HsaINT0077288 @ hg19
Intron Retention
Gene
ENSG00000120094 | HOXB1
Description
homeobox B1 [Source:HGNC Symbol;Acc:5111]
Coordinates
chr17:46606807-46608272:-
Coord C1 exon
chr17:46607690-46608272
Coord A exon
chr17:46607238-46607689
Coord C2 exon
chr17:46606807-46607237
Length
452 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGG
5' ss Score
9.46
3' ss Seq
TCTCCCTGCCCCGCCCCTAGCGA
3' ss Score
8.71
Exon sequences
Seq C1 exon
TGACGCATGGACTATAATAGGATGAACTCCTTCTTAGAGTACCCACTCTGTAACCGGGGACCCAGCGCCTACAGCGCCCACAGCGCCCCAACCTCCTTTCCCCCAAGCTCGGCTCAGGCGGTTGACAGCTATGCAAGCGAGGGCCGCTACGGTGGGGGGCTGTCCAGCCCTGCGTTTCAGCAGAACTCCGGCTATCCCGCCCAGCAGCCGCCTTCGACCCTGGGGGTGCCCTTCCCCAGCTCCGCGCCCTCGGGGTATGCTCCTGCCGCCTGCAGCCCCAGCTACGGGCCTTCTCAGTACTACCCTCTGGGTCAATCAGAAGGAGACGGAGGCTATTTTCATCCCTCGAGCTACGGGGCCCAGCTAGGGGGCTTGTCCGATGGCTACGGAGCAGGTGGAGCCGGTCCGGGGCCATATCCTCCGCAGCATCCCCCTTATGGGAACGAGCAGACCGCGAGCTTTGCACCGGCCTATGCTGATCTCCTCTCCGAGGACAAGGAAACACCCTGCCCTTCAGAACCTAACACCCCCACGGCCCGGACCTTCGACTGGATGAAGGTTAAGAGAAACCCACCCAAGACAG
Seq A exon
GTAGGGCTCAGATGTGGCCACCCCTTCTCCGGGGCCCAAAGCATCTCTGCTTCCCCTGCAGTGACATGTCCTGGGTCTGGGCTGGGTTCTTCTCTTTCAGCGGCTCTGGTAGACACAGGTAAGAGCACAACCTACGTCTCAGGTCAGGTGAGGTCTCCCCACCCAGTATGTAACCGGTCACCCCAGGAGTAAGTTTCCATACACACCCCACTTCCTGATCTGTGCACCCAGCACAGACCCAGGACCTGGTGTGCATGGGGGATGGAAGTATGGGGAAGGCTGCTCCAGACTTGGTGATCACCATGGGGGTACCTGGTGGTCCCTGGGAACTTTGACAACTGTACTTGGGCAGAATGGCAAATGGAGGTCCAGAGCCAGCCCCGGGAGGAGGGAAGCGGAAGGAGAAAGAGGTGAGAGAATTGACCTGGCCTTTCTCCCTGCCCCGCCCCTAG
Seq C2 exon
CGAAGGTGTCAGAGCCAGGCCTGGGCTCGCCCAGTGGCCTCCGCACCAACTTCACCACAAGGCAGCTGACAGAACTGGAAAAGGAGTTCCATTTCAACAAGTACCTGAGCCGGGCCCGGAGGGTGGAGATTGCCGCCACCCTGGAGCTCAATGAAACACAGGTCAAGATTTGGTTCCAGAACCGACGAATGAAGCAGAAGAAGCGCGAGCGAGAGGAAGGTCGGGTCCCCCCAGCCCCACCAGGCTGCCCCAAGGAGGCAGCTGGAGATGCCTCAGACCAGTCGACATGCACCTCCCCGGAAGCCTCACCCAGCTCTGTCACCTCCTGAACTGAACCTAGCCACCAATGGGGCTTCCAGGCACTGGAGCGCCCCAGTCCAGCCCTATCCCAGGCTCTCCCCAACCCCAGGCCTGGGCTTCACTGGCCTGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000120094-HOXB1:NM_002144:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.725 A=NA C2=0.780
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=50.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTATGGGAACGAGCAGACCG
R:
TCGCGCTTCTTCTGCTTCATT
Band lengths:
358-810
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
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)