HsaINT0076886 @ hg19
Intron Retention
Gene
ENSG00000188620 | HMX3
Description
H6 family homeobox 3 [Source:HGNC Symbol;Acc:5019]
Coordinates
chr10:124895567-124897247:+
Coord C1 exon
chr10:124895567-124895966
Coord A exon
chr10:124895967-124896573
Coord C2 exon
chr10:124896574-124897247
Length
607 bp
Sequences
Splice sites
5' ss Seq
AAGGTACCG
5' ss Score
9.67
3' ss Seq
CCGTCTGTCTGTCTCCCCAGCCT
3' ss Score
9.68
Exon sequences
Seq C1 exon
ATGCCGGAACCCGGGCCGGACGCTGCCGGCACCGCCAGCGCACAGCCCCAACCGCCGCCGCCCCCCCCACCCGCTCCCAAGGAGTCCCCGTTCTCCATCAAGAACCTGCTCAACGGAGACCACCACCGGCCGCCCCCTAAGCCTCAGCCGCCCCCACGGACGCTCTTCGCGCCAGCCTCGGCTGCCGCCGCCGCCGCCGCTGCCGCTGCCGCGGCGGCCAAGGGGGCCCTGGAGGGCGCCGCGGGCTTCGCGCTCTCGCAGGTGGGCGACCTGGCTTTCCCTCGCTTTGAGATCCCGGCGCAGAGGTTTGCCCTGCCCGCGCACTACCTGGAGCGCTCCCCAGCCTGGTGGTACCCCTACACCCTGACCCCCGCCGGCGGCCACCTCCCGCGACCTGAAG
Seq A exon
GTACCGACCTCTCTTTGAACTTTCGTTGTCCCCCTGCGCGCCCGCCCCGTCCCCGCCCCGCGCTGCTTCCCTCCGCAGTTCTGGGACCCCAGCACCCGCAAACCCTCTGCTCGGTCAGTTTTTTTCGGCCCCTAGCCTGCCCTCGCGCTGGGTTGCGCTGCCCGTTAATCCAATCCCACTTGGTGAGAAAAGAAGTGGAATTGGAGCCCCGGGCACGGTGCTTCCCGGGAAAAGTGGCCTCGGGCGTGAATAGGGAGGCTTCGGACGGCCGGGGCTTGGGACACGGCCTGGAAGGAGGGGGTGATTCCAATGCGCCTAAGCCGAAAGGGAACCGTTCTGCCGGCCCCTGGCGAGGAAGCTGAGGGAATGGAAGGAGGTGGCCGCGCTACCACCATCTGCTTGCCTGTCCTCGGGAGGAGGGGGATCCCAGGACTCGGCGTCCCTTCTCTGGCCCAGCCGAGAAGGAGGCAGCCCGCGGGAATGGTGAGGCCTCATGGCCTGGGACCTGGAGGCCGGCGCGGGTTGAGCCTGCCGTCCCCAGGCGCCGGGCCTCGCTCAAGGCTGTGTCGGTGTGCATGTGTGTGCGTCCGTCTGTCTGTCTCCCCAG
Seq C2 exon
CCTCGGAGAAGGCCTTGCTGAGAGACTCCTCCCCCGCCTCCGGCACAGACCGCGACTCTCCGGAGCCACTGCTCAAGGCCGACCCCGATCACAAGGAGCTGGACTCCAAGAGCCCGGACGAGATCATTCTGGAGGAGAGCGACTCCGAGGAAAGCAAAAAGGAAGGCGAAGCGGCGCCAGGCGCGGCCGGGGCGAGCGTAGGGGCGGCGGCGGCCACTCCGGGCGCAGAAGACTGGAAGAAGGGCGCTGAAAGTCCAGAGAAGAAGCCGGCGTGCCGCAAGAAGAAGACGCGCACAGTCTTCTCGCGCAGCCAGGTCTTCCAGCTCGAGTCCACCTTCGACATGAAGCGCTATCTGAGCAGCTCGGAGCGAGCCGGCCTGGCCGCGTCCCTGCACCTCACCGAGACGCAGGTCAAGATCTGGTTCCAGAACCGCCGCAACAAGTGGAAGCGGCAGCTGGCGGCGGAGCTGGAGGCGGCCAACCTGAGCCATGCCGCGGCGCAGCGCATCGTGCGGGTGCCCATCCTCTACCACGAGAACTCGGCGGCCGAGGGCGCGGCGGCTGCAGCCGCGGGGGCCCCGGTGCCAGTCAGCCAGCCGCTGCTCACCTTCCCGCACCCCGTCTACTACTCGCACCCGGTGGTCTCTTCCGTGCCGCTGCTACGGCCGGTCTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000188620-HMX3:NM_001105574:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.634 A=NA C2=0.433
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=25.3)
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:
AAGGAGTCCCCGTTCTCCATC
R:
AGTCTCTCAGCAAGGCCTTCT
Band lengths:
349-956
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)