HsaINT0077293 @ hg38
Intron Retention
Gene
ENSG00000120093 | HOXB3
Description
homeobox B3 [Source:HGNC Symbol;Acc:HGNC:5114]
Coordinates
chr17:48548870-48553922:-
Coord C1 exon
chr17:48552027-48553922
Coord A exon
chr17:48551182-48552026
Coord C2 exon
chr17:48548870-48551181
Length
845 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCA
5' ss Score
7.88
3' ss Seq
CCCCTCCCCCTCGGATCCAGCAG
3' ss Score
5.66
Exon sequences
Seq C1 exon
GGAGTTGAACAGCTAGGCTGAATGAGATTAAAGTTTTCCAAACACACATGGCAGTATGGAGGTTTTATGAAAAGTGATGGTGAAGAGTTGGGAGAGATGGAGGGAAAAAAATGCAGTCAGAAGTTTCAGAACAAATACACAAAATCCTATGTTAGTTTGAATCTTTATTTTTCTGGCACACTTTTAAAAGGCTGTATTAAAATAGTGATTTTTTTTTTTTGCCTCAGGGAACCTCAGTCAACAGGAATACCTCTGTTTCTAACCTAGAGAATAATATTGTTAAAATTGCTTTGTTAATTTTTTTTTCCTCAGGAATAATTTTCTCTTTTGGAAAGCACTTTCCCCGTCTCAGTAGAAAAGTCTAGCAGTTGTAACTTCTTGTTTCTTATTTGCTTTGGGGGAAATCAAAGAAAACAGACGGTGAAGGAAAGGGTGGGAAAAATTAAGTCTCATGAAAAAAAAAAAAAGAGGTCCGGGGAGAGACCTGGGCCAAATGGTCACAGCACCAACTGGCGTGGCCCAGGAAATTGAAACAATCCTGCTCCATGTGGGGGCCCCACAGGGCCACTGGCTGCCCGATCCCAGGTTTGGCTGAGCAAAGACAAGGGCTGGAGGTGGTGGTACCTGCAGCAGGGCCATGGACAGATGAGTCTCGGTTCAGCTGGCTCTTGAGGTTAAAAATCATCAGGAAGTTTCTAGGTCAGGCTGTTGTTGTCTTCCTGGTGGGAGAGTGGTGGGAAGTGGAGAGGATACCTCACAAGAGAAGCTTCTCTGCTGAACTTGCTTCTCCTGCCTGTTCTTTTAGGAGATCCTTTGGTTTTCCTTCAGGCTAGACTTTGCTTGGGCAAGAGACCTAAACCGACTTGGAAGGAGGCAAAGGCTGGAAGCATAGAAGCCTCTGGGCTCAGAGGAGGGTGTTGATGATGCTTTTATTTTGGAGTCTCCTAGTGTCCCCTCCCTTGAGCCATCCTATCCCAGAGTTGGGGAGGAGAGATAGGGAGAGAGGGACTAGGGGAGGTCAGGGGCTAGTGCACAGGCAGGAGAGAAGCAATGGCCTTTGCCATAGATTCTACATCTAGGCAGTCTTGAAAGGCATATAGTCTTTATTTATTTTTTTATTTTTTAGTGGAAATGAAAACTGGTGGGCTTTTTTTTCTCAGCATCTGCTTTGGAGATGTTGGGGAGGGGAAAAGAAAAAACCCTATTGATGTCAGTTCCCTTTTCAGTTCCTAAGATGGATTCGAGCCCCAGTCCTCTTCTCCCCCTTGTGTCTCTTCTCTCGCCTCGCAGGTCAGCCGCTTGGAACAGACCCCGGAGGAGGGGGGCAGAGAGGGGAGGTGGGGGGGGGGGGTCCGGCGTGTCACGTGACCCCCAGGGTTGCCAATGTCCGGTCCTGAGGGTATCAGGCCTTTCCAAGTTGCCACCCACTGCCCAGGCCTCACCCAGCGATGCAGAAAGCCACCTACTACGACAACGCCGCGGCTGCTCTCTTCGGAGGCTATTCCTCGTACCCTGGCAGCAATGGCTTCGGCTTCGATGTCCCCCCCCAACCCCCATTTCAGGCCGCCACGCACCTGGAGGGCGACTACCAGCGCTCAGCTTGCTCGCTGCAGTCCCTGGGCAACGCTGCCCCACATGCCAAGAGCAAGGAGCTCAACGGCAGCTGCATGAGGCCGGGTCTGGCCCCCGAGCCCCTGTCGGCCCCGCCTGGCTCACCCCCGCCCAGTGCCGCACCTACCAGTGCCACTAGCAACAGCAGTAATGGGGGCGGGCCCAGCAAAAGTGGTCCCCCAAAGTGCGGTCCCGGCACCAACTCCACCCTCACCAAACAGATATTCCCCTGGATGAAAGAGTCGAGGCAAACGTCCAAGCTGAAAAACAACTCCCCCGGCACAG
Seq A exon
GTACCAGTTCTCTGCCTTCCTTGTCCTCAGCTTTTGTCGGAGCCAGGAATGTCACTGTTATTCTAGCACCCAGCCCCTAGGCGCCCGCGAGGCTGCCTGGGAACAATATTAGGTGGCCAGCGGGTACATTTTTGATACCCCTACCCCCTAATGACCCCTGACCCCGCCAACACCCTCCTCCCTCTAGCTGCCCTCCACCGGAGCTTCTGAAAGCTCCAGAAGGCCCAGTGCGTGGCCTCAAAGCCCTTCCCAAGGCCACAGAGCCAAGACGAGGCGCTGCCGGGAGGATGCAGAGTCGTCAACGATTGATTATTATTAAGTATGATTACTGTGGGTATTAATCACAATCGCTTGGACGGCCCGGGGTCCCGGCCTCCAGAAACGGCAGCCTCTTCGTGCCACACTTCCTGCCCACGAGTGTCCAGATTACCCCGAGGATTCTCCTCAGTCTCCCATCCTGTCCTCAGGACGGGGTGGGCGGGGAGGGGAAATGTCTTCCCTGACCTGGAATTGGGGATAAGGGGGAGAAAGCACGCACGCGAAAATCCAGCCCTAAATAAATGGCCATGCGGCTCTGTCTGCGTGACATGATCAAATTTTCATAAGCTGGGGCAGCGAAAGGAGAACAGGTCTCTTAATAAATGCCACTATTATAGAGTGTCCGCTAATGCGACGGGCGGTGGGGTGGGGGAGTGAGGAGGCGGCGGGGACCCGAAGGGGAGGGCGGCGGGGGCTCTGAGTCCAGGCCTGGATTTATTAAGAAACGATGCATTCAATTTCGGCGTGTTCAGTAATTATCTTTTATTTCATTTTCTCCCCTTCCCACCCCTCCCCCTCGGATCCAG
Seq C2 exon
CAGAGGGCTGTGGTGGCGGCGGCGGTGGCGGCGGCGGCGGAGGCAGTGGTGGCAGCGGGGGCGGTGGCGGCGGCGGCGGGGGAGGGGACAAGAGCCCCCCGGGGTCGGCGGCGTCCAAGCGGGCGCGGACGGCGTACACGAGCGCGCAGCTGGTGGAGCTGGAGAAGGAGTTCCATTTTAACCGCTACCTGTGCCGGCCTCGCCGTGTAGAGATGGCCAACCTGCTGAACCTCAGCGAGCGGCAGATCAAGATCTGGTTCCAGAACCGGCGCATGAAGTACAAGAAGGACCAGAAGGCCAAGGGATTGGCCTCGTCGTCGGGGGGCCCATCTCCAGCCGGCAGCCCCCCGCAGCCCATGCAGTCCACGGCCGGCTTCATGAACGCCTTACACTCCATGACCCCCAGCTACGAGAGCCCGTCCCCACCCGCCTTCGGTAAAGCCCACCAGAATGCCTACGCGCTGCCCTCCAACTACCAGCCCCCTCTCAAAGGCTGCGGCGCCCCGCAGAAGTACCCTCCGACCCCGGCGCCCGAGTATGAGCCGCACGTCCTCCAAGCCAACGGGGGCGCCTACGGGACGCCCACCATGCAGGGCAGTCCGGTGTACGTGGGCGGGGGCGGCTACGCGGATCCGCTGCCGCCCCCTGCCGGCCCCTCCCTCTATGGCCTCAACCACCTTTCCCATCACCCTTCCGGGAACCTGGACTACAACGGGGCGCCCCCTATGGCGCCCAGCCAGCACCACGGACCCTGCGAACCCCACCCCACCTACACAGACCTCTCCTCTCACCACGCGCCTCCTCCTCAGGGTAGAATCCAAGAAGCGCCCAAATTAACACACCTGTGATGGGAAAGGGCGAACGAGGATTAGGGGATGGGGAGGAAGAGAGAGACTGTGGAGCTCTGGGGGGCAACCTGGAGGTCTGAAAAGAGGAGCCAGAGAAGGTGGTACCCAGGCTTCCTGGTCAGAACCGGCCTGGAGCTCCTTCCCTTCCCCCTGGCCTGAGAGGTTGCTTTTAAGTCTTCCACCCCTTGTTCCATCTGCCTGCCAACCCATCGGAAAGGAATCCACATCATATTGGAGATGACCCCATCAACCCCAGGGCTCCAGCACTACCAAGTTGGAATTCCACGCCCGGGAGTGGGGTAGAGGAAGACGAGACAGGACGAGGCAGAAAAGCACATTTTAAAAACCAGACAAGATGGCTAGGCCATCACCAACCAACGGACTTACCTTACATCTTTGTAGGTAATTCCCCCCAAATCTTGATTTTTTTTTTTCCTCAATTATCCTTTAAAAAATAAGAAAACACATTTCAAACCCAAAAGGCACAAAACACGTTCCCTTCCAACTTTCCCAAAACCTCAAATTTGTTCCCATTTGAGGTTTATTGAGGTACACTTCTAGCCCCCGGTTTTTCTGCTCTAGAACATTCATATCTATACATCCCACCCCCATCAATTACAGTTTTTAGAGGGCTCAGGGATGGTGAGAGATCCTGAAAGAGCTGCCTATATTATAAATTATATACATTTTTTTTTAAGGAAAAGTGTGGAGGCTAGGGCAGGCAGGTTGTTAGGACTGAAGGTTTGCCCATTCTGCTGCCTCCATCTCAGCTCCAGCTCCATCCCCCTCTCCACAGAAAGCAGTTGGTGACACGAGGTTCTATACTTTTCTTCTGTTGCTCTCTTGACTTAACGTGAAAACAGGGTATATTTGAACAAACTGTCCCAGGCAGGGGCTGGGCAGGGCCTGTGTGCCTTGCTCAGCCTCCTGACAGGACACTTTTGTTGCACTTAGAATTTACATTTTAATGGATGTAAAAACAACTGTGAGAGATGTCTGGGCCTGCAGAAGTCCAGCATTGCTCAAAAAAGCGTGTGTTCTAGTGAACATTTTCATATATATTTATTGGTTATAGCCTGTTAAAATATTTTCTTTTTTGTATTATTTATCCCCCTACATTATGTATTTATATGAGGGAAAAAAAGGAAAAAATTGTACTTTTTTAGTATTTACCTGTTACAAAGGACATTGTGTTTCCTGTCATGTAAAACCAGCTATTTTAGTTACTATTGTACTCTAGAAAAGAGCTGTAGATTTATGTTAAACTCGTACTTACGAACAATTGTAATTAGTTCTAAAAGGCATGAACTCAGCTCCTAATCGTCACTGTATAGTCCTGAATTTGTAGAACTAGAGTTAATTCCCTCTTGGAACTTTCTTTGTTCTTCAGTAGTTACTTTTTTCCTTACCTAAAAGGGTTGTCTGTCAAACAATTCTTGAATAAACTTTCTGTTATCAATTTTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000120093:ENST00000470495:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.859 A=NA C2=0.853
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=20.1),PF132931=DUF4074=WD(100=23.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCAAAAGTGGTCCCCCAAAG
R:
GCAGGTTGGCCATCTCTACAC
Band lengths:
346-1191
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