HsaINT0077298 @ hg19
Intron Retention
Gene
ENSG00000108511 | HOXB6
Description
homeobox B6 [Source:HGNC Symbol;Acc:5117]
Coordinates
chr17:46673099-46675590:-
Coord C1 exon
chr17:46675098-46675590
Coord A exon
chr17:46674035-46675097
Coord C2 exon
chr17:46673099-46674034
Length
1063 bp
Sequences
Splice sites
5' ss Seq
ACAGTGAGT
5' ss Score
8.34
3' ss Seq
ATCTCCACTCTGCGTAACAGGTT
3' ss Score
6.38
Exon sequences
Seq C1 exon
GCGCGGCGCTCGGACTATAAAACACAACAAATCATAAACCCGGCGGAGCAGCAGCGGCCGCGCGCGCCTCCCCTCCCAATGAGTTCCTATTTCGTGAACTCCACCTTCCCCGTCACTCTGGCCAGCGGGCAGGAGTCCTTCCTGGGCCAGCTACCGCTCTATTCGTCGGGCTATGCGGACCCGCTGAGACATTACCCCGCGCCCTACGGGCCAGGGCCGGGCCAGGACAAGGGCTTTGCCACTTCCTCCTATTACCCGCCGGCGGGCGGTGGCTACGGCCGAGCGGCGCCCTGCGACTACGGGCCGGCGCCGGCCTTCTACCGCGAGAAAGAGTCGGCCTGCGCACTCTCCGGCGCCGACGAGCAGCCCCCGTTCCACCCCGAGCCGCGGAAGTCGGACTGCGCGCAGGACAAGAGCGTGTTCGGCGAGACAGAAGAGCAGAAGTGCTCCACTCCGGTCTACCCGTGGATGCAGCGGATGAATTCGTGCAACA
Seq A exon
GTGAGTGAGACTTCCCGTCGCCGTCGCCCCGGCTCCCCTGGGCGCCCACCCCGGGACACAGAACTAGTGAGCGCCCCCTGCCCCAATCTCCCACAGGGTGCTGGGTGGGCATCTCAGTTAGGAGATAGAAGAAGATTGGGCGCCGGCCGGGGGTCTCTCGCTGTGTCCCCTATTAGGCAGGAGTTACAAAGTTTGCAAAGTCCCAGCCGCACTGGGAGCCATGGGGAGCAAGTGTGCTCTCCTGGGGCGCCTGGCCAGAGCCGGGGTTCCAGGACAGGGAAGGGAGCAGGAGCCTGCAGTCACTGGCTTGGCTTTACTTTGAGCCCCCAACCCCCCTCTCCCAGCCCTGGTAGGGTTCCCCAACCAAAGACGGCTCCATTAAAAACGGAGTGCGTCATGCAAGGGGGTAGGGGGTGACGCTGAAGAGAAAGAGTTGAGTCTGTCTGGGACTGTGTTTCCCTGTGGGTGGGGAGCTGGGGCAAGATGAGGCACCAGGAAAGGGGTGGTAGTCAGAGGAGGGAGGAGGAATAAGGGGAAGGAAGAGAGAGGGAGCAGGCGGAGCGAGAGAGGGAGAAACAGGCGCGGGGTCTCAGGTTGGATTATTTGTTGGCCTTAAGTCCCAACTGATGTCCATTAGCCGGACTCGAAAGTGAGGAGCCGTTAATGTGGACTATGGATCGATCTACGTCATTACGGATTAACGGCCTGGATTTATCATTGGGTTGGGGGGATGACGGGGGGTGGGAACAAGATGGATGGAAAGGGAGGGAAAGACAAGATGCAACTAGGAAGAGACACACCTGACCAGCCCCTCCCCCCAGGCTCAGGTGGGAGTTCAAACTGCTCCTCCCCTCCCCCATCTAGAGTCTAGACAGACGGCACAGGCCTAGGAGACTAGGAGGGAATCTGGAGGGGGCGCTGGAGGAGTGCGAAACGGGGGAAGGGAGCCGGCAGAATAGAGGGCATCCCGGTACTGGCTGGAGTCTGTGTTCGAGGGTCGACTAGGGGAGGGGGTCCTGGGCCCGGTGACCGCAGGCCTCAGCATCTCCACTCTGCGTAACAG
Seq C2 exon
GTTCCTCCTTTGGGCCCAGCGGCCGGCGAGGCCGCCAGACATACACACGTTACCAGACGCTGGAGCTGGAGAAGGAGTTTCACTACAATCGCTACCTGACGCGGCGGCGGCGCATCGAGATCGCGCACGCCCTGTGCCTGACGGAGAGGCAGATCAAGATATGGTTCCAGAACCGACGCATGAAGTGGAAAAAGGAGAGCAAACTGCTCAGCGCGTCTCAGCTCAGTGCCGAGGAGGAGGAAGAAAAACAGGCCGAGTGAAGGTGCTGGAAAGGGAGGGAGGACGCGAGGGGAAAGGCCTGTGGGGAGCCGAGGGCGTCAGAGAGACCCGGGAAGGAAGGCTCTCGGGTGGGGGAGCCAGGAGACCTGCTCTCCGGCGCAGACAGGCGGGGCCCAGCGCTCTCCTGGACGCCCCCGCCCGCACAGCTCCCGGCGGGTGCTCTGAGGCCTCACTACTCGAGCCCACCCAGCATCCCGCGCGCCCTTCCTTCCCGAGGAACTCGCCTCAGCCTGATCAGGCTTCCTGGTGAGAACTGAGGAGCGGACTCACTTGATGTTTCCTGGAAGCAGAGCAAAATGCTCTTGTCCCTGTCGCGTCTCATTTTGTCCATGTCCCCCGTGCACGGTTCAATGGTAGATTCGCTGTCCCCTCAGCGGGGGCCTTGAAGACTCCCTGATCCCAGACCTGTCGTCTCTCCCACCCCCTCCCCAAAGCCACTGGAAGGAGCACATACTACCTAGAAGTAAGAAGAGGAGCCTCAGAAGAAAACAAAGTTCTATTTTATTAATTTTCTATGTGTTGTGTTTGTAGTCTTGTCTTAGCTCTGGACGTGAAATACTTCGATGATGATGATGATGATGATGATGATAATAATAATAATAATAACAACAACAACAACAATAATAAAGATGTGAAAACTCGACGCTCGGTCACCTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000108511-HOXB6:NM_018952:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.302 A=NA C2=0.267
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=65.5)
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:
GTGTTCGGCGAGACAGAAGAG
R:
CCCTTTCCAGCACCTTCACTC
Band lengths:
351-1414
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)