RnoINT0071653 @ rn6
Intron Retention
Gene
ENSRNOG00000007573 | Hoxb9
Description
homeo box B9 [Source:RGD Symbol;Acc:1306158]
Coordinates
chr10:84119884-84123390:+
Coord C1 exon
chr10:84119884-84120400
Coord A exon
chr10:84120401-84122970
Coord C2 exon
chr10:84122971-84123390
Length
2570 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
TATCGCTACTTCTCTTTCAGCCA
3' ss Score
8.02
Exon sequences
Seq C1 exon
ATGTCCATTTCTGGGACGCTTAGCAGCTATTATGTCGACTCGATCATAAGTCACGAGAGCGAGGACGCGCCTCCAGCCAAGTTTCCTTCGGGCCAGTACGCGAACCCGCGGCAGCCGGGCCACGCCGAGCACCTGGACTTCCCCTCGTGCAGCTTCCAGCCCAAAGCTCCGGTGTTCGGCGCCTCCTGGGCGCCGCTGAGCCCGCACGCTTCGGGGAGCCTGCCGTCGGTCTACCACCCCTACCTGCAGCCCCAGGGCGCGCCGGCGGCCGAGAGCAGGTACCTCCGTACCTGGCTAGAGCCGGCTCCCCGCGCCGAGGCCGCCCCGGGGCAGGGCCAGGCGGCCGTGAAGGCGGAGCCGCTGCTGGGCGCGCCCGGGGAGCTGCTTAAACAGGGCACGCCCGAGTACAGTTTGGAAACTTCGGCGGGCAGGGAGGCTGTCCTGTCTAATCAAAGAGCCGGCTACGGGGACAATAAAATTTGCGAAGGAAGCGAGGACAAAGAGAGGCCGGATCAAA
Seq A exon
GTAAGTTATAAAAAAAAAAGTGAGGAAATCCCCCCCAGGGCTGCAGTCCAGGCCGGGGGAGGGGAGGGGAGAGGCCATAAACCGGACAATGTAAAGGGACAGCGCGCCTGGGGCCGCAGGGCTAGAGGGGGTGGAGGGAAGAGGAAGGAAGGGACCGGGAAAGGAAAAAGCTGGGTGTCCAGGAGGCTGGGTGTCCACTGAGGCTGCCCTTCACCCTTTTAGTAGTGCAGGGACTGAGACTCAGGACCAAGTCTCTCTATCCCATCTTCCTTCTTCTCCAGGCTGGGGCTGGAAACAAGGAAAGGGACCTGCGACAGTCCAGTGAGGAACTGTAGGGGGCCGGGCCGACGGCCAGCGCGGCCGGCCGGGAGCCCGCGCGGGCACGGGGCCGAAGCGCACCCGGCAGAGCCGCCTGCGCCACGCGCAGATCGTCCCCACCGGCCAAGGGGAAGGGGGAGGGGGCTCATTAGGATTTTATTTGCGAGCAACAGCTTGGCGGAGAATTGTTCCTAGCAGATCTCACGCAGTAGCCGCGTCCGGTCGGCAGCAGGCGCCGGGAGGGGCGGGGGAAGCCCAGGAAGCAGTGACGGAGCCCCCTCCCCAGTGCGCCGGCCCCTCCCCGGGAGCCTTCCCTCGGGGTCCCCCGCCCTTCTAGGGCATCCTGCACAGGGTGGCCCGTTTCTCCTCCTGCGGTTCCCGCTGATCTCCGCGGGGCTTCTGAGAACTAGCCGGGCAGTCCACCTCTTGGAGAGTCTAGGCATCATTTGCTAAAGACAGGGCCTCCCTCTAGAAAGGAGGAGAAGACACCCGAAGGGACCTGGGGGAGGGAGGGGGAGGACTGCGCAGGGGCGGAGAACTCTACCCTTGGTGGAGTTTCTTACCACCTCCCACTCCTAAAAGCACCCTTGCTAAAATAAATCCCCAAGTGCTGCTGGCTGAGAGGAGAGGAGGCTTACTTTTTTTGTTTGCTTTTATGAATGGAGAAGACAAACTGGTTAGGGGCACGCTCTTGGTCCCAAACAAAACCGGACAAACTGCAGGTCAACTCCTCACCTCTTTCTCCTCTGGGCACATAGTTTGGTCCTTGCATCTCCCTATCAGATGTCCCACCAACAGAGTGGCCAATGGGTCTTCTGGGGGCATGTTTGCCCTCTGAAAAGCAAGGAGAGACACTACTCCCCCGTGACCCTTGTGGTCCCCTCATACCTCCAACTTGCCAGGTTGAATCATTAGGAGTTTATATCCCAAAACAGCTCTTCCCAAACCTCCAGCAAACACCCAAACAGACCCCCTCACCCCATGGCCCCAAACTCTCAGCCTGGAAGGCCCATTATTGTAAGGCAGCCATTTGGCTAGGATCAATTATTAACAGTTTTTTTTCCTCTTTCATATTTAATGAAAGAGGAAAAGGCTGCGGGTCCCATCCCAGGCAATCACATTAAGGGAATAGCGCTGCAAATTGGTAAGACACGCTACTTAGTGTAGAATTGAAGTGAATTTAAAAACATATACATATACATAGATATTCAGAGCTTTTCATTTGGGGGAAGCTGGTGGAGTGCATCTTACTTGGAATTGGCTCCGCTTTGGGGAAGCGGGCAACTTTCCTGAGTCCTGAGGTCTAGGGAGAGATGCTGGATAGAAAAAGAAAAAGAAAAAAACAAAAACAAAAACGCTGTATATGTTATTTGCTCTTTGTGCCCCTTTCCACTCAATTACACTTTTCTCTGCCTCTCCACTGGGTCAGCTAAAAGGGTTGGTGTGCTGTGAGGGGCTTTCTGCTATCCTGCCTCATTTCTGCTTCCCCACCTTGGAGCTGGAGCAATTTTGCTTCCCAGTCTCCCTGAACTTGTGTTAACCAAACTGAGCTGAGTAGCAGAAAGGAAGAGGCTATTGCCACCATAAGTTATCTGGAAGCCCTGGGGCTCCCCATCCATGGGCTGCAATTGATAAATGGTTGCAATTGGGTCGCTTGTGAGTTGGAGTGTGCTGGGTGTTCGTGGCTGTAAATGCAGGCTCTTATTTGTGGGGTGTGATGGGGAGGGCTGTCTACCCAGACTCACATGTCTGCTGCCTAGGCCCTGGGCTGAAAGAGAGCTTTCTAAGCAGGGTTCGCTGGAACTGGACTGAAGCATCAAGAGATCTCTTGGCTGTGGCTGAACAGAATTTCACTCCTTACCACTTCTTCCCCCCTTCCCCTGAAAGCTAGAGCCAAGGAACCCTTCAGGTCATCCACCTTTAGCTGGTGGTGTGATTCCAGCTCTACTGAGCTCCTCTGATCTGAGTCCAGGTCTGTTTGGACACAAATAGAGGAAGGCTGAGATGCCTGGAGCAGTCCAAGCTTTGGAGATGCTTAGGTAGTTGAGCAGCATCCCCTTCAAAGTACTATTCCCTTGGAGCTGTCCATATTCCTTCCTCCTGGCCCAGTTAGAGATACTTTCTGAGGTCTTGGAGGCCCGGGTGTCTTTCTCCAATGCCAGACGGGGAATGGATGTGAGCACACATACCTTCTTGGTCTGGGGCCCTCCACTCCCTTCCTCTCTTTGATTCTATCGCTACTTCTCTTTCAG
Seq C2 exon
CCAACCCCTCTGCCAACTGGCTGCACGCCCGCTCTTCCCGGAAAAAGCGCTGTCCCTACACCAAATACCAGACGCTGGAGCTAGAGAAGGAGTTTCTATTCAATATGTACCTCACCAGGGACCGCAGGCACGAAGTGGCCAGACTCCTCAATCTGAGTGAGAGACAAGTCAAAATCTGGTTTCAGAACCGGCGGATGAAAATGAAGAAGATGAATAAGGAGCAGGGCAAAGAGTAAAGATGACCCCACCTCTCCCCAGCTCACTCTTACTATTTATGTGTTGGCTGGAAAAGCCACTGCTGTCTGGGTTGTACCCAAGTGAGTGGGGAAGGGTATCTCCTCTTTAAAGCCCCTCATCTGCACCTGGAGCCCGGCTCCTCTCCTTTGCCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000007573:ENSRNOT00000009951:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.647 A=NA C2=0.308
Domain overlap (PFAM):
C1:
PF046178=Hox9_act=WD(100=99.4)
A:
NA
C2:
PF0004624=Homeobox=WD(100=72.2)
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:
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]