HsaINT0077286 @ hg19
Intron Retention
Gene
ENSG00000122592 | HOXA7
Description
homeobox A7 [Source:HGNC Symbol;Acc:5108]
Coordinates
chr7:27193338-27196296:-
Coord C1 exon
chr7:27195786-27196296
Coord A exon
chr7:27194842-27195785
Coord C2 exon
chr7:27193338-27194841
Length
944 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGC
5' ss Score
9.88
3' ss Seq
GTCTGCATGTCTGTTCTCAGGAC
3' ss Score
9.45
Exon sequences
Seq C1 exon
GTGCTGCGGCGAGCTCCGTCCAAAAGAAAATGGGGTTTGGTGTAAATCTGGGGGTGTAATGTTATCATATATCACTCTACCTCGTAAAACCGACACTGAAAGCTGCCGGACAACAAATCACAGGTCAAAATTATGAGTTCTTCGTATTATGTGAACGCGCTTTTTAGCAAATATACGGCGGGGGCTTCTCTGTTCCAAAATGCCGAGCCGACTTCTTGCTCCTTTGCTCCCAACTCACAGAGAAGCGGCTACGGGGCGGGCGCCGGCGCCTTCGCCTCGACCGTTCCGGGCTTATACAATGTCAACAGCCCCCTTTATCAGAGCCCCTTTGCGTCCGGCTACGGCCTGGGCGCCGACGCCTACGGCAACCTGCCCTGCGCCTCCTACGACCAAAACATCCCCGGGCTCTGCAGTGACCTCGCCAAAGGCGCCTGCGACAAGACGGACGAGGGCGCGCTGCATGGCGCGGCTGAGGCCAATTTCCGCATCTACCCCTGGATGCGGTCTTCAG
Seq A exon
GTAGGCGCAGTCGCTAGGCGGGCCAGGCTGGCGGAGCGGGACCGGGAGCGGGGAGCGCAGCGCTGGGGAGCGCGGAGCGCGGGGCGCGGGGCCGGAAGAGCGGAGCCAGGCTGTTGCGAGCCGGTAGCCCCGTGACTCCCGGCGCAGCCTTTCTGGTTTTAATTGGAGCGGAGGCGCCATTGCGTGGAGCCCATAGCATTGTATGTAAATGAGGCTCATAAAACTTTTTATGGCCCAATTAATGGGTTCGATCCTCGTAAATTTATTTAACTCCATTTGTCTTGGAATTTTAACATTAAGTTTGTTCGCTATTCTGTCTCTCTTTCTCCCTCCTCTGTCACCCTCCCTCCCTTTCTTCTTCTCTCTCTCCTCATTTTCCTTGCTGCCTGACATTTCTTTCTCAAAAGCTAGGAGAGCCAAGCCCTCCAGGGCCTCTCACCCGACCCTGTGCCAGGGTCCATTTCAAGATGGGGGCGAGGGAATGAGGACAGAGGGTCGGGGTGCCCTAGGAAGGTCCTGGGGATGAGGGCTCAGGCTGCTGGGAAGAGTCGCCCACTTGCCTAGCAAGGCAGGGGAATGGCCGGGCTCATCTTTGAATGGCAAAAGTGCAGCGTTTCCCACTTGCTCACACTCTATATTTACAGTTTTCCTTTGTCAGAGGAAGCAGGACATTGTGGAAGCTTAGCCGGCTGGAAAGGTCGGTTGTAAAGTTGAGATTCTGTGCCTTTGCTCATTACAGAGCTGCCTGCGCGTCTGGCACTGCAGTTGGGGTCTTTCCCTAACACTCCCCCTCCTCCCCTAGCTCAGTTCGGGGCCTGGGGCAGAGGGGGATGCTCGCTGGGGACTAGGCCAGGAGGAAGGTGCGGGCTCTGGGACAGCAGCCTAACGAGTGCCCTGTCTACTTGTCTGTCCTTGTGTTCATGTGTCTGCATGTCTGTTCTCAG
Seq C2 exon
GACCTGACAGGAAGCGGGGCCGCCAGACCTACACGCGCTACCAGACGCTGGAGCTGGAGAAGGAGTTCCACTTCAACCGCTACCTGACGCGGCGCCGCCGCATTGAAATCGCCCACGCGCTCTGCCTCACCGAGCGCCAGATTAAGATCTGGTTCCAGAACCGCCGCATGAAGTGGAAGAAAGAGCATAAGGACGAAGGTCCGACTGCCGCCGCAGCTCCCGAGGGCGCCGTGCCCTCTGCCGCCGCCACTGCTGCCGCGGACAAGGCCGACGAGGAGGACGATGATGAAGAAGAGGAAGACGAGGAGGAATGAGGGGCCGATCCGGGGCCCTCTCTGCACCGGACAGTCGGAAAAGCGTCTTTAAGAGACTCACTGGTTTTACTTACAAAAATGGGAAAAATAAAAGAAAATGTAAAAAACAAAAACAAAAACAAAAAAGCAACCCAGTCCCCAACCTGCACTCTACCCACCCCCATCACCTACTCCAGCTCCCAACTTTTGTGGACTGAGCGGCCGCAGAGACTGGGTCGCCTTGGATTCCCTCTGCCTCCGAGGACCCCAAAAGACACCCCCAACCCCAGGCCAGCCGGCCCTGCTCTGGCGCGTCCAAAATACTACCTAGCACAGGCCTCTGCTCGAGGCACCCCCAAACTACCTATGTATCCAGCCCCAGAGGGCCTCCATTCCCAGGAAGTCCCTATGTATCCCAACACTGGCAGACACCCAGCACCACCCTCCCAGACCCGCAAGAAAGTGAATCTCACTACTACCTACTCCCCTAAAACTACCTATTTTGTGCTGGCTGGCTTGCCTGCTACCTAGTGCCGACTGCTCCCAGGCAAGTCCCCTGCTGCTTACAGCCCGCAGCTTTTGGGGTCCCTGAGGCTGCCCTGAGAATGTGCTGAGGTCCAGGATCAGGGTATTGGCATCTATTTAAATCGAAAAATAATATATTTATTCCAAAAAGCATCCTAAGTGCTTGCACCCTAGAATCAATCCCTCCTTCTCTGGCTTGGCACCCACAGCTCAGGCCCATCAACCCCCACTTCTGGAGGGGAATGTTCCTGAGCTGGCTGCAGATCTGTGGGTTAGCTTCTGCTTAGCAGGACTGTGGAGATGCTTCCAGCTTCGCTGTCCTTTCCTCTGGCTCCTGTATCTTACTGTTCAGCTGTGTTAAATATGTACGCCCTGATGTTTCCTATAATAGCAGATACTGTATATTTGAACAAGATTTTTTTTTATCATTTCTATAGTCTTGGAGTTCATTTGTAAGGCAGTGTCTTGACTTGGAAAGGATGTGTTAATGGGGTGACTTTGTAGCATGGTATGTTGTCTTGAGTTAACTGTAGTGGGTGGGGAGGTCCAATGCCCTCCGCAATGCCCTTCATCTCCTGTGTTGTCCTGTACCCTGCTCAGCTCCATCCTGGGGTTCAGGGAAGGCACACTTCCCAGCCCAGCTGTGTTTTATGTAACCGAAAATAAAGATGCGTGGTGACAAAGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000122592-HOXA7:NM_006896:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.500
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=54.3),PF0042814=Ribosomal_60s=WD(100=59.0)
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:
TTTCCGCATCTACCCCTGGAT
R:
CCCCTCATTCCTCCTCGTCTT
Band lengths:
350-1294
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)