DreINT0078841 @ danRer10
Intron Retention
Gene
ENSDARG00000059267 | hoxd11a
Description
homeobox D11a [Source:ZFIN;Acc:ZDB-GENE-990415-117]
Coordinates
chr9:1975021-1977293:-
Coord C1 exon
chr9:1976599-1977293
Coord A exon
chr9:1975736-1976598
Coord C2 exon
chr9:1975021-1975735
Length
863 bp
Sequences
Splice sites
5' ss Seq
CGAGTAAGT
5' ss Score
10.15
3' ss Seq
TTATCATGTTCTTTTTATAGGTG
3' ss Score
11.71
Exon sequences
Seq C1 exon
TCGCGAGTCCTATCCGCACGCATATGGTGCAATAGATGGGCAAAGTTTAACAGTCAAGCAGACGAATTTTCCCCCCTCTCTACGGCTAAAGCGAGCAATGACGGACTACGATGATCGCAACAACTGTGCATCTAATATGTATTTACCATACTACGTCTCTACTCCCGATTTCTCGTCGGTTTCGTCGTTTTTGCCTCAAACTACGTCGTGTCAAGTCAATTTCCCCTATTCTTCGAACATAGCGCAAGTCCAACCTGTTCGCGAAGTGACTTTTAGGGACTATGGACTGGATCATCCGAGCAAATGGCATTACAGGGGCAATTACGCTTCGTACTATTCAACGGAGGAGATAATGCACCGAGATCTCTTGCAGTCCACAAACAGAGCGGAAATGATTTTTAAGAACGATTCCATGTACAGCCATCACGCTGGTACTAACTCCTCGTGCAGTTTCTTCACCAACGTCGGCCGAAACGGGGTACTTCCACAAGGATTTGATCAGTTTTTTGAGACGGCAAACTCCGAGAAGCCCAACCCCGAGCAGTCCAAACAAAAGCCAGATACGAGTGTCCCGGGAGATGCTGCATGTAACCCGTCTACAGATAGCGCGGAGCAGACCAAACAGGACCCGACAGACACCGTGGAGGAGGAATCCTCCGTTTCAACCTGCGATGAAGAAAAGAACAGCGGCTCGA
Seq A exon
GTAAGTCCAGGCGTTTCACGGCGCTTCAGTCTACTATATTACTTTGTCGGTTAGCTTTTATGTGCCGCTTTATAAGCATGCAAAAGTTTTTATGTAGCTAGTAAGATTCTCTTTGCTGTTGTAAAAATATTTACGATGGGAAAGGCTCTTTGGTTGCATCTCTCTCGAGTGTATGTGTGTGTGTGTTTGTTTATATATGATGTGTATTATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATCTTACACACAAAATGATTTATGATCAGAAATGTTGAGAAATGATAGGTGTGATGTGAATCGACAGTTAACACATTTCTCAAAATCCTAATTTACAAAGCTCGAGCCTGTTGCTAGTTTCAGGTTTATGTAATAATTTCACAAAATAGCTTTAAACCTAAACGCATTAACATCGCATTAAAACACTCGTTTGGATTACTCTTGTGCGCGCTTGCGTTTGGACGTGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTTGTGGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGGGCCGCTTGCATTCGTGTGTATGTCATGTGGCAGAGCTTGTTTTTTTCCGGCATATTTTAATTTCTCTAAGTGTTTTGTTTTTGTACATGTGCTGTGTGTAGCAAATGTTACTGTGAATAACAATGATTATTAATATAGATAATTTGTAGGCTAGTTGATGTGTTGATGGATTTAGCATATTAGTGCAATCATCTAAAGAATTTGTAGTTGTATTGTCACTGAGTTTGAGTTCATTCTAATGTTATCATGTTCTTTTTATAG
Seq C2 exon
GTGCGACAAAGTCCAGAAAGAAGAGATGCCCGTATTCCAAATACCAGATCCGAGAACTTGAACGAGAATTCTTTTTCAATGTGTACATAAACAAAGAGAAACGCCTGCAGTTGTCAAGAATGCTCAGTCTTACAGACCGACAAGTGAAGATTTGGTTCCAGAACCGCAGGATGAAAGAGAAAAAGCTGAACCGAGATCGACTCCAGTATTTCACTGGAAACCCATTGTTCTGAAAGTCATGATATTGGCCGCTTCAGGAGACCAAGGCTATTCTGTCATGCTTGTGGGACATCAACCATTCGTCGGACTTATTTTCACCTCAGCCCTGTATTTGTACCACTATGCAAAATACTTGCTATATCAAACAAAAACAAAAGAGTCATTTTATTCGCAACTGCACTTCTGCACAAATTACCTATTGCAGTGTATCCGCAGAGATGGACATTATCAGTTTTCATAGGTACCCCGACAATCTCTTCATACTCTGTGATTGCCATTGAAATGCAGTTGCTTTGTGTTTGTTTGTATTTATTTATTATGTTTTTTTAATTTCAGTTCTTACATTCAATACATTCAAGTAACAACTCGCACTGCGTAATAAGCAACAAACAGGTTTGGTTATATCAAATGAATTCGTTGAGGTAAAGCTGTGTATGCATTTATTCATTTGAAGCATGTATATGTATCAGTGTATTAAATAAAAATACAGGACGTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000059267:ENSDART00000082344:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.360 A=NA C2=0.104
Domain overlap (PFAM):
C1:
PF120453=DUF3528=WD(100=71.0)
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:
AACGGGGTACTTCCACAAGGA
R:
TCTTGACAACTGCAGGCGTTT
Band lengths:
342-1205
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]