HsaINT0077319 @ hg38
Intron Retention
Gene
ENSG00000175879 | HOXD8
Description
homeobox D8 [Source:HGNC Symbol;Acc:HGNC:5139]
Coordinates
chr2:176129740-176132029:+
Coord C1 exon
chr2:176129740-176130943
Coord A exon
chr2:176130944-176131316
Coord C2 exon
chr2:176131317-176132029
Length
373 bp
Sequences
Splice sites
5' ss Seq
AAGGTTGGG
5' ss Score
4.94
3' ss Seq
TTTTTTTTTGTTTTAATCAGCAG
3' ss Score
6.97
Exon sequences
Seq C1 exon
TCCGTGCAGTGCTGTGGTGCGAAAATGCCTCGCCGGTGCGCACCGGGTCGGCAGCCTCGGCGGCGGGGGCGAGATTGGCGGGAGGGGGGCGCGGGGGGGGCGCGGTAAGAGGTGGCGGCGGGCAGAGGGTGTTTTTTTTCTTTTCCCTCCAGAGCCGGGGTTTGTAAACCGAGGCCAGAGTGTCCCCGTGGGCCGAGCGCACTTTTTTCTTGTCCGGGTGCGCTCAGTCACTGGTGCCTGAGAGGAAACAGTGGAGGCAGCGGGGCAGGTCGCCTGGGGCGTCGGCGATTATATTGCGGCCGAGCCGGGGCGCGCCGGGAAAGGCCGGGAGGGCGGCGGCGCGCGGGGGCTGGGCGAGGCCCCGCGACCCGCGAGGGAGGCGGCGCGAAGCCGAGGCGGCGGGCGCAAGAGCCGGGCATGAGCGCCCAGTAGCTGAGCGCCCGCGGCTGCCTGGCCTCAGAAGCGACGCGCGAGCGCGGGCGGGCGGCAGCAGCGACGTAGCCCGGCGGTCCCGGCGGCGAGAGCAGCCGCCCCACAGGCCCCCGCGGCAGTGCGGCCGAGTCGAGGCTCGCTCTCTGGCTGCTTAGCGCCGCCCGCCCGCCCGGGGCCGCCGCCGCTGACGCCCCAATGAGTTCGTACTTCGTGAACCCGCTGTACTCCAAGTACAAGGCGGCGGCTGCGGCGGCGGCGGCGGCGGGCGAGGCCATCAATCCCACTTACTACGACTGTCACTTCGCGCCCGAGGTCGGCGGCCGTCACGCCGCCGCCGCAGCAGCCCTGCAGCTCTATGGCAACAGCGCCGCCGGCTTCCCGCACGCGCCCCCGCAGGCGCACGCGCACCCGCACCCGTCCCCGCCGCCCTCCGGGACTGGGTGCGGCGGTAGGGAAGGCCGGGGCCAGGAGTACTTCCACCCCGGCGGGGGCAGCCCGGCCGCTGCCTACCAGGCCGCCCCCCCTCCTCCTCCGCATCCTCCGCCTCCGCCGCCACCTCCCCCCTGCGGCGGGATTGCCTGTCACGGGGAGCCCGCGAAGTTTTACGGATACGATAACTTACAGAGACAGCCGATTTTTACGACCCAGCAAGAGGCCGAGCTGGTACAATATCCTGACTGTAAATCGTCCAGTGGTAATATTGGCGAGGACCCAGACCACTTAAATCAGAGCTCGTCTCCTTCTCAAATGTTTCCGTGGATGAGACCACAAG
Seq A exon
GTTGGGATGCATTTTTTTTTTAAGAAGGGAGAGGGGGAGAAATCTGCTTTCATCTCACGTTCTGGCTTTAAAACTCCCGTTCCCTCTCCCCCTCCTTTTCCTTCTTGTGTAGCCACAGTGGCTCTTATTCATAAAGTAATACAGACTTTTTTTAAAAAAGTAGGAACCATGTAAAGATGATGGGGACAGAATAATTGTGAAGACCTCTCTGCTCCTCTTGCCTGCACACCCTATATATATATATCGGAGCTAAAGAGCTCTGTGTATATTTCACCCCGTAGACCCCCGTTCCACAAACCTCCAGCAACATGCAGAGGTACCATAACATTTTTAAAACTTTTATTCCCCCCCCCTTTTTTTTTGTTTTAATCAG
Seq C2 exon
CAGCTCCTGGTAGACGAAGAGGAAGACAAACCTACAGTCGCTTCCAAACTCTAGAGTTGGAAAAGGAATTTCTTTTTAACCCCTATCTGACCAGGAAAAGAAGAATCGAGGTTTCCCACGCCCTAGCCCTCACCGAGAGACAGGTAAAAATCTGGTTCCAGAACAGGAGAATGAAATGGAAAAAGGAAAACAACAAGGACAAATTTCCCGTTTCCCGGCAGGAGGTGAAGGACGGGGAAACGAAAAAGGAAGCCCAAGAGCTGGAGGAAGACAGAGCCGAAGGCCTGACAAATTAACTTCTACCTTTAAAATTTACCACAGACTATTAAAACTAATAATCACCATATGCTGTGGACACCACCTATTTTCTTTGTTGGAAAGGACCTTACCTGTGTTTCAAGCTACCTTCATGTCACTGCTCTTGAGGTTTTCTGTGCTTTGAGAGGGATTTGGGTGTTTAAAAAAGTTTCTAGTATCACATAGAAGCTGTCCTTGAGCTGTCCTATGGAAGGGTAATTTGATACTGACCTTGTAGCTATATTTTTATAATGGTTTTTAATGTCTGAGCTAGTGATTTGCCTCAACAACGTAAACTTCCTAATGATTAGCACTTAATAATTGCATATAAAATGCTTTATTAATTAAACAAGTGCACTTGAACATTTTAATATTTGTGGTGAGTAAATTAAAAGGAGTTTATTAATTAAAAAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000175879:ENST00000313173:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.644 A=NA C2=0.502
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=57.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATATTGGCGAGGACCCAGACC
R:
GCTCTGTCTTCCTCCAGCTCT
Band lengths:
352-725
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