RnoINT0071649 @ rn6
Intron Retention
Gene
ENSRNOG00000008010 | Hoxb5
Description
homeo box B5 [Source:RGD Symbol;Acc:1562292]
Coordinates
chr10:84152152-84154360:+
Coord C1 exon
chr10:84152152-84152832
Coord A exon
chr10:84152833-84153507
Coord C2 exon
chr10:84153508-84154360
Length
675 bp
Sequences
Splice sites
5' ss Seq
ACGGTAATT
5' ss Score
7.31
3' ss Seq
CTCTCCTCTAACTGCTCTAGATA
3' ss Score
7.99
Exon sequences
Seq C1 exon
CGCATACATAGCAAAACGAAGTACAGTGCATCGCTATAATTCATTAATACATCATAAATCGTGAAGCACAGGGTTATAACGACCACGATCCACAAATCAAGCCCTCCAAAATCACCCAAATGAGCTCGTACTTTGTAAACTCCTTCTCGGGGCGTTATCCAAATGGCCCGGACTATCAGTTGCTAAATTATGGCAGTGGCAGCTCTCTGAGCGGCTCTTACAGGGATCCCGCTGCCATGCACACCGGCTCTTACGGCTACAATTACAATGGGATGGATCTCAGCGTCAACCGCTCCTCGGCCTCATCCAGCCACTTTGGGGCGGTGGGCGAGAGCTCGCGCGCCTTCCCCGCGTCCGCCCAGGAGCCCCGCTTCAGGCAGGCGACATCCAGCTGCTCCCTGTCCTCGCCCGAGTCACTGCCCTGCACTAACGGCGACAGCCACGGCGCCAAGCCCTCTGCTTCGTCCCCTTCCGACCAGGCGACCCCAGCCAGCTCCAGCGCCAATTTCACCGAAATAGACGAGGCCAGCGCGTCCTCTGAGCCTGAGGAAGCTGCGAGCCAGCTAAGCAGCCCGAGCCTGGCTCGGGCACAGCCAGAGCCCATGGCCACCTCTACAGCCGCGCCCGAGGGGCAGACTCCACAGATATTCCCCTGGATGAGGAAGCTTCACATCAGCCACG
Seq A exon
GTAATTCTCCATCTCTCTCTCTTTTTTGTCCTCTCGGCATTCCTGCCCTGTGCTGGGGGTGGGGGCGAGCAAAGCTTGGCTTTGCCTCAAATATAGATTCCTTTTTTTTTCCACCAAGAGGGAAAAGTGTCCGAAACCGTCCCCATAGCTCCATAGATAGAGCCAAACAGGATCGTTTTCTGAGGGTAAGCATTAAAAAAAAAATGTTGCCACGGTCAGCTTAGGTTTTATTTACCCAGCCAGTAGTCACCGGCTTTAGGATGAAAGATGGGATTTGTGTATTGTGGGGAAAGGTCCTGATTATTACTGAAAATTTGAGACTGCTGCTAGCAAAGGGGGAATGGGCTGTAGATAGAGGTTACTAAGGCAAAAGTGTAGCGGCTCTCTTCCCTCCCGGACGAGCTGAGCTGCCGCCTGAACCCAGCCTAGGGTGAGGCACTGGGATGGAGTCAGAGACAAAGCCGGGAGCATGCACTACCATCAGAAGTGGGGGCTGCTGAGAAGGGGGATGAGGAAATAGAGGCTGGATGCGGGCATCTGGAGTGAGGAGGATTGGAGCTGCGGTGAGCTGGATGCTGGGGACGCCTGGGTCCTGCTCCCCGCCCCCTCCCACTCAGTGCCCCCTCCTTTAACCGGAATAACATTGCCTCCGGGGCTCTCCTCTAACTGCTCTAG
Seq C2 exon
ATATGACTGGGCCAGACGGAAAAAGGGCCCGGACCGCCTATACTCGCTACCAGACCCTGGAGCTGGAGAAGGAATTCCACTTCAATCGCTACCTGACCCGGCGGCGACGGATCGAGATCGCCCACGCGCTTTGCCTGTCCGAGCGTCAGATCAAGATCTGGTTCCAGAACCGTCGCATGAAGTGGAAGAAAGACAACAAACTGAAAAGTATGAGTTTGGCTACAGCCGGCAGCGCCTTCCAACCCTGAGCCCATCCCGAGGAGCCCTGGGAGGCCCAAGAGCCCGCACCACGCCCAGCCCGACCCTTCCAATCTTCCCTGCACTGCCGCTGCCCGCTGGGGACCAGTTCCCACGCGCCTGTCCCACCCCAGCCCTGTGTTACAATTTTTCGTTTGGTCTTAGGTCTTCCCATGGCTCCCTCTCTCCTGGACTGGTTATTCTTGTTATTATTGTTAATAATAATAATAATAATTATTATTATTATTTCCCCTCCGTGCTCCCCACTTCTCTTGGCTCGCCCCCAAGTTGCCAGTGTTTCTGAATGTCCTCGTGTCTGTGGTTGCGCTCCTTTCCCCAGGAAAAAGAAAAGAAAAAGAAATTCGCATGTTTAATGTGACTTCCCACTCCCTGTCTGTGTTCTAACTTATTTATAAAAGGATGATGGCTGTATTTTGAGTTTCTGCTGGAAACTTCCATGGGGGGTAGCAGTTGAGGTTGGGTAGTGCTGGGCCCAGCTGAGCTGGCCTAGGGAATGGAGTCCATGACTGTGCTCCCACTTTTCTCCCACTTCAGCAGCCCCACCCCCCACCCCCACTCCCTAGGCTCAGGTAGCTTGTTCCTTGGGGTGGGAAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008010:ENSRNOT00000010724:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.707 A=NA C2=0.195
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=68.7)
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:
TTCCCCTGGATGAGGAAGCTT
R:
GTGCAGGGAAGATTGGAAGGG
Band lengths:
357-1032
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]