HsaINT0077319 @ hg19
Intron Retention
Gene
ENSG00000175879 | HOXD8
Description
homeobox D8 [Source:HGNC Symbol;Acc:5139]
Coordinates
chr2:176994477-176996728:+
Coord C1 exon
chr2:176994477-176995671
Coord A exon
chr2:176995672-176996044
Coord C2 exon
chr2:176996045-176996728
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
TGCTGTGGTGCGAAAATGCCTCGCCGGTGCGCACCGGGTCGGCAGCCTCGGCGGCGGGGGCGAGATTGGCGGGAGGGGGGCGCGGGGGGGGCGCGGTAAGAGGTGGCGGCGGGCAGAGGGTGTTTTTTTTCTTTTCCCTCCAGAGCCGGGGTTTGTAAACCGAGGCCAGAGTGTCCCCGTGGGCCGAGCGCACTTTTTTCTTGTCCGGGTGCGCTCAGTCACTGGTGCCTGAGAGGAAACAGTGGAGGCAGCGGGGCAGGTCGCCTGGGGCGTCGGCGATTATATTGCGGCCGAGCCGGGGCGCGCCGGGAAAGGCCGGGAGGGCGGCGGCGCGCGGGGGCTGGGCGAGGCCCCGCGACCCGCGAGGGAGGCGGCGCGAAGCCGAGGCGGCGGGCGCAAGAGCCGGGCATGAGCGCCCAGTAGCTGAGCGCCCGCGGCTGCCTGGCCTCAGAAGCGACGCGCGAGCGCGGGCGGGCGGCAGCAGCGACGTAGCCCGGCGGTCCCGGCGGCGAGAGCAGCCGCCCCACAGGCCCCCGCGGCAGTGCGGCCGAGTCGAGGCTCGCTCTCTGGCTGCTTAGCGCCGCCCGCCCGCCCGGGGCCGCCGCCGCTGACGCCCCAATGAGTTCGTACTTCGTGAACCCGCTGTACTCCAAGTACAAGGCGGCGGCTGCGGCGGCGGCGGCGGCGGGCGAGGCCATCAATCCCACTTACTACGACTGTCACTTCGCGCCCGAGGTCGGCGGCCGTCACGCCGCCGCCGCAGCAGCCCTGCAGCTCTATGGCAACAGCGCCGCCGGCTTCCCGCACGCGCCCCCGCAGGCGCACGCGCACCCGCACCCGTCCCCGCCGCCCTCCGGGACTGGGTGCGGCGGTAGGGAAGGCCGGGGCCAGGAGTACTTCCACCCCGGCGGGGGCAGCCCGGCCGCTGCCTACCAGGCCGCCCCCCCTCCTCCTCCGCATCCTCCGCCTCCGCCGCCACCTCCCCCCTGCGGCGGGATTGCCTGTCACGGGGAGCCCGCGAAGTTTTACGGATACGATAACTTACAGAGACAGCCGATTTTTACGACCCAGCAAGAGGCCGAGCTGGTACAATATCCTGACTGTAAATCGTCCAGTGGTAATATTGGCGAGGACCCAGACCACTTAAATCAGAGCTCGTCTCCTTCTCAAATGTTTCCGTGGATGAGACCACAAG
Seq A exon
GTTGGGATGCATTTTTTTTTTAAGAAGGGAGAGGGGGAGAAATCTGCTTTCATCTCACGTTCTGGCTTTAAAACTCCCGTTCCCTCTCCCCCTCCTTTTCCTTCTTGTGTAGCCACAGTGGCTCTTATTCATAAAGTAATACAGACTTTTTTTAAAAAAGTAGGAACCATGTAAAGATGATGGGGACAGAATAATTGTGAAGACCTCTCTGCTCCTCTTGCCTGCACACCCTATATATATATATCGGAGCTAAAGAGCTCTGTGTATATTTCACCCCGTAGACCCCCGTTCCACAAACCTCCAGCAACATGCAGAGGTACCATAACATTTTTAAAACTTTTATTCCCCCCCCCTTTTTTTTTGTTTTAATCAG
Seq C2 exon
CAGCTCCTGGTAGACGAAGAGGAAGACAAACCTACAGTCGCTTCCAAACTCTAGAGTTGGAAAAGGAATTTCTTTTTAACCCCTATCTGACCAGGAAAAGAAGAATCGAGGTTTCCCACGCCCTAGCCCTCACCGAGAGACAGGTAAAAATCTGGTTCCAGAACAGGAGAATGAAATGGAAAAAGGAAAACAACAAGGACAAATTTCCCGTTTCCCGGCAGGAGGTGAAGGACGGGGAAACGAAAAAGGAAGCCCAAGAGCTGGAGGAAGACAGAGCCGAAGGCCTGACAAATTAACTTCTACCTTTAAAATTTACCACAGACTATTAAAACTAATAATCACCATATGCTGTGGACACCACCTATTTTCTTTGTTGGAAAGGACCTTACCTGTGTTTCAAGCTACCTTCATGTCACTGCTCTTGAGGTTTTCTGTGCTTTGAGAGGGATTTGGGTGTTTAAAAAAGTTTCTAGTATCACATAGAAGCTGTCCTTGAGCTGTCCTATGGAAGGGTAATTTGATACTGACCTTGTAGCTATATTTTTATAATGGTTTTTAATGTCTGAGCTAGTGATTTGCCTCAACAACGTAAACTTCCTAATGATTAGCACTTAATAATTGCATATAAAATGCTTTATTAATTAAACAAGTGCACTTGAACATTTTAATATTTGTGGTGAGTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000175879-HOXD8:NM_019558:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.612 A=NA C2=0.503
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
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
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)