HsaINT0077290 @ hg38
Intron Retention
Gene
ENSG00000173917 | HOXB2
Description
homeobox B2 [Source:HGNC Symbol;Acc:HGNC:5113]
Coordinates
chr17:48542655-48544989:-
Coord C1 exon
chr17:48544521-48544989
Coord A exon
chr17:48543748-48544520
Coord C2 exon
chr17:48542655-48543747
Length
773 bp
Sequences
Splice sites
5' ss Seq
CAGGTCGGT
5' ss Score
7.53
3' ss Seq
CGAGCCTGTTTTCCCTGCAGATG
3' ss Score
11.77
Exon sequences
Seq C1 exon
GGGTGCAGGAGGGGGGTCCCTTCCGATCCTCCCTCCTGACGCCCCCCCCAGCAGCCCCCTCCCCCACCATTGAAAGCCATGAATTTTGAATTTGAGAGGGAGATTGGGTTTATAAACAGCCAGCCGTCGCTCGCCGAGTGTCTGACTTCCTTCCCCGCTGTCTTGGAGACATTTCAAACTTCATCAATCAAGGAGTCGACATTAATTCCTCCTCCTCCTCCTTTCGAGCAAACCTTCCCCAGCCTCCAGCCCGGCGCCTCCACCCTTCAGAGACCCAGGAGCCAAAAGCGAGCCGAAGATGGGCCTGCTCTGCCGCCGCCACCGCCGCCGCCACTCCCCGCTGCCCCCCCGGCCCCCGAGTTCCCTTGGATGAAAGAGAAGAAATCCGCCAAGAAACCCAGCCAATCCGCCACGTCTCCTTCTCCGGCCGCCTCCGCCGTTCCGGCCTCCGGGGTCGGATCGCCTGCAG
Seq A exon
GTCGGTAAGCGTGGTGGGGGTGGGGTGAGGGGCAGCTAGAAGAGGGGGAGAAAAAGCAGTGGAAGGAGGTTTAAAAAAAATGGTGGCGAGCCTGTTGGGGTTCCTTACCCCCTCCATTCCTGGGATGGGGAAGTAGAATATCCCACTGGGGTTCAGGCCTGGCCGCTAACAGCGTCTTTTTTTTTTTCTGTCTCTCTCTCTCTTTCTCTCCCTATGGCTGATTTTGGAAGCTGGTTGGGGAAACGCCTTTTTTTCTGCTAGAAGAAAATGATTTGATTGAGGTTTTCACCCGTATCTGTGTAGGGGAATGAGTATGTTGTTGCTGGGATAGACCCTAGAAGCAGAAAAGATTCGGTCCTTTCTGCCCCAACTCTAGGAGAAGAGGAAGAATTCAGAGCTAGGGAGGAAGAGGGGTGAAGAACAATCTTTCTGACCCTCGCTCCGGTTGAGTTGGAAAGTTCCGAATTGAGGGGTCCACTGGGAGGGCTTGGGAGGGGGATCTGAGGTTCCGGCGCCGAAGGGAGCCGCTCTCCGCCCCCTGCGTGGCCCGTGGGCGGCTCTGAATGCTTTGCCCTGACCCGGGCCGGGGCTGTAGACTAGAGAGGGAGAGAAGAAAACCCAAAAGCAGTAAAGCGAGCGGCTTTGGGGTGGGGGCGGGGGTGGGGTGGCGAGGAAGGGGAGAGGTGATACTGGTTTTGGAGGATGGGGTAGTCCGAACTGAGGTTGGGCTGAGTACACGGCCCGCTATGACGCCGAGCCTGTTTTCCCTGCAG
Seq C2 exon
ATGGCCTGGGACTGCCGGAGGCTGGTGGCGGCGGGGCGCGCAGGCTGCGCACGGCTTACACCAACACGCAGCTGCTGGAACTGGAGAAGGAATTCCACTTTAATAAGTACCTGTGCCGGCCACGCCGCGTCGAGATCGCGGCCTTGCTGGACCTCACCGAAAGGCAGGTCAAAGTCTGGTTTCAGAACCGGCGCATGAAGCACAAGCGGCAGACGCAGCACCGAGAGCCGCCGGATGGGGAGCCTGCCTGCCCGGGAGCCCTGGAGGACATCTGCGACCCTGCCGAGGAACCCGCGGCCAGCCCGGGCGGCCCCTCCGCCTCGCGGGCGGCGTGGGAAGCCTGCTGTCACCCGCCGGAGGTGGTGCCGGGGGCCTTAAGCGCGGACCCCCGGCCTTTAGCCGTTCGCTTAGAGGGCGCAGGCGCGTCGAGTCCCGGCTGCGCGCTGCGCGGGGCCGGCGGGCTGGAGCCCGGGCCATTGCCAGAAGACGTCTTCTCGGGGCGCCAGGATTCACCTTTCCTTCCCGACCTCAACTTCTTCGCGGCCGACTCCTGTCTCCAGCTATCCGGAGGCCTCTCCCCTAGCCTACAGGGTTCTCTCGACAGCCCGGTCCCTTTTTCCGAGGAAGAGCTGGATTTTTTCACCAGTACGCTCTGTGCCATCGACCTGCAGTTTCCCTAACCTGTTTCCTCCTCCCGGTCCTTTCGACCCCCGCGCTCCTTGGCCGTCTACTGGAAAAATCGAGCCTCTCCCACCCTCAGTCGCATAGACTTATGTGTTTTGCTAAAATTCAGGTATTACTGAATTAGCGTTTAATCCACTCCCTTTCTTCTTCTTCTAAAATATTGGGCACTCGGTTATCTTTTAAAATTCACACAGAAAAATTCCGTTTGGTAGACTCCTTCCAATGAAATCTCAGGAATAATTAAACTCTAGGGGGACTTTCTTAAAAATAACTAGAGGGACCTATTTTCCTCTTTTTTATGTTTTAGACTGTAGATTATTTATTAAAATTCTTTAATAATAGGAAAAGGGGAAAGTATTTATTGTACATTATTTTCATAGATTAAATAAATGTCTTTATAATACCAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000173917:ENST00000330070:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.740 A=NA C2=0.473
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
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTCCTCCTCCTCCTTTCGAG
R:
CTTCTCCAGTTCCAGCAGCTG
Band lengths:
351-1124
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