BtaINT0073199 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004835 | HOXD3
Description
homeobox D3 [Source:HGNC Symbol;Acc:HGNC:5137]
Coordinates
chr2:20776408-20779895:-
Coord C1 exon
chr2:20779266-20779895
Coord A exon
chr2:20777166-20779265
Coord C2 exon
chr2:20776408-20777165
Length
2100 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGCC
5' ss Score
7.13
3' ss Seq
CTCTCTCCCTCCTGGCCCAGGAG
3' ss Score
8.15
Exon sequences
Seq C1 exon
GTTATCTGGAGCCTGGGGCTGCCCCAGCTCTCTCAGGATTTGGCAGACATTGGAGGTGGTGGTGAAGGAGACAGTGGTGGTCAATGTTATTTGAGCAGGGTCAGCAGGCCCCGGAGGTTCCTGAGTACACGATGCAGAAGGCTGCTTACTATGAGAACCCAGGACTCTTCGGAGGCTATGGCTACAGCAAAGCTGCTGACACTTACGGCTATAGTGCCCCTCATCAGCCTTATCCACCCCCTGCTGCTGCCAACTCCATGGACACTGATTACCCAGGCTCTGCCTGCTCCATCCAGAGCTCTGCGCCTCTCCGAGCCCCAGCCCATAAGGCGGCTGAACTCAATGGAAGCTGCATGAGGCCTGGCACTGGGAACAGCCAAGGTGGGGGTGGTGGCAGCCAGCCTCCAGGTCTGAACTCAGAGCAGCAGCCACCACAGCCCCCTCCACCGCCACCGCCACCAGCCCTGCCCCCATCCTCTCCCACCAACCCTGGAGGTGGAGTACCTGCCAAGAAGGCCAAAGGTGGGCCCAATGCTTCTGGCTCCTCAGCCACCATCAGCAAGCAGATCTTTCCCTGGATGAAAGAGTCCCGCCAGAACTCCAAGCAGAAGAACAGCTGTGCCACTGCAG
Seq A exon
GTAGCCCTCCGAGGGGCCTCATCTCTGGGCCTTCCCCCAGATTGACCCCAAGAAGCTAGCTCACCTAGGAATTAAGAGACTCAGGGCTGGACGTACAACTTTGGAGGCCATATGTGTACACTCGCAATGCAGAAATTGTGGGGGTTTTTTTGGCCATACTGCATGGCTTTGAGGGATCTCAGTGCTCTGACTGGGGGCTGCAGGGATTGAACCCAGGCCATGGCAGTGAAAGTGCTGAATCCTAACCACTGGACCACCAGGGAGCTCCCTGTTCTTTCTTTTTAGTGTCTCTGGTTGTGGTCATATCCTTACAGTGACAGGGTGCTGATGTCCACTCCAGGCTGCTGGCACCGCTGCTGGACATGTCTCATAGTTATTCATAGACAGCTCTTCCTTATACTGCCCTAATATCTGGACTGCTGGTCATAACTCAACTCCTTCCAGCCAATAGATCTTCAAAACTTGAAGATAGGTACTATGATCCCCAAGCCCAGGGGGTGATATAGCCCATATCACATGAATCCCACTTCCTTAAATTAATAAGAACTAAAAGGCTATTGAACACTATGTTAAGAATCATGTTAAGTGCTTTATAAGCACTAATTTTCCAAAGAACGCTTTGAGGTAGGTATTAATAAGACATCCATTTTAACAGATAAAGAAAATGTTAGAGATGATAAGTCACTTGCCCAAGATAACTAAACTACCAAATGGCACACCTGGGGAATTCCCGGGTGGTTCAGTGATTAAAGACTGTGCACTTTGACTGCCGAAGGGCACAGGTTCAATCCCTGGCTGGGGAACTAAGATCCTGCAAGCTGAAAGGCACGGCCAACCCTTTCCTGCCCCAACAAAACAAAATAACATGTACAAAAAACAAAACCTCAAATGGCATATCTCAGGCCACTCCCACTCAATTCTCCCCCTCCCCAGGAAATCCCTAATGTGGAGGCTCATATCCTAGGGAAAGAGGCTGTACTCTGAAACAGGAGCAGCCTTGGGTTTTTTCCCTGGAAAGGGAGACTCTGGTGTTGAGAAAAATTTCCCTAGGTCCGTTTAGTCTGTGTGGAAGAAGAAGGGCAGGATCAGCAGCTCTGAGACCTTCTGCCACTCTCTGCTCAGCTTGCTTGATGCCTGAACTTTTCTGGCCTTGTGTTCTCTGATGCACTTTTTATCTTCAGGTAGATGAACTTGCTCCCAGGTCCAGGGCTAGCTTGAGGTGTAGTTAGCTGGGGATGTACTTAGTTTGTTATCAGATCTCTGGTTTGCCTGTTGCTCTTTGGGGCTGCTGCTCCTAGGGGGAAAGAGTCTTTAAGTCTTGTAAGCTCCTTCTCCTGCCCCTCCTTCCCAGCTGCAGGCCTAGGCCCTCCCTCCCAGGAGAAATCCATTTGTCTTCCTAGGGAGGGAGTGGACAAGCTGCTGAGAGGTGGCAGGGGTGGTGGAAACCACTGCTGAAGCTGCTGCTCCCAGCACTGTAATACTCAAAATATGCCCAGCCTGGCCTTGAATGCCCTAAAAATCTGGGGCCATATTTTCATGGTATGTCACCTCCCTGCATTTGAGTACTGGGCACATGGGTGCAATTGAGCTGGAGTGAGCTGCCAAGATTGCCACCCTCATTCCATGCTTGGGGTGCTTTGCCCAGGAGCCAGCCTCTGAGCAAGGTAGTTTGAGGCTGCCTCCAACATTCCCCCCACCTACCTTCCCAGCAGCAGTGGCTGGAAGGAGTGTTCAAAGTGAAGTCTGGCCCTTCTTTGACAGGGTGGGAAGCCTTACCAGCTGCTACTAGTCTCTCATTAAACTCCTCCTCAGCCTTGGGAACGGGATGATGGACTAGGCTGAAGGGGAAGGGGTGGGCTGAATGAGTTGGACTTCAGAAGGCAGATGGGAGTTTCAGGTGCCACTGATAGGTAGGCCTGGGGCCTTTGAGTTCTGGGAATCTCTTGGAATCTCACCGCTCTAACGCCCCTCCCTCGCTCCAGCCAGGATTAAAATGGGGCGGGGGGAGGAAGAGGAAGGAGTCAGGGAAGCACCCCTCTACGGCCCAGGGTGTCCCCACATCTCCTGCTCAGCGACCTCTCTCTCTCCCTCCTGGCCCAG
Seq C2 exon
GAGAGAGCTGCGAGGACAAGAGCCCGCCGGGCCCAGCGTCCAAGAGGGTGCGCACGGCGTACACAAGTGCACAGCTGGTGGAGCTGGAAAAGGAATTCCACTTCAACCGCTACTTGTGCCGGCCACGCCGCGTGGAGATGGCCAACCTGCTGAACCTCACCGAGCGGCAGATCAAGATCTGGTTCCAGAACCGGCGCATGAAGTACAAGAAGGACCAGAAGGCCAAGGGCATCCTGCACTCGCCGGCGGGTCAGTCTCCGGAGCGCAGCCCGCCGCTCGGCGGCGCCGCGGGCCACGTGGCCTACTCAGGGCAGCTGCCACCCGTGCCCGGCCTGGCCTACGACGCGCCCTCGCCGCCCGCCTTCGCCAAATCTCAGCCCAACATGTACGGCTTGGCCGCCTACACGGCGCCGCTCAGCAGCTGCTTGCCTCAGCAGAAGCGCTACGCGGCGCCCGAGTTCGAGCCCCACCCCATGGCGAGCAACGGCGGCGGCTTCGCCAGCGCCAACCTGCAGGGCAGCCCGGTGTACGTGGGCGGCAACTTCGTCGACTCCATGGCGCCCGCGTCCGGCCCCGTCTTCAACCTGGGCCACCTCTCGCACCCGTCTTCGGCCAGCGTGGACTACAGTTGCGCCGCGCAGATTCCAGGCAACCACCACCACGGACCGTGTGACCCTCATCCCACCTACACAGATCTCTCGGCCCACCACTCGTCTCAGGGACGCCTGCCCGAGGCCCCCAAACTGACGCATCTGTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004835:ENSBTAT00000006353:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.896 A=NA C2=0.472
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=22.5),PF132931=DUF4074=WD(100=24.9)
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:
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]