C1 exon
ACCTTGGGTGGGAGCGCGGGGCGCCTCAAAATGTCCTCCAGTGGCACCCTCAGCAACTACTACGTGGACTCGCTCATAGGCCATGAGGGCGACGAGGTGTTCGCCGGGCGCTTCGGACCTCCAGGGCCTGGCGCGCAGGGCAGGCCCGCAGGTGTGGCCGACAGCCCGGCCGCTGCCGCCGCCGAGTTCGCCTCGTGTAGTTTTGCCCCCAAATCGGCCGTGTTCTCCGCCTCGTGGTCCGCGGTGCCCGCCCAGCCCCCGGCGGCGGCGGCGATGAGCGGCCTTTACCACCCATACGTGCCCCCGCCGCCCCTGGCCGCTTCCGCCTCCGAACCCGGCCGCTACATGCGCTCCTGGATGGAGCCGCTGCCCGGCTTCCCGGGCGGTGCGGGCGGCGGCGGCGGCGGCGGCGGTAGCGGCGGTGGCCCGGGCCCCGGTCCCAGCCCCGGCCCCAGCGGCCCACCCAACGGGCGCCACTACGGGATTAAGCCTGAAAGCGGAGCGGCACCGACCCCCGCCGCCGCCTCCACCACCTCCACCTCCTCCACTTCCTCGTCTTCCTCCTCCAAAAGGACTGAGTGCTCCGCGGCCCGAGAGTCCCAGGGGAGCGGCGGTCCCGAGTTCTCGTGCAACTCGTTCCTACGGGACAAGGTGGCAGCGGCGGCGGCTGGGGGAACCGGGCCCGGGGCGGGGATTGGATCCGGGTCCGGGGCAGGCGGCACATCGGAGCCCTCAGCTTGCAGCGACCACCCGAGCCCGGGCTGTCCGCTGAAGGAGGAAGAGAAGCAGCATTCGCAGGCGCCGCAGCAGCAACTTGACCCAA
Seq A exon
GTAAGTGCAAAAGAAATTGCCCCCTGATTTATTGCTGAAACCTGTAAGGCTCGAATGTGCAAAACTGATAGTTTTACTAACCTATAAAAACGTCTAGACGCCTACCCTAGCCTGGGCGAGCTACACGCGTCCATAAAAAAAGCGTCCCATAACCACCTACCCTGGGCACGCGGTTTGTACGGTAAACAGAGCTCGGGCATTAAGGCTTTTTATGATAATTCCCCCCCAAGTTGTGAAAACCGGCCATCCTTGGTGAAATTAATTTAACGACCTTTTCTCTCCCCCACCCCGTTGTCTCTCCCTGCCTCCCCTCCGCCCCTCGCTCCCCTTCTTCAAACCCCCCTCTTCATAG
Seq C2 exon
ACAACCCCGCAGCAAACTGGATCCACGCTCGCTCCACCCGGAAAAAGCGCTGTCCCTACACCAAATACCAGACGCTTGAGCTGGAGAAGGAATTCCTCTTCAACATGTACCTCACTCGGGACCGGCGCTATGAGGTGGCAAGGATTCTGAACCTCACAGAGAGACAGGTCAAAATCTGGTTCCAGAATCGTAGGATGAAAATGAAAAAGATGAGCAAGGAGAAATGCCCCAAGGGAGACTGACCCGGCGAGGCGCCAGCAGGACCACTCTGCTTTGCAATGGCAGTGGGGTTTTTTTCTTTGTGGGTGCTTGATTTCCAGAACTTCTCCAGCCATTCGGACATTCCCCCCACCCCATTTTATGTAGAAGTGACTGTGTGGTTGGTTTCTGTGAGGTAATTTGGGGGACTCTGTATTTGCTCGCTTATGTGTTGGAGAAACCAAGTGGCTTTGGGGTTTTGCCCTATCCTGCTCCCCTCTTTTCCTGTTCCGTTGGTTCCTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000016033:ENSBTAT00000021336:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.749 A=NA C2=0.325
Domain overlap (PFAM):
C1:
PF046178=Hox9_act=WD(100=45.1)
A:
NA
C2:
PF0004624=Homeobox=WD(100=70.4)
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:
CCTCCACTTCCTCGTCTTCCT
R:
TGTAGGGACAGCGCTTTTTCC
Band lengths:
342-694
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]