HsaINT0077294 @ hg19
Intron Retention
Gene
ENSG00000182742 | HOXB4
Description
homeobox B4 [Source:HGNC Symbol;Acc:5115]
Coordinates
chr17:46652869-46655743:-
Coord C1 exon
chr17:46655225-46655743
Coord A exon
chr17:46654383-46655224
Coord C2 exon
chr17:46652869-46654382
Length
842 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGT
5' ss Score
9.89
3' ss Seq
CTCTCTCCGTGTGTGTCCAGTAA
3' ss Score
7.11
Exon sequences
Seq C1 exon
GGAAAACGAGTCAGGGGTCGGAATAAATTTTAGTATATTTTGTGGGCAATTCCCAGAAATTAATGGCTATGAGTTCTTTTTTGATCAACTCAAACTATGTCGACCCCAAGTTCCCTCCATGCGAGGAATATTCACAGAGCGATTACCTACCCAGCGACCACTCGCCCGGGTACTACGCCGGCGGCCAGAGGCGAGAGAGCAGCTTCCAGCCGGAGGCGGGCTTCGGGCGGCGCGCGGCGTGCACCGTGCAGCGCTACGCGGCCTGCCGGGACCCTGGGCCCCCGCCGCCTCCGCCACCACCCCCGCCGCCCCCGCCACCGCCCGGTCTGTCCCCTCGGGCTCCTGCGCCGCCACCCGCCGGGGCCCTCCTCCCGGAGCCCGGCCAGCGCTGCGAGGCGGTCAGCAGCAGCCCCCCGCCGCCTCCCTGCGCCCAGAACCCCCTGCACCCCAGCCCGTCCCACTCCGCGTGCAAAGAGCCCGTCGTCTACCCCTGGATGCGCAAAGTTCACGTGAGCACGG
Seq A exon
GTGAGTGCGTGGGCACCCCTTCCCCCTCCCACCCCTGGAGCTTTACACCAAAGGGACTTCGGAGGCATGGGTTGGGGGGGGGTTGAGCTGGGGAAGCCAATTGTCCCCGCTATAAACTCGCCATTGCCGGAGATTTACGGTCGCCTGTTTTCAGAGCCACATAATTACATCCCCCATAAATTTTTATGGCCTGGTGGGCCCTGCGCCTTTGAAGTAGGTTCCCCATCCTCTTCACCATTCTCACCAGCGACTTTTTCGCCAGGGAGATACAGTCTTAATGAAGTTGGAAGTTGGGGAGGGGTGGAGGAGGTGGAGGAGGAGAAGGAGGAGGAGGTAATCCGTATTTAAGCAGAGAGTTGAGTCAACTCCCAGTATTTATTTTTTCCTTTCTTCCAGTCTGACTCCTTGGCTGGAGAAGTGAGCAAAAGTTTTCAGTAGGGGTAGGCACTGCTTGGAATCTGAGCAGCAAGGGTGGGAACTAAACAGAGGAAAGGTTTAGGGAAACCTCCCCTCCCTCTTCCACCCCCTCATTCTCCCATTCTGGGGGCCCCAAGCTGAGGGGGAGAGAGGAGCAATTAAAACCTTGGGGGAGTCCTCACACGCCCCCCTTCCCCACCACACACCCAAACAAGGACACAGCACAGCCCTCCAAAACTTGGAGGTCTCTTTCTCATTCTTGGGTCTTGCATTCTTCCCTTTTCGTTTTTCCCCGCTCTCCCTCAGAAGGAAGAAGAGGTGGCGGGAGAGGGAGGGAGGGAAACGCTGTGTTCCCTGGAAGAAAGGACTCTCTCTTTCGGGGGCAATAAAACTTTCTCTTTCTCCCTCTCTCCGTGTGTGTCCAG
Seq C2 exon
TAAACCCCAATTACGCCGGCGGGGAGCCCAAGCGCTCTCGGACCGCCTACACGCGCCAGCAGGTCTTGGAGCTGGAGAAGGAATTTCACTACAACCGCTACCTGACACGGCGCCGGAGGGTGGAGATCGCCCACGCGCTCTGCCTCTCCGAGCGCCAGATCAAGATCTGGTTCCAGAACCGGCGCATGAAGTGGAAAAAAGACCACAAGTTGCCCAACACCAAGATCCGCTCGGGTGGTGCGGCAGGCTCAGCCGGAGGGCCCCCTGGCCGGCCCAATGGAGGCCCCCGCGCGCTCTAGTGCCCCCGCACGCGGGAGCCACGAACCTCGGGGTGGGGGTGGGCAGTGAGTGCAGGGGATGGGGTGGGGGGACAGGAGGGGGCCCTGGGGCCTGGGCCCCGGAAAAATCTATCTGCCCTCCCCCACACTTTATATACGAATAAACGCAGAAGAGGGGGAGGGGAAGCTTTATTTATAGAAATGACAATAGAGGGCCACGGGGAGGCCCCCCCAGAAGCAAGATTCAAATCTCTTGCTTTCTTTCTTAAAAAAAAGAAAAAGAAAAAGCAAGAAGAAGGAAGAAAGAAAAAGACAGAAAGAGAAATAGGAGGAGGCTGCAGCTCCTCGTTTTCAGCTTTGGCGAAGATGGATCCACGTTTCATCTTTAATCACGCCAGGTCCAGGCCCATCTGTCTTGTTTCCTCTGCCGAGGAGAAGACGGGCCTCGGTGGCGACCATTACCTCGACACCCGCTAACAAATGAGGCCCGGCTCGGCCGCCTCCGCCTCTGCTACTGCCGCTGCTGGAAGACAGCCTGGATTTCCTTTCTTTGTCCCCCACTCCCGATACCCAGCGAAAGCACCCTCTGACTGCCAGATAGTGCAGTGTTTTGGTCACGGTAACACACACACACTCTCCCTCATCTTTCGTGCCCATTCACTGAGGGCCAGAATGACTGCTCACCCACTTCCACCGTGGGGTTGGGGGTGGGCAACAGAGGAGGGGAGCAAGTAGGGAAGGGGGTGGCCTTGACAACTCAGGAGTGAGCAGGAAAATTGAGTCCAAGGAAAAAGAGAGACTCAGAGACCCGGGAGGGCCTTCCTCTGAAAGGCCAAGCCAAGCCATGCTTGGCAGGGTGAGGGGCCAGTTGAGTTCTGGGAGCTGGGCACTACTCTGCCAGTCCAGAGTTGTACAGCAGAAGCCTCTCTCCTAGACTGAAAATGAATGTGAAACTAGGAAATAAAATGTGCCCCTCCCAGTCTGGGAGGAGGATGTTGCAGAGCCCTCTCCCATAGTTTATTATGTTGCATCGTTTATTATTATTATTGATAATATTATTATTACTATTTTTTTGTGTCATGTGAGTCCTCTCTCCTTTTCTCTTTCTGACATTCCAAAACCAGGCCCCTTCCTACCTCTGGGGCTGCTTGAGTCTAGAACCCTTCGTATGTGTGAATATCTGTGTGCTGTACAGAGTGACAATAGAAATAAATGTTTGGTTTCTTGTGACCAGCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000182742-HOXB4:NM_024015:1
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.693 A=NA C2=0.606
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
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGAGGCGAGAGAGCAGCTTC
R:
GCCGGCGTAATTGGGGTTTA
Band lengths:
353-1195
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)