RnoINT0071647 @ rn6
Intron Retention
Gene
ENSRNOG00000008313 | Hoxb3
Description
homeo box B3 [Source:RGD Symbol;Acc:1310780]
Coordinates
chr10:84193043-84195796:+
Coord C1 exon
chr10:84193043-84193639
Coord A exon
chr10:84193640-84194468
Coord C2 exon
chr10:84194469-84195796
Length
829 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCA
5' ss Score
7.88
3' ss Seq
CTCCCCCTCGGGTCCAGCAGAAG
3' ss Score
3.81
Exon sequences
Seq C1 exon
GTCAGCCGCTTGGAACAGACCCGGGAGGAGGGGGGCAGAAAGGGGAGGGGGGTCCGGCGTGTCACGTGACCCCCAGGGGTGCCAATGTCCGGTCGTGAGGGTATCAGGCCCTTGCAAGTTGCCACCCACTGCCCGGGCCTCGCCCAGCGATGCAGAAAGCCACCTACTACGACAACACCGCAGCTGCGCTCTTCGGAGGCTACTCCTCGTACCCTGGCAGCAATGGTTTCGGCTACGACGGGCCTCCCCAGCCCCCCTTTCAGGCCGCTACACACCTGGAGGGTGACTACCAGCGCTCAGCGTGTTCCCTGCAGTCCCTGGGCAATGCCGCCCCACATGCCAAGAGCAAGGAGCTCAACGGCAGCTGCATGAGGCCAGGCCTGGCCCCAGAGCCCCTGCCCGCACCGCCGGGTTCACCCCCACCCAGCGCCGCACCTACCAGTACCACTAGCAACAGCAATAACGGGGGTGGGCCCAGCAAAAGCGGCCCCCCCAAGTGCGGTGCCAGCTCCAACTCCACCCTCACCAAACAGATATTCCCCTGGATGAAAGAGTCAAGGCAAACGTCCAAGCTGAAAAACAGCTCCCCGGGCACAG
Seq A exon
GTACCAGCTCTCTGCCTTCCTAGTCCATCAGCTTTTGTCCAGCCCAGGAATGCCACTGTTATTATAGCATCCGACCCCAAGGCGCCCACAAGGCGGCCTGAAAACAATATTAGGTGGCTGCCTAGTGTTTTTTAGCTACCTCTCACCACCTGATGACCTCTGACCTGACCAATACCCAGTCCCTCCAACCATCCTCCGCCTGGGCTTTCAAGAGTTTCCAGGAGGTGGGCCTCACAGACCTTCCCAAGGCCGCACTGCCTAGAGGTACAGAGTCATCAAGGACAGATTATTATTAAATATGATTACTGTGGGTATTAATCACCATCGCTCAGGCAGCCTGGGGTCCAGGCCTGCAGCCACTGCAGCCTCCACGTGCCACACTTCCAGGCCCTGCCCACCAGTGTCCAGTCCCCCCAAGGTGTTCCCAAGTCACCTGTCTTGTAAAGAGGGTGGACAGAAGGCAGGAATCATCTCAGACTTAGATTTGGATATATGGGGAGGGGTGCGCGCACACGCAAAAACCTAGCCCTAAATAAATGGCCACGCAGCTCTGTCTGTGTGACATGATCAAATTTTCATAAGCCGGGGCAGTGAGAGGAGAACAGGTCTCTTAATAAATGCCACTATTATAGAGTGTCCGCTAATGCGACGGGAGGTAGGAAGTGGGGGGGTGTAGAGGAGGAGGCGGGGACGCGAAGGGGAGGGCAGCGGGGCCTCCGAGTCCAGGCCTGGATTTATTAAGAAACGATGCATTCAATTTCGGCGTGTTCAGTAATTATCTTTTATTTCATTTTCTCCCCTTCCCACCCCTCCCCCTCGGGTCCAGCAG
Seq C2 exon
AAGGTTGTGGTGGCGGCGGCGGCGGCGGTGGCGGCGGCGGTAGTAGCAGCGGCGGGGGCGGCAGCGGCGGCGGGGGAGGGGACAAGAGCCCCCCGGGGTCGGCGGCGTCCAAGCGGGCGCGGACGGCATACACAAGCGCGCAGCTGGTTGAGCTGGAGAAGGAGTTCCACTTCAACCGTTATTTGTGCCGGCCGCGCCGCGTCGAGATGGCCAATCTGCTGAACCTCAGCGAGCGGCAGATCAAGATCTGGTTCCAGAACCGCCGCATGAAGTACAAGAAAGACCAGAAGGCCAAGGGGCTGGCCTCGTCCTCCGGGGGTCCCTCTCCGGCCGGAAGCCCCCCGCAGCCCATGCAGTCCACGGCCGGCTTCATGAACGCCTTACACTCCATGACCCCCAGCTACGACAGCCCGTCCCCACCAGCCTTCAGCAAAGGCCACCAGAATGCCTACGCGCTGCCTTCCAACTATCAGCCCCCTCTCAAGGGTTGCGGCGCCCCACAGAAGTACCCCCCGACCCCGGCGCCGGAGTATGAGTCCCACGTCCTCCAAGCCAACGGGGGAGCCTACGGGACGCCCACCATGCAGGGCAGTCCTGTCTATGTGGGCGGGGGTGGCTACGCGGATCCGTTGCCGCCCCCTGCCGGCCCCTCCCTCTACGGCCTCAATCACCTTTCCCACCACCCCTCGGGGAACCTGGACTACAACGGGGCGGCCCCTATGGCCCCCGGCCAGCATCACGGACCCTGTGACCCTCACCCCACGTACACAGACCTCTCCTCTCACCACGCACCGCCTCAGGGTAGAATCCAAGAAGCGCCCAAACTGACACACCTGTGATGGGAGGGGCGGGCTGGGGAGGGGGGGGTGAGGTTAAGGGACAGGGAGACCGTGGAACTGGGGGATGGGCGCGGTTTGGAGTCCTGAAAAAGGTATGTGTTGGGGTTGTCGCCAGGCTTCCATTAACAGAAGAGGCCTTGGGGGTGCCTTCCCTGCTCTCAGGCCCCGAGGGGCTGTCTTTTAAGTCCTCCAGGCCTGGTTCCATCTGCCTGCCAACACCCTTGGAAAGGAATCCACAGCAGGTTGGAGACGGGACCACATCAACCCCAGAGTTCCCAGGGTTCCAGCACTACCAAGTTGGAATTCCAGATTGGAGGGGTGAGGTGGAGTCGGGTAGAGAGGGAGCCAAGATAGACAAGCAGGGCAGAGAAGCACATTCAAAACTTAATGGCTTGGCTATCATCAAACAATCAACTTACCTTGCATCTCTGTGGGTAATTCCCCCAAATCTTGATTTTTTTTTTGATTCTCCCTTTCAGTCTCCTTATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008313:ENSRNOT00000011027:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.840 A=NA C2=0.853
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=20.4),PF132931=DUF4074=WD(100=23.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCAAGGCAAACGTCCAAGCT
R:
CCCTTGGCCTTCTGGTCTTTC
Band lengths:
342-1171
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]