HsaINT0077318 @ hg38
Intron Retention
Gene
ENSG00000170166 | HOXD4
Description
homeobox D4 [Source:HGNC Symbol;Acc:HGNC:5138]
Coordinates
chr2:176151222-176153226:+
Coord C1 exon
chr2:176151222-176152066
Coord A exon
chr2:176152067-176152607
Coord C2 exon
chr2:176152608-176153226
Length
541 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGG
5' ss Score
10.17
3' ss Seq
CTGTCTGTTTTGTCTCGCAGTGA
3' ss Score
10.83
Exon sequences
Seq C1 exon
ATAGGAGGATTCATTCTCCCTTGAGCTGTGCCTACTTGGTGTCGGGGGGCGGGGGTTGCATTCAGCTGGGGGTGAGTGGAAGGGCCACGGAAGGTTGGCAAAATCAGTGGCAGACAAAAGCTGGGATTACCTGAGGGGAATGGGGTGCTGGGGACTGGAACTACATTAATATCTGGCAGGGGCTCTCAAATGTGCCATAGCAAGCTACTTGATTACACGTATGTTATTTAGTTAAATTTGTGAAAATTATGAGATGCTCACCAACCCGGTGATAAACTTGCTCCCTCGCCATTGGCTGGCCTGGTCACATGGCTGCCCAACTTTATTCAGTTGACAGCAAGTAGGAGGGCCCTATGGAAGGAGAAAAAAAGACAACACGAGAAAAATTAGTATTTTCTACCTTCTGAAATTAATGGTCATGAGTTCGTATATGGTGAACTCCAAGTATGTGGACCCCAAGTTCCCTCCGTGCGAGGAGTATTTGCAGGGCGGCTACCTAGGCGAGCAGGGCGCCGACTACTACGGCGGCGGCGCGCAGGGCGCAGACTTCCAGCCCCCGGGGCTCTACCCACGGCCCGACTTCGGTGAGCAGCCTTTCGGAGGCAGCGGCCCCGGGCCTGGCTCGGCGCTGCCTGCGCGGGGTCACGGACAAGAGCCAGGCGGCCCCGGCGGTCACTACGCCGCTCCAGGAGAGCCTTGCCCAGCTCCCCCGGCGCCTCCGCCGGCGCCCCTGCCTGGCGCCCGGGCCTACAGTCAGTCCGACCCCAAGCAGCCGCCCTCCGGGACGGCACTCAAGCAGCCGGCCGTGGTCTACCCCTGGATGAAGAAGGTGCACGTGAATTCGG
Seq A exon
GTAAGGCTAGGGTCCAGTAACCTTTCTGTCCACATCCCAGCCCGTTAGCCTGGGTCCTCTGGAAGGGGGTGCGAGTAGGTGGGGGCGTGTGGAGCTTCCATGGGCGCCGCAATTACTCTCCCCATAAATTTTTATAGCTGAGGGAGCAGGTCAGGACCATGTGGCTGGCTGCTCGGCTGTGGGCGCAAAAGGGGGTGGGGATGGGGGGGTGGGGGAGGACTCCATTTTCAGAGCAGGGGGAAGGCTGTGGAGGAGCGGGGGATTTCCAAAATGCTTGAGGGTTCCGGACCTGGTGGTGGGCCCAGAAGAAGGAGCACATTTGGGGATCCCGCAAGCCTGGGGTATGTGGGTGTGTTTGAGGAGGTGGGTGGGAGTGAGCGTGTGCGCCGGGGAGAGGGCGGGAGGGAGGAAGCAAGCGAGCTTGGGAGCGCGCGGGGAGGGCCGCGGGCCTCGGGGCGCGCCAGGAAGTGAGCGGCGGAGGCGAGGGGCCTAACTAGTGGCCGGGCGCTGACCTGCCTGTCCTGTCTGTTTTGTCTCGCAG
Seq C2 exon
TGAACCCCAACTACACCGGTGGGGAACCCAAGCGGTCCCGAACGGCCTACACCCGGCAGCAAGTCCTAGAACTGGAAAAAGAATTTCATTTTAACAGGTATCTGACAAGGCGCCGTCGGATTGAAATCGCTCACACCCTGTGTCTGTCGGAGCGCCAGATCAAGATCTGGTTCCAGAACCGGAGGATGAAGTGGAAAAAAGATCATAAGCTGCCCAACACTAAAGGCAGGTCATCGTCCTCATCTTCCTCCTCATCTTGCTCCTCCTCAGTCGCCCCCAGCCAGCATTTACAGCCGATGGCCAAAGACCACCACACGGACCTGACGACCTTATAGAAGTGGGGACCCTGGGCCCATCTCTCCCTGCGCACCAGGCTGAGCCGAAGCTGCGGGGGCAGGCCGGGCCTGCTGTCACCTCGCTGGGCTCTAAGGTACTGTGGGGTGGACCTGGGACAAGCAGGCCGCCCTCGGACTAGGTTAGCATCCTGCCCGAGGGCAGCCCCCTCCCTAGAGCGGGATGGGGATGGGAGGGGGGGCGGGATTCTCTCTCTAAGTATATTATATGGCAGGAGCTACTGAGAACATAAAATCTTGGCGAGTCATTAAACTTATGAAAATCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000170166:ENST00000306324:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.738 A=NA C2=0.631
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=50.9),PF105004=SR-25=WD(100=68.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGAAGGTGCACGTGAATTCGG
R:
ATAAGGTCGTCAGGTCCGTGT
Band lengths:
354-895
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