HsaINT0077290 @ hg19
Intron Retention
Gene
ENSG00000173917 | HOXB2
Description
homeobox B2 [Source:HGNC Symbol;Acc:5113]
Coordinates
chr17:46620019-46622393:-
Coord C1 exon
chr17:46621883-46622393
Coord A exon
chr17:46621110-46621882
Coord C2 exon
chr17:46620019-46621109
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
AATCTCCCCCTCCCAAAATCGCTCCATTACATAAATCGGGGGGGGTGCAGGAGGGGGGTCCCTTCCGATCCTCCCTCCTGACGCCCCCCCCAGCAGCCCCCTCCCCCACCATTGAAAGCCATGAATTTTGAATTTGAGAGGGAGATTGGGTTTATAAACAGCCAGCCGTCGCTCGCCGAGTGTCTGACTTCCTTCCCCGCTGTCTTGGAGACATTTCAAACTTCATCAATCAAGGAGTCGACATTAATTCCTCCTCCTCCTCCTTTCGAGCAAACCTTCCCCAGCCTCCAGCCCGGCGCCTCCACCCTTCAGAGACCCAGGAGCCAAAAGCGAGCCGAAGATGGGCCTGCTCTGCCGCCGCCACCGCCGCCGCCACTCCCCGCTGCCCCCCCGGCCCCCGAGTTCCCTTGGATGAAAGAGAAGAAATCCGCCAAGAAACCCAGCCAATCCGCCACGTCTCCTTCTCCGGCCGCCTCCGCCGTTCCGGCCTCCGGGGTCGGATCGCCTGCAG
Seq A exon
GTCGGTAAGCGTGGTGGGGGTGGGGTGAGGGGCAGCTAGAAGAGGGGGAGAAAAAGCAGTGGAAGGAGGTTTAAAAAAAATGGTGGCGAGCCTGTTGGGGTTCCTTACCCCCTCCATTCCTGGGATGGGGAAGTAGAATATCCCACTGGGGTTCAGGCCTGGCCGCTAACAGCGTCTTTTTTTTTTTCTGTCTCTCTCTCTCTTTCTCTCCCTATGGCTGATTTTGGAAGCTGGTTGGGGAAACGCCTTTTTTTCTGCTAGAAGAAAATGATTTGATTGAGGTTTTCACCCGTATCTGTGTAGGGGAATGAGTATGTTGTTGCTGGGATAGACCCTAGAAGCAGAAAAGATTCGGTCCTTTCTGCCCCAACTCTAGGAGAAGAGGAAGAATTCAGAGCTAGGGAGGAAGAGGGGTGAAGAACAATCTTTCTGACCCTCGCTCCGGTTGAGTTGGAAAGTTCCGAATTGAGGGGTCCACTGGGAGGGCTTGGGAGGGGGATCTGAGGTTCCGGCGCCGAAGGGAGCCGCTCTCCGCCCCCTGCGTGGCCCGTGGGCGGCTCTGAATGCTTTGCCCTGACCCGGGCCGGGGCTGTAGACTAGAGAGGGAGAGAAGAAAACCCAAAAGCAGTAAAGCGAGCGGCTTTGGGGTGGGGGCGGGGGTGGGGTGGCGAGGAAGGGGAGAGGTGATACTGGTTTTGGAGGATGGGGTAGTCCGAACTGAGGTTGGGCTGAGTACACGGCCCGCTATGACGCCGAGCCTGTTTTCCCTGCAG
Seq C2 exon
ATGGCCTGGGACTGCCGGAGGCTGGTGGCGGCGGGGCGCGCAGGCTGCGCACGGCTTACACCAACACGCAGCTGCTGGAACTGGAGAAGGAATTCCACTTTAATAAGTACCTGTGCCGGCCACGCCGCGTCGAGATCGCGGCCTTGCTGGACCTCACCGAAAGGCAGGTCAAAGTCTGGTTTCAGAACCGGCGCATGAAGCACAAGCGGCAGACGCAGCACCGAGAGCCGCCGGATGGGGAGCCTGCCTGCCCGGGAGCCCTGGAGGACATCTGCGACCCTGCCGAGGAACCCGCGGCCAGCCCGGGCGGCCCCTCCGCCTCGCGGGCGGCGTGGGAAGCCTGCTGTCACCCGCCGGAGGTGGTGCCGGGGGCCTTAAGCGCGGACCCCCGGCCTTTAGCCGTTCGCTTAGAGGGCGCAGGCGCGTCGAGTCCCGGCTGCGCGCTGCGCGGGGCCGGCGGGCTGGAGCCCGGGCCATTGCCAGAAGACGTCTTCTCGGGGCGCCAGGATTCACCTTTCCTTCCCGACCTCAACTTCTTCGCGGCCGACTCCTGTCTCCAGCTATCCGGAGGCCTCTCCCCTAGCCTACAGGGTTCTCTCGACAGCCCGGTCCCTTTTTCCGAGGAAGAGCTGGATTTTTTCACCAGTACGCTCTGTGCCATCGACCTGCAGTTTCCCTAACCTGTTTCCTCCTCCCGGTCCTTTCGACCCCCGCGCTCCTTGGCCGTCTACTGGAAAAATCGAGCCTCTCCCACCCTCAGTCGCATAGACTTATGTGTTTTGCTAAAATTCAGGTATTACTGAATTAGCGTTTAATCCACTCCCTTTCTTCTTCTTCTAAAATATTGGGCACTCGGTTATCTTTTAAAATTCACACAGAAAAATTCCGTTTGGTAGACTCCTTCCAATGAAATCTCAGGAATAATTAAACTCTAGGGGGACTTTCTTAAAAATAACTAGAGGGACCTATTTTCCTCTTTTTTATGTTTTAGACTGTAGATTATTTATTAAAATTCTTTAATAATAGGAAAAGGGGAAAGTATTTATTGTACATTATTTTCATAGATTAAATAAATGTCTTTATAATACCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000173917-HOXB2:NM_002145:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.754 A=NA C2=0.483
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
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
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)