HsaINT0077294 @ hg38
Intron Retention
Gene
ENSG00000182742 | HOXB4
Description
homeobox B4 [Source:HGNC Symbol;Acc:HGNC:5115]
Coordinates
chr17:48575513-48580111:-
Coord C1 exon
chr17:48577863-48580111
Coord A exon
chr17:48577021-48577862
Coord C2 exon
chr17:48575513-48577020
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
GAGAATTGAAAACCTTGTAATCCCAAGAACAGACTCGCACTGCCTTTTTCTGTTCCCAGAGCTCAAAACTAGAACAAAACGAAATAAAACCAAAGCACTCAAACCACACCCCAAACGAAGAAGGCGCGGAAAGTAGGAGAACTGGAAAATTTCTGGGCCAAGAAGATCTGTCTGTCTTCTGTATATACCCTGTAGATCCGAATTTGTGTAAGGAATTTTGTGGTCACAAATTCGTATCTAGGGGAATATGTAGTTGACATAAACACTCCGCTCTTATTTTTCCAGAAGAAAAAAATATATATATATGTATATGTAGTATTTTTCTGAATGAGGACAGTCTGGTGACTGGCCACACGAAGACTCCTTCCTCTTTATTCCTCTATCTTTTCCTCCTTCAACTGGTTAGAGATGGAGAAATCATCTACCTGAACTCTCCCCACGCCTGCCCCTGGGAGCCTTGGTCCCTTTTCACATCTCTTTAAGAGGTTAATGTTATTGTTGTTGAAGTTTTAAATTTATCTTCTCGTCCCAAACGCACCCATTTTCTATTCTGGGCTCAGGGAGGCTTTATTGGAAATTGCGAAAAAAAATGACTTGTCTTCAGTGTGCGAAGAAGGCAAAGGAAATTTGTTTAACAAACGGATGCTGAGGCCGCCTTTCCGTTTCAGTTCAGAACAAGATGACCTGGAAATACTCGATTACCAAGGAGTGTTATTGTCTGTGTGGGTCACCTCTATGGCTGTATCCCCAGTATCAAAGGGATGTGAGATTTCTATTCGCCGCGGAGGCGGCGACAATTAGAACGTCTCGGACCCATGGTTAGTATTGCTCGGGTGGTTATGGAATTAGCAAATTGCTAATCAATTTTGCTCTCAAAAGTTGCAGGTTTTTTTACCCCAGCGCTCTGTCTATAGTGTGGGAAACCAAGTCGTTTCTCCAGGCTTGGGCCGTGTGGGTTAAAGGGAGGAGTGGATAGGAGAAGGGGGACAGACGGACTGACGGACACAGTCTAGCTAACCGTGCAGCTAAATGAGATTTGGAAGGCGAAGTCTCCCCGAATTAGTGCATGAATTTCCTATCGATCCGCCCGCGGTTCCATTCATCTCTGACAAGTCCCTCTGCGCACCCGCCCTCTAGCTCTGGACGCCTCCTCTCTCACCCCTACCCTTCCCCATCCAGCTGCAGAGAAAAGCCCCAAGCTCTGTGCTCTGGCCCCCGTATGGGTTCCCCTTTCGAGACGGAGCCCCCAACCCGCCAGTAACCTAACTCCCCATAGAGACGCAGGGTGCTAGCGCTCCCTCCCGCCGAGGGGAGGAGACTGGGGCCTTTGGAAGGTACAGAATGCTGGGCAGAGGTGAGGCAGAACAGGAGGGCTACACCGGGAGCCCCAACTTCTTAAGGGATCTAGGGTTTGCGCTCTGCCTAGCGCCCCAACAGGCCCTCCAGTCGCAACCTGCGCGCGCTCTCTCTCTCGCTCTCTCTCTGATCCCGGAGAGAGCGAGGCAAGGAGGGGGTCGCCCCGCAGGAGCCCTATGTAAATCCTGGTGTTGGGTGGGTGGGTGGGGAGGGGGAAGGGAAGAAGGGGAAATAAACCTCTTTGGCTGGAGTGGGGTCCGGGTGAGCAGATTTCCTTATCCGGGAATCGCAGGCGGGGCGGCCATTGGCTCGGAGGATCACGTGGGCGCCTAACTTTGTTCACTTGACAGTAAGTAGGAGGGCTTTCGGAAACAGGAAAACGAGTCAGGGGTCGGAATAAATTTTAGTATATTTTGTGGGCAATTCCCAGAAATTAATGGCTATGAGTTCTTTTTTGATCAACTCAAACTATGTCGACCCCAAGTTCCCTCCATGCGAGGAATATTCACAGAGCGATTACCTACCCAGCGACCACTCGCCCGGGTACTACGCCGGCGGCCAGAGGCGAGAGAGCAGCTTCCAGCCGGAGGCGGGCTTCGGGCGGCGCGCGGCGTGCACCGTGCAGCGCTACGCGGCCTGCCGGGACCCTGGGCCCCCGCCGCCTCCGCCACCACCCCCGCCGCCCCCGCCACCGCCCGGTCTGTCCCCTCGGGCTCCTGCGCCGCCACCCGCCGGGGCCCTCCTCCCGGAGCCCGGCCAGCGCTGCGAGGCGGTCAGCAGCAGCCCCCCGCCGCCTCCCTGCGCCCAGAACCCCCTGCACCCCAGCCCGTCCCACTCCGCGTGCAAAGAGCCCGTCGTCTACCCCTGGATGCGCAAAGTTCACGTGAGCACGG
