RnoINT0071683 @ rn6
Intron Retention
Gene
ENSRNOG00000001580 | Hoxd9
Description
homeo box D9 [Source:RGD Symbol;Acc:1582908]
Coordinates
chr3:61621002-61622359:+
Coord C1 exon
chr3:61621002-61621038
Coord A exon
chr3:61621039-61621385
Coord C2 exon
chr3:61621386-61622359
Length
347 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
GCAAACCCCCCTCTTCCTAGACA
3' ss Score
5.57
Exon sequences
Seq C1 exon
GAGGAGGAGCAGCCGCCGCAGCAGCAACTTGACCCAA
Seq A exon
GTAAGTGCAAAAGAAATTGCCCCCTGATTTATTGCTGAAACCTGTAAGGCTCGAATGTGCAAAACTGATAGTTTTACTAACCTATAAAAACGTCTAGACGCCTACCCAAGCCTAGGCGAGCAACACGTATCCATAAAAAAGCTTCCCATAACCACCTACCTTGGGCGCGCGGTTTGTACGGTAAACAGAGCGCGGGCATTAAGGTTTTTTATGATAATTCCCCCAAGTTGTGAAAAGCGTCCATCCTTGGTGAAATTAATTTAACGACCTCTCTTCCCCACCCTGTCGTCTCTCCCTGCCTCCCCTCCGCCCCTCGCTCCCTTGTCTGCAAACCCCCCTCTTCCTAG
Seq C2 exon
ACAACCCTGCAGCGAACTGGATCCACGCTCGCTCCACCCGGAAAAAGCGCTGTCCCTACACCAAATACCAGACGCTAGAGCTGGAGAAGGAATTCCTCTTCAACATGTACCTCACCCGGGACCGGCGCTACGAGGTGGCCAGGATTCTGAACCTTACAGAGAGACAAGTCAAAATCTGGTTCCAGAACCGTAGGATGAAAATGAAAAAGATGAGCAAGGAGAAATGTCCTAAAGGAGACTGACCCAGTGCGGGTCAGGCCTGCAGCGCTCAAAAGGCAGCGGGTTTTGGTTTTTTGTTGTTGATTGTTTTCTTTGTGGGTGCTTGATTCAGAAACTCTGCAGCGATTCGGACATTCTTCTTTTTTTTTTAGGTAGAAGTGACTGTGTGGTTGGTCTCTGTGAGTTATTTGGGGGACGCTGTATTTGCTCGCATATGTATTGGAGAATCCAAGTGGCTTTGGAGTCTTGTCCTATCTCACTCCCTCCCTTTCCCACTCCCTTGGTTCCTTAGGAAATGCTTTATTTTGTGAGTGCACGCAGGCTTGATGGAGCCCTATCCTGTGTAAATGTTCCTCATGTTTCTGGAAAGTGCTGTAGTGTAGTCTCACCCCATCCAGCCTCCCAAACAGGGCCAACTATCTAATTCCGAGAATCTGAAAGAAGAGAAAGACTGTGGACACACACCCCCTCCCCCAAAAAACCCAGCTCAGCTGCAGGAAAACCCCTATCCTCAGGGAGCCCGCGGACTGACTTCCAGAGAGGCCTACCAAGAAGCCCTGGGCCCTGGGACACGAGGTTGGGGTGGGGTTGAGGAGAGGCTTAGTCCTTGGAGCACGGGGAAGCTACTTTCTCCCCAGGAGGGCTGGGCTCCCTGGGGCGGCCTCGGGAGGTGGCCCTCCATATTCCTGCCTGAGGACCAGTTGTAAATGTTACCGCTTCCTACAAATAAATGCTGATCTGAACAAATGGAGCCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000001580:ENSRNOT00000065426:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.338
Domain overlap (PFAM):
C1:
NO
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:
GCAGCAGCAACTTGACCCAA
R:
AGTTTCTGAATCAAGCACCCACA
Band lengths:
356-703
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]