RnoINT0071652 @ rn6
Intron Retention
Gene
ENSRNOG00000007585 | Hoxb8
Description
homeo box B8 [Source:RGD Symbol;Acc:1586211]
Coordinates
chr10:84131495-84133246:+
Coord C1 exon
chr10:84131495-84131918
Coord A exon
chr10:84131919-84132697
Coord C2 exon
chr10:84132698-84133246
Length
779 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
GTCCTTTCCCCCATTCCCAGCAG
3' ss Score
6.62
Exon sequences
Seq C1 exon
ATGAGCTCTTATTTCGTCAACTCACTGTTCTCCAAATACAAAACCGGGGAGTCCCTGCGCCCCAATTATTATGACTGCGGCTTCGCCCAGGACCTGGGCGGCCGACCCACCGTGGTGTACGGTCCCAGCAGCGGCGGCAGCTTCCAGCACCCTTCGCAAATCCAGGAGTTCTACCACGGGCCATCGTCGCTGTCCACGGCTCCCTACCAGCAGAACCCGTGCGCCGTGGCGTGCCACGGGGACCCGGGCAACTTCTACGGCTACGACCCTCTGCAGCGCCAGAGCCTGTTCGGTGCGCAGGATCCAGACCTGGTGCAGTACGCAGACTGCAAGCTCGCGGCAGCCAGCGGCCTGGGCGAGGAGGCCGAGGGGTCTGAGCAGAGCCCGTCGCCCACACAGCTCTTCCCCTGGATGCGCCCTCAAG
Seq A exon
GTGAGCTCGCGTCGGACCTGGACCTGACGGGGTGGGAAGGGGCCAGGAGGGTCCCAGGCCGGTCAGCGGGGGAGGGCTGGTGGGCAGTCCCGGAGCATCTTCTGCTCCTAGAGGACTTGCAGGTTCTGTTCCAAACACCTACCTCCTCTCCCTTCCTCCCCACTTTCTTTTCTTCTTTTTTTCCCCTTTTCTTTTTGCTTCCTTTGAAGGGGGGGTCTCTAAGCGAACTTCCTGAATCCATAAACTCCTCACCCTCCTTTACTTTTCTTCTTCAACCCCTTTCCCCTTTTACTGTTTTATGGGGGCTGTGGAGGAAGAGTGGTGGGAGTGGGGGCGCTCAACGTTTGCACTTCTCAATTGCTTTATAGTTTAATTACCCTGAAGAAACTTTTCTTCTGGGGCAGAGGCTCTGGGGGCTTTTCAAGGTGGGTTCGTGGTCCCCACTCTGGCTTTTTATTTTTACTTCCCCCCCCCACCACCACATTCATCCCCTTAAACTTTATGCACTTTTACTATATCTGAACCCCCTATTCTGGGTCTAGTTACCAGAGGAAGGGGCTCCTCCTTTATGAGCCCTGCAGATTCAGGGCTGTCTAGTTCCCCCCTCTCGCCTCCCCTCCCCCGCTGACCGCGTCCTCCGCGCTCCCCCTCCCGCCCCCGCATAAGGGTCCCCTGCCCTTATTATCCTGGTCTCTAGGCTGGTTCACGAATCTTCCAACTCTCTGTCTCTGCCCCCTCCCCCATCCTCCCCTCTGTCTCGTCCTTTCCCCCATTCCCAG
Seq C2 exon
CAGCCGCCGGACGCAGGCGAGGCCGCCAGACCTACAGCCGCTACCAGACCCTGGAGCTGGAGAAGGAGTTCCTATTTAATCCCTATCTGACTCGCAAGCGGAGGATCGAGGTATCGCACGCGCTGGGACTGACAGAAAGACAGGTCAAAATCTGGTTCCAGAATCGGAGAATGAAGTGGAAAAAGGAGAACAACAAAGACAAGTTCCCCAGCAGTAAATGCGAGCAGGAGGAGCTGGAGAAAGAGAAGCTGGAGCGGGCGCCAGAGACCGCCGAGCAGGGCGATGCGCAGAAGGGTGACAAAAAGTAGGCTCCAGCTGGGACTGCTCGGGCCCGGACTAGCCCGCACGTCCGCCGGTCCCTCCCGCGACCACGCCGCCGCCGCCCGCCCCCCGCCTCCGAGAGCTCCGGCCCCGCGAGCGGAGCCAGGAGCTGGGCCTCCCACCGCAGCGTCCCCCGCCGCGCCAGTCCCCGCTAGTGGTAGTATCTCGTAATAGCTTCTGTGTGTGAGCTACCGTGGATCTCCTTCCCTTCTCTTGGGGGTCCGAGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000007585:ENSRNOT00000009986:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.261 A=NA C2=0.500
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=55.3)
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:
CACCCTTCGCAAATCCAGGAG
R:
AGGAACTCCTTCTCCAGCTCC
Band lengths:
350-1129
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]