HsaINT0077320 @ hg19
Intron Retention
Gene
ENSG00000128709 | HOXD9
Description
homeobox D9 [Source:HGNC Symbol;Acc:5140]
Coordinates
chr2:176987413-176989645:+
Coord C1 exon
chr2:176987413-176988313
Coord A exon
chr2:176988314-176988661
Coord C2 exon
chr2:176988662-176989645
Length
348 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
CCAAACCTCCCTCTTTGTAGACA
3' ss Score
7.04
Exon sequences
Seq C1 exon
CGCGACCAATGGTGGAGGCTGCAGCCTGCGAACTAGTCGGTGGCTCGGGCGCCGGCGGGGAGCTGCTCGGCGGCGGACAGTGTAATGTTGGGTGGGAGTGCGGGACGCCTCAAAATGTCTTCCAGTGGCACCCTCAGCAACTACTACGTGGACTCGCTTATAGGCCATGAGGGCGACGAGGTGTTCGCGGCGCGCTTCGGGCCGCCGGGGCCAGGCGCGCAGGGCCGGCCTGCAGGTGTGGCTGATGGCCCGGCCGCCACCGCCGCCGAGTTCGCCTCGTGTAGTTTTGCCCCCAGATCGGCCGTGTTCTCTGCCTCGTGGTCCGCGGTGCCCTCCCAGCCCCCGGCAGCGGCGGCGATGAGCGGCCTCTACCACCCGTACGTTCCCCCGCCGCCCCTGGCCGCCTCTGCCTCCGAGCCCGGCCGCTACGTGCGCTCCTGGATGGAGCCGCTGCCCGGCTTCCCGGGCGGTGCGGGCGGTGGCGGTGGTGGTGGAGGCGGCGGTCCGGGCCGCGGTCCCAGCCCTGGCCCCAGCGGCCCAGCCAACGGGCGCCACTACGGGATTAAGCCTGAAACCCGAGCGGCCCCGGCCCCCGCCACGGCCGCCTCCACCACCTCCTCCTCCTCCACTTCCTTATCCTCCTCCTCCAAACGGACTGAGTGCTCCGTGGCCCGGGAGTCCCAGGGGAGCAGCGGCCCCGAGTTCTCGTGCAACTCGTTCCTGCAGGAGAAGGCGGCAGCGGCGACGGGGGGAACCGGGCCTGGGGCAGGGATCGGGGCCGCGACTGGGACGGGCGGCTCGTCGGAGCCCTCAGCTTGCAGCGACCACCCGATCCCAGGCTGTTCGCTGAAGGAGGAGGAGAAGCAGCATTCGCAGCCGCAGCAGCAGCAACTTGACCCAA
Seq A exon
GTAAGTGCAAAAGAAATTGCCCCCTGATTTATTGCTGAAACCTGTAAGGCTCGAATGTGCAAAACTGATAGTTTTACTAACCTATAAAAACGTCTAGACGCCTACCCAAGCCTAGGCGAACAACATGCATCCATAAAAAGAGCTTCCCATAACCACCTACCCTGGGCGCTCAGTTAGTACGGTAAACAGAGCGCGAGCATTAAGGCTTTTTATGATAATTCCCCACAAGTTGTGAAAAGCGACCATCCTTGGTGAAATTAATTTAACGACCTCTCTTCCCCACCCTGTGGTCTCTCCCTGCCTCCCCTCCTCTCCTCTCTCCCCGTCTCCAAACCTCCCTCTTTGTAG
Seq C2 exon
ACAACCCCGCCGCGAACTGGATCCACGCTCGCTCCACCCGGAAAAAGCGCTGTCCCTACACCAAATACCAGACGCTTGAGCTGGAGAAAGAATTCCTCTTCAACATGTACCTCACCCGGGACCGGCGCTACGAGGTGGCCAGGATTCTCAACCTAACAGAGAGACAGGTCAAAATCTGGTTTCAGAACCGTAGGATGAAAATGAAAAAGATGAGCAAGGAGAAATGCCCCAAAGGAGACTGACCCGGCGCGGTGCTGGCGGGAGCGCTCAAGGGCAGCGGATTTGTTGTTGTTGCTGTTTTCCTTTGTGGGTGTTTGGTGCTTGATTTCCAGAAACTCTCCAGCGACTTGGACTTCTTCTTCTTTTTTTTTTTCTTTTTAGATAGAAGTGACTGTGTGGTTGGTCTCTGAGGTATTTGGGGGACTCTGTATTTGCTCGTTTACGTGTTGGAAAAACCAAGTGGCTTTGGGGTTTCGCCCTATCCCACTCCCTCTCTTTCCTGCTCCATTGGTTCCTTAAGAAATGCTATATTTTGTGAGTGCAAGCTGGCTTGGGGAGCCCTCTCTTGTGTAAATGTCCCCCATGTTTCTGAAAAGTGCTGTAGTTTAGTCCCCTCACCCCCAGCACTGCCCAAACAGGGGCCAAGTGCGCCCCAATTCCAAGAATGAAGGCAGAGCGACAACAGTGCGGACACCCCGGCTGCTAGCCCACGGTGAAGCCCGGCGGGGTTGCCCACCAGTTGCGAAAGCCCCCTTTCCTCAGGGAGCACGCGGGACCTCGGTGGAGATCTCCAGTGAGGCTTAGAGGAGCCCAGGGCCTCGGGCGGGTTGGGGTTTGTCCTCAGTGCATTGGACGCGCTGCTCTCTCCCCTGAAGGCTGGGCTCGCGTGGGCGGCCGCGGGTGGTGGCCCTCCCGGTTCCTGCCCGAGGACCAGTTGTAAATGTTACTGCTTCCTACTAATAAATGCTGACCTGATCAAATGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000128709-HOXD9:NM_014213:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.777 A=NA C2=0.312
Domain overlap (PFAM):
C1:
PF046178=Hox9_act=WD(100=45.4),PF046178=Hox9_act=WD(100=29.3)
A:
NA
C2:
PF0004624=Homeobox=WD(100=70.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACCTCCTCCTCCTCCACTTC
R:
TGTAGGGACAGCGCTTTTTCC
Band lengths:
350-698
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)