DreINT0078846 @ danRer10
Intron Retention
Gene
ENSDARG00000059274 | hoxd9a
Description
homeobox D9a [Source:ZFIN;Acc:ZDB-GENE-990415-121]
Coordinates
chr9:1963208-1964930:-
Coord C1 exon
chr9:1964293-1964930
Coord A exon
chr9:1963977-1964292
Coord C2 exon
chr9:1963208-1963976
Length
316 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
TCTTATTTTTCTGTTTTTAGGCA
3' ss Score
10.88
Exon sequences
Seq C1 exon
GAAGGTGAAGGCAGCAAAAATACTACGATTGTTCGGAGGCAAGGTTTCGGAAACAGAGTACCGTTTTATATGAGTTCGAAGGGATCCAAAAATGTCGACTAGTTCAGCTCTCAGCAGTTATTATGTGGACACTATTATGGGGCACGAGGCTGAGGATGTGTACGGAGCGCGTTATATCCAGGGTTCTCACACCGCGCCCGCGAGGCCGTCAGGTGTGGTTGAAAATGCGGACTTTTCCTCGTGCAGCTTCGCTCCCAAATCAGCCGTGTTCCCTGCGTCCTGGTCCTCGGTTCATCAGCCATCTACTGCTGCTGTGTCCGGGATTTACCATCCATACGTTCACCAGACCCATCTTTCAGACAACAGATACGTCCGATCCTGGATAGAGCCAGTCGCAAACCATATCTCTTTAACGGGCTTCCACCCCAACAGTCGGCACAGCGGTACAAAGACTGAAAGTTTACCCCCGAAAAGGACCGAAAGCGCCGCGTTTGAAACGGAGACACCGTCGGTTCCCGAGTTTAGCTTAAATGCTGTGTCCGAGAGCGCGGACAAAGCTACCGAAGAAAGAGTTGGAAGTGATAATTCGAGTCACGGTGAGCCTAAAGACGAAAAACAACAACAACAACTTGACCCAA
Seq A exon
GTAAGTAAAATGAATTGCCCCGTGATTTACAGCTGTCGAAGTGTCCTAAACTGGAGGTTTTACAAACCTATAAAAGTGTCCAGGCGTTTACCACGGGCCGAAATTTTTCATTTATCCCAAAAGTGGCTATTTTAAAGCATTATACATAGTTGTATTTACATATCAACTAATTTAATACACAAATTACTAAATAATTGAATGGATGAATATTAAAATATATCCATATATATACATTGTGCTTTGGACGTGACCTTTAATTGAGTGACTTGACGATGTGAAGCCTGTTTATTTTATTGTCTTATTTTTCTGTTTTTAG
Seq C2 exon
GCAACCCTGCTGCCAACTGGATCCATGCGAGATCAACAAGAAAGAAGCGTTGTCCGTACACCAAATATCAGACTCTGGAATTGGAAAAGGAGTTTCTTTATAACATGTATTTAACGAGGGATCGTCGCTATGAAGTTGCACGAATCCTGAATTTAACAGAGCGCCAGGTGAAAATCTGGTTTCAGAACAGAAGAATGAAAATGAAGAAGATGAACCGAGAGAGGAGCAGCAAAGATCCGTAATGGAAAGCGTGCAAGAAGCTAATGCGCGTTTCTTTAGCACGCTTGGTTTAGGATACAAGTTTTGTCCATTTTTTGTTTTAGTCACTCAAGATTAAATTGGCGTATATTCTATTTAATTTGATATATTTTTAAATATATATATTTTTTCCTCAGATAATAATTAGTATTTGAGTAACTTTAAATAAAAGGGTATTTCAATCCTCCTAAATTGTATTTCCCAGGTCTGAGCATTTCTTATTTTGCACAGTGTCAGCATACTCATACTCATTTAAATATCTTGCAAGTAATTAGGACATCTGCTAGTTCTTAATCTGATGATCTGATGAGATTTAAATATTTGTCCACAATGCATGCAAATAGCCTACCTTCCATCTTCATACAGCCACATGTAGTCATTTACTGTGCCATTAATTTTACTTTTTCCTTTTTTTAATTGGACCTTTTGTACAGTCTCATTTTGATTCTAGTGTATTTCTCGTTGAAACTGTTGTCGCATCGAAAAGGTCTAAATTATAAACTAAAACGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000059274:ENSDART00000082354:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.459 A=NA C2=0.350
Domain overlap (PFAM):
C1:
PF046178=Hox9_act=WD(100=99.5)
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:
ATTCGAGTCACGGTGAGCCTA
R:
CCAAGCGTGCTAAAGAAACGC
Band lengths:
342-658
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]