HsaINT0077313 @ hg19
Intron Retention
Gene
ENSG00000128713 | HOXD11
Description
homeobox D11 [Source:HGNC Symbol;Acc:5134]
Coordinates
chr2:176972084-176974316:+
Coord C1 exon
chr2:176972084-176972864
Coord A exon
chr2:176972865-176973634
Coord C2 exon
chr2:176973635-176974316
Length
770 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGC
5' ss Score
9.88
3' ss Seq
CTGGTCTCTTTGCCTTGCAGTTG
3' ss Score
10.12
Exon sequences
Seq C1 exon
ATGAACGACTTTGACGAGTGCGGCCAGAGCGCAGCCAGCATGTACCTGCCGGGCTGCGCCTACTATGTGGCCCCGTCTGACTTCGCTAGCAAGCCTTCGTTCCTTTCCCAACCGTCGTCCTGCCAGATGACTTTCCCCTACTCTTCCAACCTGGCTCCGCACGTCCAGCCCGTGCGCGAAGTGGCCTTCCGCGACTACGGCCTGGAGCGCGCCAAGTGGCCGTACCGCGGCGGCGGCGGCGGCGGCAGCGCGGGGGGCGGCAGCAGCGGGGGCGGCCCCGGCGGGGGCGGCGGCGGCGCGGGGGGCTACGCTCCCTACTACGCGGCGGCGGCGGCGGCGGCTGCGGCGGCCGCGGCGGCCGAGGAGGCGGCCATGCAACGCGAGCTTCTCCCGCCCGCGGGCCGCCGGCCGGACGTGCTCTTCAAGGCGCCTGAGCCGGTGTGCGCTGCGCCGGGGCCGCCGCACGGCCCCGCGGGCGCCGCCTCCAACTTCTACAGCGCGGTGGGCCGCAATGGCATCTTGCCACAGGGCTTCGACCAGTTCTACGAGGCAGCGCCCGGGCCCCCGTTCGCCGGGCCGCAGCCCCCGCCGCCACCCGCGCCGCCACAGCCCGAGGGCGCAGCCGACAAGGGCGACCCCAGGACCGGGGCTGGTGGCGGCGGGGGCAGTCCCTGCACCAAGGCGACCCCTGGCTCGGAGCCCAAGGGGGCAGCAGAAGGCAGCGGTGGCGACGGCGAGGGCCCCCCGGGAGAGGCGGGGGCCGAGAAGAGCAGCAGCGCAG
Seq A exon
GTAGGCACCGGGTACTGGGCAAGCGGTGGGCCCGGGGGCCGCGGGGGAGGGGGGGGGGGCGGAGGCCTCCCTCTGCTTGCGCCTTTTTATGTGCTACTTTATAAGCATTCGAAGAGGTTTATACATCCTATAAGATTTCCTGGGCCGTTGTAAAGTGTGTTTATGGTAGGAAACCAATTTAGGTGGGCTTAAGGTAGACTTCGAGGAGGACATTAATAGCTGTCGAGAGCCTTTTCCCAGTTTTGGGCAGGGGGTTGCTAGATACCATGGAGGGAGGGAGGGAGGGAGATTTCAAGCCAGTGTGAGTGCATACACCGGAGCCTCCTGCTTTTAAGGGAGAGAGGCGGGGGGTGGGGAAGTGGGGGGAGTTTGATCCTTGCACTGGACTTTATCCAAGCCGCTAGCTGACGCGCGCCGCTGGAGTCAAGCAGATGCCCCGGCGGGCCTGCTCTTGTCTCTGTTCCCTCAGGTTCCAGTTTAGAGCCTGCCTTGCCCTCTGCTTCCCCACCTCCGTGCCAGGCTCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTCCGGGCGTGAACACATGTCCACGCCCGCACTCTCTCCTGTGCCCGCCCATATATCATCCCCCACGACGCAGGCAGGGCCTTTCGGCCGCGGCAGAGAACGTCCCCAACGGGGCCAGGGCCTGGCCCTCGCTCAGTGGCCCGGGCGGGCGGGCGGGTGGGGGCTGTCAGGCAGCGGCCTCTCTCACCCCCTGGTCTCTTTGCCTTGCAG
Seq C2 exon
TTGCCCCCCAGCGGTCCCGGAAAAAGCGCTGTCCCTATACCAAGTACCAGATCCGCGAACTGGAACGCGAGTTTTTCTTTAACGTGTACATAAACAAAGAGAAAAGACTTCAACTCTCTCGGATGCTCAACCTCACTGACCGGCAAGTCAAAATCTGGTTCCAGAATCGCAGGATGAAAGAAAAGAAACTGAACAGAGACCGTCTGCAGTATTTCACTGGAAACCCCTTATTTTGAGAGCTCCAGGAAGCGCCCTCACCCCAGCCCCACTCACCCACCCTCCTTCCCACCAGCCTGCTCTCCGCAGGCCCACTGTCCTTGGGTTTAATGACGTCTCTTCTCTGTGGAACTTCACGATTCCTTCCCACGGTCAACTCGGGACCTCCCAGCGACCACTGCAGCCTGCGGACGAGGCCGGGACTTGGCCGAGCGGATCCTAATAAGGGGAAAATGGTAAATGCAAACGTCCCGTTACAATTTTACCGCCAGTGTGCTGTCGTTCCCCCTCCCCCTCTCCGAGTCCTCGTGGGGACACGGCGGGGTCTGTAGGAAGTTGGGCCGGGTTGGGGGTTGCTAGAAGGCGCTGGTGTTTTGCTCTGAGTTTTAAGAGATCCCTTCCTTCCTCTTCGGTGAATGCAGGTTATTTAAACTTTGGGAAATGTACTTTTAGTCTGTCATATCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000128713-HOXD11:NM_021192:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.638 A=NA C2=0.157
Domain overlap (PFAM):
C1:
PF120453=DUF3528=WD(100=69.3)
A:
NA
C2:
PF0004624=Homeobox=WD(100=72.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCCAACTTCTACAGCGCGG
R:
ACTTGGTATAGGGACAGCGCT
Band lengths:
344-1114
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)