RnoINT0071646 @ rn6
Intron Retention
Gene
ENSRNOG00000008313 | Hoxb3
Description
homeo box B3 [Source:RGD Symbol;Acc:1310780]
Coordinates
chr10:84190087-84193639:+
Coord C1 exon
chr10:84190087-84190174
Coord A exon
chr10:84190175-84193042
Coord C2 exon
chr10:84193043-84193639
Length
2868 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
TCTCTTCTCTCGCCCCGCAGGTC
3' ss Score
14
Exon sequences
Seq C1 exon
GAGGGGAGATTTCTCGCCTGCCGCTCGCGCTGGGGCTCGATGTGAATATATATTATGTCTGCCTGTTCTCCCCTCGTCGGTGGCTAAG
Seq A exon
GTAAGCTGGACTGAGAATAGGCTATCATTTGTGAATGGCGGAGAGTATGTCTCAATGATTTATGGCCCATATGACTCCAATCTCGGTTCAAGAAGAGTTCACAAGCTTTAAGCTTCCTTCCACGCAGCGACTGACTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCCTTTCCGCTTTTCTCCTTTTCTCTCTCTTCTCTTCTAGCAGCCTGATCCAGGGCGGAATCCTCTCTCCCCCGTTTGCTAAGAAGAGCCAAACCTTTCTCTTTCCCTTTCTTAATCCTTTTATTTTTCTTCCTTTCATTATTTTTTTTAAAGTCCTGGAAGGTGGCCTGTCCTCTCTCCTGAGGTTTCTTCAGCTATTGTTACCCTTCCCGGCTCTCCCCAGGAGTGTGCCTGGAAAGGTGGGGTTCTGGAGGGGGGGCTTGCCTCCCTTCTCTAGCGAGACCCTGAGGGAAAGCCCGGAGCCACTGTCTCCTTCCCACCCTTCCGAGAAGCCATATGGAGCCTGAATTTTTCCAACATGGAGGCAAGGGAAATAGACTTGTTTGGCTGGGTAGAGCTGTTCCCCACCCCCTCTTCTGGATCCCAGATTTCTGATCCCTGTGGCACCTTCGGGTTCCTTACTGTCCCATTGCGCCAGGCCTCTGTGCCTTCCAGCCTGGAGCCCTGTTAGGCAAAGTCCCGGAGCAGAGTTGCTAAGGCGCCTTTTAATTCGGTTACCTCCAGCGCCAAACTTGCTGCCGCGGAGCTCGGCCCGGGCCCAGCCCGGTGTGCTTGGAACCTGCCGCGGCTAACCAGTTCGGCGTCCGGGTCGGTTTCTCCTCATCTCCTTGAGCCTTGAGCAGGAGGCTGGTAGCTCCTCGCCAGCCACCGCCGCCGCAGCGGCCAGACAGCCCGCCAGCAGCGGCAGCTGGAGGCTCTCCGAATCCACAAACCTTCCTGGCCTTGTCTCACCGCCAGAGGAGTCTCCTCTTTCCTATCAAGTCTCTGGCTCCTTCGCTTCCCACACTCGCCTGGCCTCTGTCCTGCGATGGTTTGGGGCTTACTGCTGGGGGAGCGACAGGAATTTCGGCCCCAGGCGCCTAGTCAAATTACTGGGTTTTTATTTCTTCTTCTTGTTGTTATTATTATTATTATTATTACCATCATCATCGTTATTGCTGTAACAATCATCTAGACTAAATAAAGCCAGGGCCCAGCCAGCTACCCCCCTCCAAGGTTTTTATTTCATTCTCTTCTCTATCTATTAATAACAAACTCAACTGATGTCGGTTAATTAATTCTCCCTTTCAGCCAGGGCTGCTCCGAAGCTAATTTTGGTTAAATCATCAGAGGCTAATGGTAATAATAATAAAAGGATTGGGTCAGCCTGGTCAATTGAACTCCAGTCCTCCCTGGAAGGACCTGCTGCTTTGCAGACCCATGTGTATTTCCAGAAACAAAAATTTCCCAGAAACCAATTGGAACTCAAGGCTACACCAGCTCCCTTTTAAGTACGGATCTGTGTCATAAGGGCAGCAAGCGCGTTTGCGTGTGGGAGGGGCTCACCCCACCTGAAGTCCTTTCATTTTATTTTTATCAAAATAAAACCAGCTGGGCCGAATGGTATTTTAAGTTTTGCCCAAAGCACATGACTCAGCGAGGATCAGTCTGGAGGTTTTAGGGAATTATTCATAGAGGGCTGGAGACGACACAGAGAAAAGGGGAGATATGGTCAGAAATCTAGGAACAAATTCAAAATCCCCTGACACAGTGAGCTTTCAAAAGGCTGTGTTAAAATAGTGACCACAATTTTATTTTATTTTATTTTATTTTTTTGCTGTTGGGAACCTCAGTAAACAGCCTCCCCTTTTGAATCCAGAGACGAATACTGTTCAGATTTTTTTGTGACTCTGTCATCCTGAATAATTCCTCCCATCTCAGTAGAAAAGAGATTCCAGCAGCTGCACAGGTTTTTTTCTTTTTTCTTTTTCTTTTTTATCCTGAGAAATAAAAAACAAAAAACAAACAAACAAAACAAAAACAAAAACAGACTTGTGGAAAGGACAGGGGAGGTCCCACACCAAATGGCCATAGCACCAACCGGTCTTGCCTGGGAACTCTAAACAGTCATGGTCCATTTGGATGCTCCATAGGGGCCTCTGGCTTCTTGGTCCCAGGCCTGCCTGAGCCAAGACTGGAGGTGAAGGTACCTTCAGATGGGACATAGATGGATGAAGCCTGGTTCCACTGCCTCTGAGGTTAAAAATCTTCAGGAATTTTCTGTCTAAGGCTGCTATGATCTTCTTGGAGGGCAGGGTCCCAGATGAACTTGCTTTTCAGTCCGGCTTGGGTCCAAGACCTGCTAGACTTTGCTTAGGTGGAAGGAGAAGGGAGGAAGAGAGACAGGAAGCAGAGAGGCCTCACTAGGGGAAGGAGGACCTCCGGGATGCTTTTATTTTAGAGTCTAATAGTGCCTACTCCCTGGATTGCCCCACCCCAGGGTTGGGGAGTAGGGGGAGGCATAAGGAGAAATTGTAGGAGAGGCAAGAGGTTAGTGCAGGCGCCAGAGAGAGGCGGTGGTCCACGAGGCAGTGGTATTTTATTCCTAAGTATTCACCAAAGGAGTACAGTCTTGATTTTGTAGAAAATGGAAATGGAAATCGGTGTTTTCTTTTTCCCTTTAAAATTAAAGTTGAAGCGAGAAGCATCCATGTCAGGTTAGATACTTGGTCTCAGCGCCTGCTGCAGAGATAGTGGCGAGGGGAGAAGAAAAAGAAAACCTATTGATGTCAGTTCCCTTTTTAGTTCCTAAGATGGATTCGAGGCCCAGTCCTCTTCTCCCCCTCTGTCTCTTCTCTCGCCCCGCAG
Seq C2 exon
GTCAGCCGCTTGGAACAGACCCGGGAGGAGGGGGGCAGAAAGGGGAGGGGGGTCCGGCGTGTCACGTGACCCCCAGGGGTGCCAATGTCCGGTCGTGAGGGTATCAGGCCCTTGCAAGTTGCCACCCACTGCCCGGGCCTCGCCCAGCGATGCAGAAAGCCACCTACTACGACAACACCGCAGCTGCGCTCTTCGGAGGCTACTCCTCGTACCCTGGCAGCAATGGTTTCGGCTACGACGGGCCTCCCCAGCCCCCCTTTCAGGCCGCTACACACCTGGAGGGTGACTACCAGCGCTCAGCGTGTTCCCTGCAGTCCCTGGGCAATGCCGCCCCACATGCCAAGAGCAAGGAGCTCAACGGCAGCTGCATGAGGCCAGGCCTGGCCCCAGAGCCCCTGCCCGCACCGCCGGGTTCACCCCCACCCAGCGCCGCACCTACCAGTACCACTAGCAACAGCAATAACGGGGGTGGGCCCAGCAAAAGCGGCCCCCCCAAGTGCGGTGCCAGCTCCAACTCCACCCTCACCAAACAGATATTCCCCTGGATGAAAGAGTCAAGGCAAACGTCCAAGCTGAAAAACAGCTCCCCGGGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008313:ENSRNOT00000011027:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.840
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]