RnoINT0071650 @ rn6
Intron Retention
Gene
ENSRNOG00000007823 | Hoxb6
Description
homeo box B6 [Source:RGD Symbol;Acc:1562142]
Coordinates
chr10:84147836-84149600:+
Coord C1 exon
chr10:84147836-84148250
Coord A exon
chr10:84148251-84149340
Coord C2 exon
chr10:84149341-84149600
Length
1090 bp
Sequences
Splice sites
5' ss Seq
ACAGTGAGT
5' ss Score
8.34
3' ss Seq
TTCTCCTCTCTGCGTAACAGGTT
3' ss Score
8.83
Exon sequences
Seq C1 exon
ATGAGTTCCTATTTCGTGAACTCCACCTTCCCCGTCACTCTGGCCAGCGGGCAGGAGTCCTTCCTGGGCCAGCTGCCGCTCTACTCGTCTGGCTATGCGGACCCGCTGCGGCACTATCCCGCGCCTTACGGGCCGGGACCCGGCCAGGACAAGGGCTTTGCGGCGTCCTCCTATTACCCACCAGCCGGCGGCGGCTATGGTCGGGCGGCGCCCTGTGACTATGGGCCGGCGCCTGCCTTCTACCGGGAGAAGGACGCGGCCTGCGCCCTCTCCGGCGCCGACGAGCCGCCCCCGTTCCACCCCGAGCCGCGCAAGTCCGACTGCGCACAGGACAAGAGCGTGTTCGGAGAGACCGAGGAGCAGAAGTGCTCCACGCCCGTCTACCCGTGGATGCAGCGCATGAATTCGTGCAACA
Seq A exon
GTGAGTGTGACTTCCCGCTGTCCCACGCAGGGGGGAGGGAGGTGCGGTGCAAACAGAAAGGCAAAACTAGCGAGTGTCAGCATCCTCTCACCCCAACTCTCCTACTGGGAACTAGATGGGCATCTCAGCAAATAGGGCAAGATTGGGCCCTGGCCTCCAGATCAGTCCTCCTGCCCGCAGAAGTTGCAAAGTTTGCAAAGTCCCAGCTGCACAGTAAGGCAGGGGGAGTAAGTGGGCTCTCTGAGAGAGGAGAGAGTCAGGCTAGGATTATTGATCAGGAAGAGGACAGGGGACTCAGTCTCTGATTTTGCTTTCCTCTATATTCTCCGGATATATTCCCTCTCTTGTCCGGATCTGCGGGGGGGGGGGTGTCCCGCACCCAAAGACCACTCCATTAAAAACAAGAGTGCGTCATGAAAGGGGAGGGGTAGCATGACGCCTGCAAGGGCGAGTTTACAGGGTCCTGGATTGTGTTTCCCTTGGGCTGGGGGAGGGGAACTGGGGACGGGGGTACTAGGGAGCTGTGAGACACTACCACAGGGGTAGTATAGTCTGAGGAAGGAAGAATGAGAAGGGACAGGCGGAGGGAGTGAGAAGAACAAACTGGCGCCTGGGTCTCACGTTGGTTTATTTGTTGGCTTCAAGTCCCAATTGATGTCCATTAGCACGACACGAAAGTGAGGAGCTGTTAATGCGGACTATGAATCGATCCGTGTCATTATGGATTAAGGGCCAGAATCTATCATCGAGTAGGGCAGGGAGAGCTGGATGAATGGAAAGAAGGGAAAGAAAAGATACAGCTCGTAGGAGACTCACCTGGCCAGCCCCTCCCCCAAGCTCAGGTGGGAGTCAAACTGCCCCTCCCCTCCCCCACCGAAAGTCTAGACAGAAAGAAAGCACAGCACAGGCCTCGGAGTCCAGGAGGGAATCTGGAGGGGGCGCTGGAGGAGTGGGAAACGGGGATCAGGGAATGGGAGGGGGAAAAGACAACTCCCGACCGGCTAGCTTTACGTTTGAGGGCCCAGTGGGGGAGGGGCTATGGGTTTGGTGTGGTGACCCCAGGCCTCAGTTTCTCCTCTCTGCGTAACAG
Seq C2 exon
GTTCCTCTTTTGGGCCCAGCGGTCGGCGAGGCCGCCAGACCTACACCCGCTACCAGACCCTGGAGCTGGAGAAGGAATTTCACTACAATCGCTACCTGACCCGCCGGCGGCGCATAGAGATCGCGCACGCCCTGTGCCTGACCGAGCGGCAGATCAAGATCTGGTTTCAGAACCGGCGCATGAAGTGGAAAAAGGAGAGCAAACTGCTCAGTGCGTCTCAGCTCAGTGCGGAGGAGGAGGAAGAAAAGCCGGCCGAGTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000007823:ENSRNOT00000010527:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.281 A=NA C2=0.279
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=65.5)
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:
CCTGCCTTCTACCGGGAGAAG
R:
CCAGATCTTGATCTGCCGCTC
Band lengths:
348-1438
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]