DreINT0078845 @ danRer10
Intron Retention
Gene
ENSDARG00000059280 | hoxd3a
Description
homeobox D3a [Source:ZFIN;Acc:ZDB-GENE-990415-120]
Coordinates
chr9:1936252-1938435:-
Coord C1 exon
chr9:1937852-1938435
Coord A exon
chr9:1937638-1937851
Coord C2 exon
chr9:1936252-1937637
Length
214 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGG
5' ss Score
9.99
3' ss Seq
TTTCTGCTCTTTGTGTTCAGGAG
3' ss Score
10.12
Exon sequences
Seq C1 exon
GTCAATGCAATCTTTACTAAAACTGGCTTATTTTCTTAGCAGGTCAAAGGACAGAAAATCTGTGGGAAGCTCCAATCACGTGATTCACAAGTCCATGCTATTGGACAGGAGTTCACAGGATCTCTAAGTTTGAACCTTCGCAATGCAGAAAGCCACTTATTATGACAATGCTGGACTTTTCGGAGGATATTCGTACCCTAAATCTGACTCCTACACGTACGGTCCAACACACCAGGGCTTCTCATCCTCCAGTATAGAGAATGACTATCAAAGCCCAATTTGTCCAATTCAAACTACATCAGTCCGGCAAGCAACCCATAAAAACGGAGACATCAATGGCAGTTGTATGCGACCAAGTGCCAGTCAGGGCAACAGTCAGCCAGAGAGTATCAGTGAGCAGCAGCAGGCTGCTCCATTAGCGGCCAGCTCTCCCAGCCCCAGCACTAACTCCACACAAAAAAAGAAATCCCCCAGCTCTAATGGATCCAGCACTGCCACCCCAGTCATCTCCAAGCAAATTTTCCCCTGGATGAAAGAGACCCGCCAAAATGCAAAGCAGAAAAGCACCAACTGCCCAGCAGCAG
Seq A exon
GTATGGGCTTTGCTTGAGTGAGTGTGTGTGCGCGGCTGGAGAGAATAGTTTTATCTACCCAGTATAAGATGAATAACTACAGTCGGAGACAGCTACTATCATTATGACCCAGTTCCTTTTGTTTACAGTAGGCTGTCTCGCTTTGGCCTTTAAGTGATGTAATAGGCTGTGTAACACAATTAATCCATTGCACATTTCTGCTCTTTGTGTTCAG
Seq C2 exon
GAGAAACCTGCGATGACAAGAGTCCGCCTGGCCCTGCGTCGAAACGAGTGCGCACTGCCTACACCAGCGCCCAGCTAGTCGAGCTGGAGAAGGAGTTTCATTTCAACCGCTACCTGTGTCGCCCCAGAAGAGTGGAGATGGCCAATCTGCTCAACCTCACCGAGCGCCAAATAAAGATCTGGTTTCAAAACAGAAGGATGAAGTACAAAAAAGATCAGAAATCTAAAGGCATAATGCACTCTCCCTTAGGACACTCTCCGGACAGGAGCCCGCCGTTAAGTGGCTCGAATCACATTGGATATTCTGGTCAGCTTCCGAACGTAAACAGCCTCAGCTACGACGCGCCGTCGCCTCCGTCATTCGCCAAGCCGCAGCAGAATATATACGGCTTGGCGGCATACACGGCGCCATTGGGCGGCTGCATACCGCAGCAGAAAAGGTACCCGGGAACAGAGTACGACCACCACAGCATGCAGGGGAACGGTAGCTTTGCTAATGCTAATTTACAAAGTAGCCCCGTGTACGTCGGGGGAAACTTCGTTGATTCAATGCCAGCCTCCGGCCCCATGTTCAACCTCGGTCATCTTCCCCATCCCTCATCCGCTAGTGTGGACTACAGCTGTGCCGCTCAGATTCCGGGTAACCACCACCACGGACCGTGTGACCCCCACCCCACATACACAGACCTCAGCTCTCATCATGCGTCTCAGGGAAGGCTGCAGGATGCGCCCAAACTCACGCACCTGTAAGGATCCCATCTGTGTGCTCAAGCGAAGGGTCGCTTTTTGTATTACCTCACTAGCTAAACTAATTTATAAAAACTACACTCGGAGAGAAACATAACGTATTATCCTGTATTATTATTGATATTACTATTACTGCTATGATTGTAATTATTTTTTAATAATAATAGCTGTGGTCCATTTCTCTTTGACTGTTGAAGACACACACAAGGTTGTTTGTTGCCGGGTTCTCCAAAGAACCGAATCGGCAATAATGAGGGCAATTTCCATGACGTATTATACTTGAAGGTAAGTTCTGTAGATTTGACCGTATAGACATTCGTCTTTATAGAGGTGGGTTTTTGTAGAGGATTAAAAACCATCGCGTCGTCTGTTACTCACGGGTTTTTCGCCATACCATTATTTATTTTCCACCAAGATTGTATGACAAGCATTTATAATGACTGAGTATTATATTTATTATTTATCGTTTTAATTAACGCACATTATTTATATTCTCATGTATATTATTTATATAGCAGGTGTAGAATTTATTTTGGAGCAGAAGGCATTTCTTTGAACTGGTGCAAACAAGGTAATAATGTGAGATTGGTGTATTCCCTTCTTCATTCAGTAATAAAATATTGTGAAAATGAAGAACTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000059280:ENSDART00000146131:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.851 A=NA C2=0.530
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=22.8),PF132931=DUF4074=WD(100=25.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCGCCAAAATGCAAAGCAGAA
R:
CCGGAGAGTGTCCTAAGGGAG
Band lengths:
305-519
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]