HsaINT0077283 @ hg19
Intron Retention
Gene
ENSG00000197576 | HOXA4
Description
homeobox A4 [Source:HGNC Symbol;Acc:5105]
Coordinates
chr7:27168126-27170399:-
Coord C1 exon
chr7:27169737-27170399
Coord A exon
chr7:27169191-27169736
Coord C2 exon
chr7:27168126-27169190
Length
546 bp
Sequences
Splice sites
5' ss Seq
CCGGTACGT
5' ss Score
10.49
3' ss Seq
TCGGGGTTCTGGGTTTTCAGTTA
3' ss Score
4.53
Exon sequences
Seq C1 exon
AAAACGACAACGCGAGAAAAATTAGTATTTTTGCACTTCACAAATTAATGACCATGAGCTCGTTTTTGATAAACTCCAACTACATCGAGCCCAAGTTCCCTCCCTTCGAGGAGTACGCGCAGCACAGCGGCTCGGGCGGCGCAGACGGCGGCCCGGGCGGGGGCCCCGGCTACCAGCAGCCCCCAGCGCCCCCGACCCAGCACCTGCCGCTGCAGCAGCCCCAGCTCCCTCACGCGGGCGGCGGCCGAGAGCCCACTGCCTCCTACTACGCGCCGCGGACCGCCCGCGAGCCCGCCTACCCTGCTGCCGCGCTGTACCCCGCGCATGGGGCCGCGGACACCGCCTACCCCTATGGCTACCGCGGCGGCGCCAGCCCCGGGCGGCCGCCCCAGCCCGAGCAGCCCCCGGCGCAAGCCAAGGGCCCAGCGCACGGCCTGCATGCGAGCCACGTCCTGCAGCCCCAGCTGCCGCCGCCCCTGCAGCCTCGCGCCGTGCCCCCAGCGGCCCCGCGGCGCTGCGAGGCGGCCCCCGCCACCCCAGGCGTCCCGGCAGGGGGCAGCGCCCCCGCGTGCCCGCTGCTCTTGGCCGACAAGAGCCCGCTGGGCCTGAAGGGCAAGGAGCCCGTGGTGTACCCCTGGATGAAGAAGATCCATGTCAGCGCCG
Seq A exon
GTACGTGGCGCCGCTTGGGAGGCGCGGGAGGTGGGCCGGGGCTGGGCCTGGGTTCGAGGGTCGGGGTCAGGAGGGAGAGGCTCAGGGGAAGGGGGCCTCGGGAGGGGAGCCCCCATCTGACCCGGGCTGCGGTGAGATGTGGGTATGTGCGCGCCAGCCAGCCGCCTGATCCCAACATGAGAACCCTTTTGTACCCAGGGTCCCTTTATCAGGAGATTTACGAGACGCCAAACTGTTAGGGCAGTAATTATAGCCCCCATAAATTTAATTGCCCTGGCAGAGGCTTCAGGCCATGTGTCTTTGAAGCTTTTCTTCAGCCCCAATGCCCAGCACCATTCTTTATGGCTCTCGGGTGTTTCCCGTTGTCAATAGCCTGTGAAACATTTTCTTTGCCGTTTTATGTATCTTGCGTGAACTTGGTGTCAGGTTATTATATAATGATGATGTCCAATTGCTCTTCCCCACCCCACCTTCTCTCTCCTCCTCCTTTCCCTCTCTTCCGCTCCCTCCTCCTTGGCCTTCTATTTCGGGGTTCTGGGTTTTCAG
Seq C2 exon
TTAACCCCAGTTATAACGGAGGGGAGCCTAAGCGCTCTCGAACCGCCTACACCCGGCAGCAGGTCTTGGAGCTGGAGAAGGAGTTCCACTTCAATCGATACCTGACCCGGCGGCGCCGCATCGAGATCGCCCACACGCTCTGTTTGTCTGAGCGCCAGGTCAAGATCTGGTTTCAGAACCGGAGGATGAAGTGGAAGAAAGACCACAAACTGCCCAACACCAAGATGCGATCCTCCAATTCGGCCTCGGCCTCTGCCGGCCCACCAGGGAAAGCACAAACTCAGAGCCCACACCTCCATCCCCACCCCCACCCGAGCACCTCCACACCCGTTCCCTCCTCCATATAATCTTCTAGAGATCTTAACCAGTTTCTATCCCTTACCTGCTTTTCTCTTCTCTTCTCCTGCTCCGTTCCTCATCCACCCCTCCCCATCTGGACCATAATAGACACCAAAACAAACCCAAATTGGTGAAAAGAATAATCAAAAAGAAGACATTATCCGGTTAAGAGTCTGTGCTGGTTGCCACCCAAGAGAGAACAGTTGTCCAGGATGCTGGCTGGTGGAACAACCTGCTGGCCCGAAACAAGGCTGCCAGGTGTGGATACCTGAGAAGGACTACTTGGTATCAAATACTTTTGAGATGGCTACAGTCAGCTAGCTGGACAGCCCATGCTGAGTGGGGACATACACTTGCATCTTTGTTGAAAGCAGAAGAAGACAGACCCTTTCCCCACCTTCCTTACCTCCTCTTCCCCCATTAAGGCAGCTCATCCAAGCTTGTATTTAACTGAATAAATGAGTAGACATTGTGGACCTCACAAGATTATTTAATTCTTAAGATGTGTAGACCTTGATGGTAGGTGTGACATGTTAGTTTTTCTTACTTGCATTTATTTAAGACACTGTTACAGAGATACTGTTGTCCCCTTCTGGGGCACGGTCTTTGGGGAGAGGGGAGTGCATTTAGACTTATGTGGAACTGTACAAATTGTGATGTGGCTACATAGAAAGCCATGTGCTAAGAATAAACTCCATTTAAAAAACATTAAAAATCTAAGATTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000197576-HOXA4:NM_002141:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.699 A=NA C2=0.600
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=49.1)
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:
CCTACCCCTATGGCTACCGC
R:
CCCCTCCGTTATAACTGGGGT
Band lengths:
345-891
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)