HsaINT1015861 @ hg38
Intron Retention
Gene
ENSG00000198353 | HOXC4
Description
homeobox C4 [Source:HGNC Symbol;Acc:HGNC:5126]
Coordinates
chr12:54053160-54054361:+
Coord C1 exon
chr12:54053160-54053276
Coord A exon
chr12:54053277-54053916
Coord C2 exon
chr12:54053917-54054361
Length
640 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
AAAATTATTTTCCACTCCAGAAA
3' ss Score
6.59
Exon sequences
Seq C1 exon
CGGGGGCTCAACCCCCAGACCTCCAGAAATGACGTCAGAATCATTTGCATCCCGCTGCCTCTACCTGCCTGGTCCAGCTGGGACCCTGCCTCGCCGGCCGCATGGCCAGAGGGTTGG
Seq A exon
GTGAGTGTGTATGGGGAAGAGGGGCTGGACTCTGGTATCCTTGGATGGGGGGCACTCCAGGCTCTCCAGCCTCCTCGGCTCAGCCTGGGCCCCTCCCCATCCAACATCCACTCCAGTCCTCATTCAACTTCCTCTTCCTGCGAAAGAGGGGCGCTGCCCCGTGACCTACACAGACTGAGACACGATCGCCATGAATGGAGACCTCTGGAAAAGCTCAGGAGCCGAGGCCCACGGGGCCCAGCAGAGGCCTGAGGGGAGACCCTGGGCGGGGGCTGAATCACTGCCTCCCGACAGTCCCCCAATGCCCGGGCTTTGGAGGGGAGCCGGGAGCTTCCCATCTCCTTTTGCAGGGGAGGGTTGTCAGTCTGGCGGGATGTGCACTGGGGGCACTCCAACCTCTGCTAGCTAACCCCACATCACCACCCACCCCCGCCTCCCAGCACCACCACCACCACACACACAAAAAAATTGGATACATTTTGAATAAAGCGATTCGGTTCCTTATCCGGGGACTGGGTTGCTCCGTGTGATTGGCCGGAGGAGTCACATGGTGAAAGTAACTTTACAGGGTCGCTAGCTAGTAGGAGGGCTTTATGGAGCAGAAAAACGACAAAGCGAGAAAAATTATTTTCCACTCCAG
Seq C2 exon
AAATTAATGATCATGAGCTCGTATTTGATGGACTCTAACTACATCGATCCGAAATTTCCTCCATGCGAAGAATATTCGCAAAATAGCTACATCCCTGAACACAGTCCGGAATATTACGGCCGGACCAGGGAATCGGGATTCCAGCATCACCACCAGGAGCTGTACCCACCACCGCCTCCGCGCCCTAGCTACCCTGAGCGCCAGTATAGCTGCACCAGTCTCCAGGGGCCCGGCAATTCGCGAGGCCACGGGCCGGCCCAGGCGGGCCACCACCACCCCGAGAAATCACAGTCGCTCTGCGAGCCGGCGCCTCTCTCAGGCGCCTCCGCCTCCCCGTCCCCAGCCCCGCCAGCCTGCAGCCAGCCAGCCCCCGACCATCCCTCCAGCGCCGCCAGCAAGCAACCCATAGTCTACCCATGGATGAAAAAAATTCACGTTAGCACGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000198353:ENST00000303406:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.792
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATCCCGCTGCCTCTACCTG
R:
TGATTTCTCGGGGTGGTGGT
Band lengths:
357-997
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains