RnoINT0071644 @ rn6
Intron Retention
Gene
ENSRNOG00000008365 | Hoxb2
Description
homeobox B2 [Source:RGD Symbol;Acc:2319509]
Coordinates
chr10:84200880-84202688:+
Coord C1 exon
chr10:84200880-84201267
Coord A exon
chr10:84201268-84202008
Coord C2 exon
chr10:84202009-84202688
Length
741 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGT
5' ss Score
8.56
3' ss Seq
CAGGGGTGCTTTCCCCGCAGATG
3' ss Score
10.23
Exon sequences
Seq C1 exon
ATGAATTTTGAATTTGAGAGGGAGATTGGGTTTATAAACAGCCAGCCATCGCTCGCCGAGTGTCTGACTTCCTTCCCCGCTGTCTTGGAGACATTTCAAACTTCATCAATCAAGGAGTCGACATTAATTCCTCCTCCTCCTCCTCCTCTGGAGCAAACCTTCCCCAGCCTCCAGCTCGGCGCCTCCACCCTTCAGAGACCAGGGAGCCAAAAGCCAGCCGGAGATGGGCCTGCTCTGCGGCCACCGCCGCCACTCCCCGTCGCCCCCCCAGCCCCCGAGTTCCCCTGGATGAAAGAGAAGAAATCCGCCAAGAAACCCAGCCAATCCGCCGCAACCCCTTCTCCAGCCGCCTCCTCGGTCCGGGCCTCCGGGGTCGGATCACCATCAG
Seq A exon
GTGGGTTAGCGTGGTAGGGGTGGGGTTAGGGCAGTTGGAAGAGAAGGGGAGAATGTGAGGTGATGGGGAACCTGGTGGGGTTCCCAAGGTCGACGGATATGGGGTTAGGGAAGCAGAGTATCCTGCTGGGGTTCAGGCCTAGCCACTACTAGCACCCTCCACCCCCCCCCCGAAGATTTTGGAAGCTGGTTAAGGGTGGGGAGGGTGCTTTTTTCTTATGTGCTTAGAAGAAACCGATTCGATTGAGGTGTTTCCCCATTTTCTGTGTAGAGGAATGAAGTGTGCCTGGAATTGAATCTGGAGCCTGGAAAAGATGCGAGCCTTCTAGCTCTCCTAAACCTAGGGGAGAAGAGGGAATTCAAAACCTAGGAAGGAAAGGGTTGAAGAACAATCTGTGATCCCTCTCCCCAGGTTGAGTTGGAAAGTTCCGAATTGAGGGGTCCATTGGGAGGACTGGGGGAGGGGGCTTTGAGGTTCTGGGAGCTAAAAGAAATTGCTCCCCGCCCCCTACGTGGCCCGTGGGCGGCTCTGAAGGCACCGATTTGACCCGGGCCGGGTCTGCCTACGAGGAAGAGCGCTAAAAAAAAAACCAAAGACACAGAGGAAAGCCCTGTGGGGGGTGGGGTAGGAGCCTGAGTAGGACTGCTGATAGTCTTTTTAGCCGATGGAGTGCTCCTGGTCTCAGCTAAACCCAGGCTGCGTTTAGACCTCTCTGCTTACACAGGGGTGCTTTCCCCGCAG
Seq C2 exon
ATGGTCCCGGACTGCCGGAGAGCGGCGGCAGCGGCTCCCGCAGACTGCGCACGGCCTATACCAACACGCAACTGCTGGAGCTGGAGAAGGAGTTCCACTTCAACAAGTACCTGTGCCGGCCGCGGCGGGTTGAGATCGCCGCCTTGCTGGACCTCACCGAAAGGCAGGTCAAAGTCTGGTTCCAGAACCGACGCATGAAACACAAGCGACAGACTCAGCATCGAGAACCGCCCGATGGAGAACCAGGCGGGCTGAGCGCCCAGGACGACGCGGGAGAGCCAGCCGAGGAGCCCACGGTCAGCCCCGGCGACGTGGCGTCACATCGGCTGAGGGAAGCCTGCTTTCTCCCAGCCGAGGCCGCACAGGGACCCCGGGGCGCACCGCCGCCGCTGCCTCCTGCCACTGCCCTGGAGAGTGTGGGTGCATCGAGCCCCGGCTGCACAATGCTCAGAGCCGGAGGCCTGCAGAGCGAGCCCCTGCCCGAAGACGCCTGCCCCGAGCGGCAGGATTCGCCTTTCCTGCCGGACCTCAACTTCTTCGCTGCAGATTCCTGTCTCCCGATGTCCGGAGGCCTTTCGCCCAGCCTGCAGGGCTCGCTGGACAGCCCCGTGCCCTTTTCTGAGGAAGAGCTGGACTTCTTCACCAGCACGCTCTGTGCCATCGACTTGCAGTTTCCCTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008365:ENSRNOT00000011213:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.731 A=NA C2=0.615
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=25.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATTCCTCCTCCTCCTCCTCCT
R:
CTTCTCCAGCTCCAGCAGTTG
Band lengths:
351-1092
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]