HsaINT0077300 @ hg19
Intron Retention
Gene
ENSG00000120068 | HOXB8
Description
homeobox B8 [Source:HGNC Symbol;Acc:5119]
Coordinates
chr17:46689708-46692301:-
Coord C1 exon
chr17:46691643-46692301
Coord A exon
chr17:46690872-46691642
Coord C2 exon
chr17:46689708-46690871
Length
771 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
GCCCTTTCCCCCATTCCCAGCAG
3' ss Score
6.95
Exon sequences
Seq C1 exon
CCTTTTCTATTCCTGGAAACCACAAAAAGTGTGTCGGCTTCGAGATCTTCTTCGCCTTTTCTTTCTTTTCTTTTTTTCCCTCCTCTCTTTCCCTCTCCTTTCCTGGCGAGGGTGACTAGGAGCCGGCGAATCCGCGTTTTTTTCTCTCTCTCCCTCCCTTTCCCCCTCCCCACCCCCTCCCCAACAGCCCCCAACTATAGCCTCCGCCGCCGCCGCCGCCTCAAAATTCAATAAAATGAGCTCTTATTTCGTCAACTCACTGTTCTCCAAATACAAAACCGGGGAGTCCCTGCGCCCCAATTATTATGACTGCGGCTTCGCCCAGGACCTGGGCGGCCGACCCACCGTGGTGTACGGTCCCAGCAGCGGCGGCAGCTTCCAGCACCCGTCGCAAATCCAGGAGTTCTACCACGGGCCGTCGTCGCTGTCCACGGCTCCCTACCAGCAGAACCCGTGCGCCGTGGCGTGCCACGGGGACCCCGGCAATTTCTACGGCTACGACCCGCTGCAACGCCAGAGCCTATTCGGTGCGCAGGATCCAGACCTGGTGCAGTACGCAGACTGCAAGCTTGCCGCCGCCAGCGGCCTGGGCGAGGAGGCCGAGGGCTCCGAGCAGAGCCCGTCGCCCACACAGCTCTTCCCCTGGATGCGCCCGCAAG
Seq A exon
GTGAGCTCGCCTCGGGGCCGACAAGGGCAGGAGGGGGCCGGAAGGGCCCAAGGCCTGGCAGGCCGGGGCGCATTTCCTCCAGCTTCTGGAAGACTTGCCGGCTCCGTTCCGATCGCCTGCCGCTTTTCCCCTTTCTTTCTTATCTTTCTTTCTTCTTTCTTTTTTCTTTCCCTTGAAGGGGGTCGCTTAGAAACATTTCCTGAATCTATAAACCCCTCATCCTGCCTTACTTTTCTTCTTCTTCTCCTCCTTTTTTTCCCCTTTTACTGTTTTATGGGGGGTAGTGAAGAGAGGGTGGTGGGAGTGGGGGCGCTCAACTTTTGCACTTCTCAATTGCTTTATAGTTTAATTACCCTGAAGAAACTTTTCTTCTGGGGCAGAGGCTCTGGGGGCTTTTCAAGGTGGGTCCATTCGTCCCCACCCGGCTTTTTTATTCTTATTTTCCCCCCTCCTTCACATCCTTCCTCCTAAAGTTTATGGCACTTCTAATAGATCTGAACCACCTCCTACACAACTCTGGTGCTGGTTACCGGGGGAGGGGGCTCCCCTTTCTGGCTCCCTTAGATTCACTTGTGTCTAATCCCCCTCGCCCCTCCTCCTCCGCCGACCGCGGCCTTCTTGCGCCCCCCCCGCCCCCGCACGGGGTAGAAGGTCCCCTGCCCTTATTATAATGGTCTCCCAGGCTCGTTCACGAATCTTCCAACCTTCTCCGTCCCTGCCCCCTCCCCCACCCTCCCCTCCCCTCTGTCTCGCCCTTTCCCCCATTCCCAG
Seq C2 exon
CAGCCGCCGGACGCAGGCGAGGCCGACAGACCTACAGCCGCTACCAGACCCTGGAGCTGGAGAAGGAGTTCCTATTTAATCCCTATCTGACTCGTAAGCGGCGAATCGAGGTATCGCACGCCCTGGGACTGACAGAGAGACAGGTCAAAATCTGGTTCCAGAACCGGAGGATGAAGTGGAAAAAAGAGAACAACAAAGACAAGTTCCCCAGCAGCAAATGCGAGCAGGAGGAGCTGGAGAAACAGAAGCTGGAGCGGGCCCCAGAGGCGGCGGACGAGGGCGACGCGCAGAAGGGCGACAAGAAGTAGGCTTCAGCTGGGACTGCCAGGGCCGCGGCCGCCCGCACGTCCGCGGGTCCCGGCCGCGCCGCCGCCGCGCGCCCCTGCCCGAGAGAGCTCTGGCCCCGCTAGCGGGGCCAGGAGCCGGGCCTCCCACCGCAGCGTCCCCCGCCGCGCCAGTCCCCGCTAGTGGTAGTATCTCGTAATAGCTTCTGTGTGTGAGCTACCGTGGATCTCCTTCCCTTCTCTTGGGGGCCGGGGGGAAAGAAAAGGATTTAAGCAAAGGCTCCCTCGCCCTGTGAGGGCGAGCGGCAAAGGCCCGGCTGAGCCCCCCATGCCCCTCCCCTCCCCGTGTAAAAAGCCTCCTTGTGCAATTGTCTTTTTTTTCCTTTGAACGTGCTTCTTTGTAATGACCAAGGTACCGATTTCTGCTAAGTTCTCCCAACAACATGAAACTGCCTATTCACGCCGTAATTCTTTCTGTCTCCCTTCTCTCTCTCTCTCTCGCTCGCTCGCTCTCGCTCTCGCTCTCTCTCGCTGCGTCCTCATTTCCCCTCCCAATCCTCTCTCCCCTCTGCAACCCCCCAGCTCGCTGGCTTTCTCTCTGGCTTCTCTCTTTTCCTCCTCCACCCACCCCCTTTGGTTTGACAATTTTGTCTTAAGTGTTTCTCAAAAGAGGTTACTTTAGTTAGCATGCGCGCTGTGGGCAATTGTTACAAGTGTTCTTAGGTTTACTGTGAAGAGAATGTATTCTGTATCCGTGAATTGCTTTATGGGGGGGAGGGAGGGCTAATTATATATTTTGTTGTTCCTCTATACTTTGTTCTGTTGTCTGCGCCTGAAAAGGGCGGAAGAGTTACAATAAAGTTTACAAGCGAGAACCCGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000120068-HOXB8:NM_024016:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.261 A=NA C2=0.500
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=55.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGTCGCAAATCCAGGAGTTCT
R:
AGGAACTCCTTCTCCAGCTCC
Band lengths:
346-1117
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)