HsaINT1015862 @ hg38
Intron Retention
Gene
ENSG00000198353 | HOXC4
Description
homeobox C4 [Source:HGNC Symbol;Acc:HGNC:5126]
Coordinates
chr12:54053917-54055327:+
Coord C1 exon
chr12:54053917-54054361
Coord A exon
chr12:54054362-54054849
Coord C2 exon
chr12:54054850-54055327
Length
488 bp
Sequences
Splice sites
5' ss Seq
CGGGTAGGC
5' ss Score
7.5
3' ss Seq
TGCTTTTCCCCTCCCCCCAGTGA
3' ss Score
10.91
Exon sequences
Seq C1 exon
AAATTAATGATCATGAGCTCGTATTTGATGGACTCTAACTACATCGATCCGAAATTTCCTCCATGCGAAGAATATTCGCAAAATAGCTACATCCCTGAACACAGTCCGGAATATTACGGCCGGACCAGGGAATCGGGATTCCAGCATCACCACCAGGAGCTGTACCCACCACCGCCTCCGCGCCCTAGCTACCCTGAGCGCCAGTATAGCTGCACCAGTCTCCAGGGGCCCGGCAATTCGCGAGGCCACGGGCCGGCCCAGGCGGGCCACCACCACCCCGAGAAATCACAGTCGCTCTGCGAGCCGGCGCCTCTCTCAGGCGCCTCCGCCTCCCCGTCCCCAGCCCCGCCAGCCTGCAGCCAGCCAGCCCCCGACCATCCCTCCAGCGCCGCCAGCAAGCAACCCATAGTCTACCCATGGATGAAAAAAATTCACGTTAGCACGG
Seq A exon
GTAGGCAACTTTGCTTTTTGCTCCCCCCCTCCCTCCCTTCTTCCCTAGCGCTCCCCACCCTCCTCGGCCCCCTCTGGCCCCCGTCCTCCTTTCTCTCCTTCCCCCTCTCTCTCCAGGAGCGACTCTGGGTTAGCACAATTGAACTGGATTTACGAGCGAGAATGGGTAATTACATCCCCCATAAATTTTATGGCTTAGCTACTCTGGGCAGTCCGAGCCATGTGCTACGATCTGTTATGTATGTGTGAAAACTATGCTCGCTTTCTAAGGGCGCATAAATAATTCAGTGTCGTTACAATGAGGATTCCCCTCTTATTACACTACAAAGTCTTCAGCTTCCTTCAACTTCTTTATAACCCATTTAAGCTTGATGACTTTATTTCCACCACTCCCTCCTCCTGTTTCTCAGAGCTGAGGATGGGGTGAGGGTGGGGGGCGGGGAGCCTGCTGCCTCTGAACCCCACTATTTGCTTTTCCCCTCCCCCCAG
Seq C2 exon
TGAACCCCAATTATAACGGAGGGGAACCCAAGCGCTCGAGGACAGCCTATACCCGGCAGCAAGTCCTGGAATTAGAGAAAGAGTTTCATTACAACCGCTACCTGACCCGAAGGAGAAGGATCGAGATCGCCCACTCGCTGTGCCTCTCTGAGAGGCAGATCAAAATCTGGTTCCAAAACCGTCGCATGAAATGGAAGAAGGACCACCGACTCCCCAACACCAAAGTCAGGTCAGCACCCCCGGCCGGCGCTGCGCCCAGCACCCTTTCGGCAGCTACCCCGGGTACTTCTGAAGACCACTCCCAGAGCGCCACGCCGCCGGAGCAGCAACGGGCAGAGGACATTACCAGGTTATAAAACATAACTCACACCCCTGCCCCCACCCCATGCCCCCACCCTCCCCTCACACACAAATTGACTCTTATTTATAGAATTTAATATATATATATATATATATATATATAGGTTCTTTTCTCTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000198353:ENST00000303406:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.792 A=NA C2=0.669
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=47.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATAGCTGCACCAGTCTCCAGG
R:
TTCTCCTTCGGGTCAGGTAGC
Band lengths:
357-845
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains