HsaINT0076885 @ hg19
Intron Retention
Gene
ENSG00000188816 | HMX2
Description
H6 family homeobox 2 [Source:HGNC Symbol;Acc:5018]
Coordinates
chr10:124907638-124910188:+
Coord C1 exon
chr10:124907638-124908162
Coord A exon
chr10:124908163-124909085
Coord C2 exon
chr10:124909086-124910188
Length
923 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGG
5' ss Score
9.08
3' ss Seq
TGTCTGTTCTCGCTCCTCAGGTA
3' ss Score
11.68
Exon sequences
Seq C1 exon
CGGGCGAGGAAGGGGCATTTGCACCGGGGCTGGGCGGGCGCACCCAGAGCCAGGCGGGCAGGAACCCCTGCGCAGCCATCCGGTGCCTGCATGTCCCTGGCGCGGAAGGGACGCCTCACCAGCCTCGGCGCCCCCTCCCCCTAGATTTCCTCCCCGCCCCTCCCCACTGCCTGCCTGCTGCACCACCTTCCACCCAGATCACCCAGATCGTCTCTAAAGGGAGTTCTTGGTTTCCTTCGATTTCTTATGAACCCAGGATGGGCAGCAAAGAAGATGCGGGCAAGGGGTGTCCGGCGGCCGGTGGCGTCTCCAGCTTCACCATCCAGTCCATCCTGGGCGGGGGCCCCTCGGAGGCACCGCGGGAGCCCGTCGGCTGGCCAGCCAGGAAGCGCAGCCTGTCCGTGTCCTCGGAGGAGGAGGAGCCGGACGACGGCTGGAAGGCGCCCGCCTGCTTCTGCCCAGACCAGCACGGCCCTAAGGAGCAGGGCCCCAAGCACCATCCCCCCATCCCTTTTCCTTGCCTGG
Seq A exon
GTAAGGATCGCACGTCGCCAGTGTGGCAGCGAGCGAGCGCGAGGGGAGGGAGGCTGAGCGCCCCGCCAAGACTCCCGCGCCGGGCCCCCTCTGGCCAGAGCTGCGGCAGCCGGGGGTTCGGGACCGCGGGGAGAGGGGCGCGCACTGTGGTGCCTCCTCCGCCCGGTGGGCCCCTGGGAGCAGGCGAACACAGACCCGTGCCGGCTTGGGCTTCCTGGGGAAGGTTGAGTTGTTGAGAGAGTGGACCACAGCGAGAGGGACACGCGGCCGGCCTTACACCCGGCTGTCCTCAATCACTGCACATCTGGTACTTTCTTTCCGGACACGAGGTGGAGATCTGCAAGTCGGGTCTGGGCAGTCTGTCTCCACCGTAATCTCTTTCTGAGTCTTCTTCCTCACTCGCTCCGTATCTCTGCCTTTCTCTCTCTCTCCTCCTTGGAATGATTAGCACTCCAAGATGATTGACAATGGTGCATTTCAGAGACGGTTCCTCTTTACAACATTTGACGAAGGGGAGTCCTGCGTTAGTCCTTAGCGTGATTTCCAAACAAACGGCCTGTGAAATGATGCCACCCTATAAAGCTCGAGGAACTCTTCCAGCTCAATTACCACCAAGCAAATTCGCCTTTTAAAACCATGCTAATGTTTCCCCCTCCAGACCTCCTCTCCCTGTTGCCCCTGGCCCATTCATAAAGGTGGGAGCACAGAGACCCCATACTCCAAGTAGCTGGGTCCCTCTCTTGTCGCTTTTAAAGGACGGGGTGCTGGGTTTGGGGGGCCAGTGAGAGGGATAAGAGGAGGGGATTGGTAAGGTGGGACCAAGGCTGCAGGCGCTTGCCAACCGCTTGGTCCCAGGGAGAGCTGGCGGTCTCCGAGGCTCCCCAACCAACTCCATGGCCTTTCTGTCTGTTCTCGCTCCTCAG
Seq C2 exon
GTACCCCCAAGGGCAGCGGAGGCTCGGGCCCGGGCGGCTTGGAGCGCACGCCTTTCCTCTCTCCTTCGCACTCGGACTTTAAAGAAGAGAAAGAGAGGCTCCTGCCCGCGGGCTCGCCCTCGCCGGGGTCCGAGCGGCCGCGGGACGGCGGCGCTGAGCGGCAGGCCGGCGCGGCCAAGAAGAAGACGCGCACCGTCTTTTCGCGCAGCCAGGTGTACCAGCTCGAGTCCACCTTCGACATGAAGCGCTACCTGAGCAGCTCGGAGCGCGCCTGCCTCGCCTCCAGCCTGCAGCTCACGGAGACCCAGGTAAAGACTTGGTTCCAGAACCGCCGCAACAAGTGGAAGCGGCAGCTCTCGGCTGAGCTGGAGGCGGCCAACATGGCGCACGCGTCGGCGCAGACTCTGGTGAGCATGCCGCTGGTGTTCCGGGACAGTTCGCTGCTGCGCGTGCCGGTGCCGCGCTCGCTCGCCTTTCCCGCGCCGCTCTACTACCCGGGAAGCAACCTCTCGGCCTTACCTCTCTACAACCTATACAACAAGCTCGACTACTGACCGGCCCGCCGCCCCGCGCCGCCCCCAGCTGCCCGCAGAGCCGGGCGCGTACTGTACTGTAAGCAGGGCTCCGGAGCAAGGCGGCGTGTTTCCAGAAATATGAAGAAATACACCATGTGTATTCATTAGCTCTTATTTATGGTCTCTGCCCTACTTTTTGTTTTGATTGTTTCGGGTATTTATTGGCATTCCCTAAGTCAGAGAGCCTGCTTCCTACCTAGACCGAACCAGTACGCTTTGAAAACCATTCGGAGTGAGATGTTCTCGGGTGGTGGTGGGAAAGGGAGTTTTGGCCAGACAGGCTGTGGTTGGTAGGGAAAAAAATCAGGAAAACACCTACAAAACCAGGTACACTCCTCCCCCATATATACACCTGTATATATGTACATGCATACACGCTCGGCCAAGCCAGGCCCTCAGAGGCTTTGGACAATTACTAAATTGCTTCTTTTCGTTTCCCTCATCCCGAGGATGGTAGGGACGAAAAGGGGAGAGTTCAGATCTGTAAATATTTTTAAAAAGAAAAAAAAATAAAACATTTTAAACATC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000188816-HMX2:NM_005519:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.348
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=30.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGGATGGGCAGCAAAGAAGA
R:
AAAGTCCGAGTGCGAAGGAGA
Band lengths:
352-1275
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)