Seq A exon
GTGAGTGCGTGGGCACCCCTTCCCCCTCCCACCCCTGGAGCTTTACACCAAAGGGACTTCGGAGGCATGGGTTGGGGGGGGGTTGAGCTGGGGAAGCCAATTGTCCCCGCTATAAACTCGCCATTGCCGGAGATTTACGGTCGCCTGTTTTCAGAGCCACATAATTACATCCCCCATAAATTTTTATGGCCTGGTGGGCCCTGCGCCTTTGAAGTAGGTTCCCCATCCTCTTCACCATTCTCACCAGCGACTTTTTCGCCAGGGAGATACAGTCTTAATGAAGTTGGAAGTTGGGGAGGGGTGGAGGAGGTGGAGGAGGAGAAGGAGGAGGAGGTAATCCGTATTTAAGCAGAGAGTTGAGTCAACTCCCAGTATTTATTTTTTCCTTTCTTCCAGTCTGACTCCTTGGCTGGAGAAGTGAGCAAAAGTTTTCAGTAGGGGTAGGCACTGCTTGGAATCTGAGCAGCAAGGGTGGGAACTAAACAGAGGAAAGGTTTAGGGAAACCTCCCCTCCCTCTTCCACCCCCTCATTCTCCCATTCTGGGGGCCCCAAGCTGAGGGGGAGAGAGGAGCAATTAAAACCTTGGGGGAGTCCTCACACGCCCCCCTTCCCCACCACACACCCAAACAAGGACACAGCACAGCCCTCCAAAACTTGGAGGTCTCTTTCTCATTCTTGGGTCTTGCATTCTTCCCTTTTCGTTTTTCCCCGCTCTCCCTCAGAAGGAAGAAGAGGTGGCGGGAGAGGGAGGGAGGGAAACGCTGTGTTCCCTGGAAGAAAGGACTCTCTCTTTCGGGGGCAATAAAACTTTCTCTTTCTCCCTCTCTCCGTGTGTGTCCAG
Seq C2 exon
TAAACCCCAATTACGCCGGCGGGGAGCCCAAGCGCTCTCGGACCGCCTACACGCGCCAGCAGGTCTTGGAGCTGGAGAAGGAATTTCACTACAACCGCTACCTGACACGGCGCCGGAGGGTGGAGATCGCCCACGCGCTCTGCCTCTCCGAGCGCCAGATCAAGATCTGGTTCCAGAACCGGCGCATGAAGTGGAAAAAAGACCACAAGTTGCCCAACACCAAGATCCGCTCGGGTGGTGCGGCAGGCTCAGCCGGAGGGCCCCCTGGCCGGCCCAATGGAGGCCCCCGCGCGCTCTAGTGCCCCCGCACGCGGGAGCCACGAACCTCGGGGTGGGGGTGGGCAGTGAGTGCAGGGGATGGGGTGGGGGGACAGGAGGGGGCCCTGGGGCCTGGGCCCCGGAAAAATCTATCTGCCCTCCCCCACACTTTATATACGAATAAACGCAGAAGAGGGGGAGGGGAAGCTTTATTTATAGAAATGACAATAGAGGGCCACGGGGAGGCCCCCCCAGAAGCAAGATTCAAATCTCTTGCTTTCTTTCTTAAAAAAAAGAAAAAGAAAAAGCAAGAAGAAGGAAGAAAGAAAAAGACAGAAAGAGAAATAGGAGGAGGCTGCAGCTCCTCGTTTTCAGCTTTGGCGAAGATGGATCCACGTTTCATCTTTAATCACGCCAGGTCCAGGCCCATCTGTCTTGTTTCCTCTGCCGAGGAGAAGACGGGCCTCGGTGGCGACCATTACCTCGACACCCGCTAACAAATGAGGCCCGGCTCGGCCGCCTCCGCCTCTGCTACTGCCGCTGCTGGAAGACAGCCTGGATTTCCTTTCTTTGTCCCCCACTCCCGATACCCAGCGAAAGCACCCTCTGACTGCCAGATAGTGCAGTGTTTTGGTCACGGTAACACACACACACTCTCCCTCATCTTTCGTGCCCATTCACTGAGGGCCAGAATGACTGCTCACCCACTTCCACCGTGGGGTTGGGGGTGGGCAACAGAGGAGGGGAGCAAGTAGGGAAGGGGGTGGCCTTGACAACTCAGGAGTGAGCAGGAAAATTGAGTCCAAGGAAAAAGAGAGACTCAGAGACCCGGGAGGGCCTTCCTCTGAAAGGCCAAGCCAAGCCATGCTTGGCAGGGTGAGGGGCCAGTTGAGTTCTGGGAGCTGGGCACTACTCTGCCAGTCCAGAGTTGTACAGCAGAAGCCTCTCTCCTAGACTGAAAATGAATGTGAAACTAGGAAATAAAATGTGCCCCTCCCAGTCTGGGAGGAGGATGTTGCAGAGCCCTCTCCCATAGTTTATTATGTTGCATCGTTTATTATTATTATTGATAATATTATTATTACTATTTTTTTGTGTCATGTGAGTCCTCTCTCCTTTTCTCTTTCTGACATTCCAAAACCAGGCCCCTTCCTACCTCTGGGGCTGCTTGAGTCTAGAACCCTTCGTATGTGTGAATATCTGTGTGCTGTACAGAGTGACAATAGAAATAAATGTTTGGTTTCTTGTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000182742:ENST00000332503:1
Average complexity
IR
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