RnoINT0071648 @ rn6
Intron Retention
Gene
ENSRNOG00000008191 | Hoxb4
Description
homeo box B4 [Source:RGD Symbol;Acc:1560113]
Coordinates
chr10:84167331-84169907:+
Coord C1 exon
chr10:84167331-84167994
Coord A exon
chr10:84167995-84168808
Coord C2 exon
chr10:84168809-84169907
Length
814 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGT
5' ss Score
9.89
3' ss Seq
CTCTCTCTGTGTGTGTCCAGTAA
3' ss Score
7.84
Exon sequences
Seq C1 exon
GGAAAATAAACCTCTTTGGCTGGAGTAGGGTCCGGGTGAGCAGATTTCCTTATCCGGGAATCGCAGGCCGGGTGGCCATTGGCTCGGAGGATCACGTGGGCCTCTAACTTTGTTCACTTGACAGTAAGTAGGAGGGCTTTCGGAAACAGGAAAACGAGTCAGGGGTCGGAATAAATTTTAGTATATTTTGTGGGCAATTCCCAGAAATTAATGGCTATGAGTTCCTTTTTGATCAACTCAAACTATGTCGACCCCAAGTTCCCTCCGTGCGAGGAGTATTCACAGAGCGATTACCTACCCAGCGACCACTCGCCGGGGTACTACGCCGGCGGCCAGAGGCGAGAGAGCGGCTTCCAGCCGGAGGCGGCCTTTGGGCGCCGGGCGCCGTGCACTGTGCAGCGCTACGCGGCCTGCCGAGACCCCGGGCCCCCGCCACCTCCGCCGCCCCCGCCGCCCCCGCCACCGCCCGGGCTGTCCCCTCGGGCTCCCGTGCAGTCAACAGCCGGGGCCCTCCTCCCGGAGCCCGGGCAGCGCAGCGAGGTGGTCAGCAGCAGTCCCCCGCCGCCTCCCTGCGCCCAGAACCCCCTGCATCCCAGCCCGTCCCACTCCGCGTGCAAAGAGCCCGTCGTCTACCCCTGGATGCGCAAAGTTCACGTGAGCACGG
Seq A exon
GTGAGTGCGTGGGCACCCCTTCCCCTCCCACCCCAGGCGCTTTACAGTGAAGGGACCTCCAAGGCATGTGGGGGAGGGAGCTGGGGGAAGCCAATTGTCCCCGCTATAAACTCGCCATTGCCAGAGATTTACGGTCTCCTGTTTTCAGAGCCACATAATTACATCGCCCATAAATTTTTATGGCCTAGTGGGCCCTGCGCCTTTGAAGTCATCCTCTTCTTCATTCTCCCAGTGACTTTTTCGCCAGGGATATGCAGTCCCAGTAAAGTTGGAAGTTGGGGAGGGGTGTGGGAGGAGGGGAGAAGGAGGAGGAGGAGGAGGAGGTAGAAATCCGTATTTAAGCAGAGAGTTGAATCAACTTCCTGTATTTCTTTTTTTGCCCCCTTTCTTCCAATCTGGTACCTTGGCTGGAGAAGTGGGCAAAAGTTTTTACTGAGGGGAAGGCGCTGCTTGGAATCTGAGCAGTGAGGGTGGGGACTAAGCCCCGGAAAGGTCTAGGGCAACACCCCTCCCACTCCCACACTTCATTCTCTCACCCGGGGTCCTCAGGCCAAAGAGTGAGATGAAAATCTTTCCAAGATTCCTCACAGTGCCCCCTCCCCCAGGCAACAAGGACAACAACACAGCTCTCCAAAAGTTTGAGGCTTTTTCTTTTCTGTGTGTTCCAATGTCTTCCTTTTTCGATGGCCTCCCTCCAAGATGAGGTAGTGGGAGCTGGAGGCTTGGTGTTAGCTGGAAGAAAGAAAGGGTTTTCCCTCCTCCCTTTCGGGGGCAATAAAACTTTCTCTTTCTCCCTCTCTCTGTGTGTGTCCAG
Seq C2 exon
TAAACCCCAATTACGCCGGCGGGGAGCCCAAGCGCTCCCGGACCGCCTACACTCGCCAGCAGGTCCTGGAACTGGAGAAGGAGTTTCACTACAATCGCTACCTGACGCGACGCCGGAGGGTGGAGATTGCCCACGCGCTCTGCCTGTCCGAGCGCCAGATCAAGATCTGGTTCCAAAATCGGCGCATGAAGTGGAAAAAAGACCACAAGTTGCCCAACACCAAGATCCGCTCGGGTGGTACCGCGGGCGCAGCCGGAGGCCCCCCTGGCCGGCCCAACGGAGGCCCCCCTGCGCTCTAGTGCCCCCCAAGCAGGAACTCGAACTTGGGGGGCGGGGGGGGACTGCGAACACCGAAGGGGGTATGCGGGGTATGGGAAGGTCCCCAGGCTTGAGCCCAGAAAAACCTATCTACCCTACCCCCACTTTATCTATAAGGAATAAACGCAGAGAAGGGGGGTAGGGAAGCCTTATTTATAGAAACGACAATAGGGAGCCGGGTAAAGTCCTCCGGAAGCAAGATTCGAGTCTCTTGCTTTCTTCCTTAAAAAAAGAGAGAGAGAGAAAGAAAAGAAAAAAGAAGAAAGAAAGGAAGAAAGAAAGAAAAGGAAGAAAGGAAAAGACAGAAGAGAAATGGAGAGGCTTTTGCGCCTGGCTTTCAGCTTTGGTGAAGATGGATCCATGTTTCATCTTTAATCATGCCAGGCCTCGGCCCATCTGTCTTGTTTACTCCGCCGAGGAGAAGACGAGCTTCGGTGGCGACCATTACCTCGACACTTGGCTAACAAATGAGGCCGGCTCGGCCGCTGCCGCTGCCTTTGCTGCTGCCGCTGCTGGACCACAGCCTGGATTTTCTTTCTTTGTCCCTTATTCCTGACACCCAGCGAATGCACCCTCAGACTGCCAGATAGCACAGTGTTTTGGCCACGGTAACAAACACACACACACACATAACTTTCCTCCCTGTCTGTGCCCACTTTGGGGTGGGGGTGGGAAGACCGCTCCCCTCCCTTCCACCATAGACTTAGAAGGGGAAAAAGAAGGGAAGCGAGGGGTGGTCTGCACAATGTGGGTTCCCAAATCTGAACCCAAGAAATAAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008191:ENSRNOT00000010965:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.717 A=NA C2=0.596
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=57.0)
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:
GATGCGCAAAGTTCACGTGAG
R:
AAGTTCGAGTTCCTGCTTGGG
Band lengths:
351-1165
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]