HsaINT0077287 @ hg19
Intron Retention
Gene
ENSG00000078399 | HOXA9
Description
homeobox A9 [Source:HGNC Symbol;Acc:5109]
Coordinates
chr7:27202057-27205149:-
Coord C1 exon
chr7:27204497-27205149
Coord A exon
chr7:27203461-27204496
Coord C2 exon
chr7:27202057-27203460
Length
1036 bp
Sequences
Splice sites
5' ss Seq
CCAGTAAGT
5' ss Score
9.09
3' ss Seq
AGTGTTTCTCTTCCCCGCAGATA
3' ss Score
12.67
Exon sequences
Seq C1 exon
AGTTGTTACATGAAATCTGCAGTTTCATAATTTCCGTGGGTCGGGCCGGGCGGGCCAGGCGCTGGGCACGGTGATGGCCACCACTGGGGCCCTGGGCAACTACTACGTGGACTCGTTCCTGCTGGGCGCCGACGCCGCGGATGAGCTGAGCGTTGGCCGCTATGCGCCGGGGACCCTGGGCCAGCCTCCCCGGCAGGCGGCGACGCTGGCCGAGCACCCCGACTTCAGCCCGTGCAGCTTCCAGTCCAAGGCGACGGTGTTTGGCGCCTCGTGGAACCCAGTGCACGCGGCGGGCGCCAACGCTGTACCCGCTGCGGTGTACCACCACCATCACCACCACCCCTACGTGCACCCCCAGGCGCCCGTGGCGGCGGCGGCGCCGGACGGCAGGTACATGCGCTCCTGGCTGGAGCCCACGCCCGGTGCGCTCTCCTTCGCGGGCTTGCCCTCCAGCCGGCCTTATGGCATTAAACCTGAACCGCTGTCGGCCAGAAGGGGTGACTGTCCCACGCTTGACACTCACACTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAACAACCCAGCGAAGGCGCCTTCTCTGAAAACAATGCTGAGAATGAGAGCGGCGGAGACAAGCCCCCCATCGATCCCA
Seq A exon
GTAAGTGTCTCCTCCCTTCAAATCCGCCGCCGCCTCCACGCCGGCCTCCCGGATCTGCTGGCCCGCCAGGTTTCTCTCGAGCCTGCCTTCGTCCTCGCTGGAAGCCTCTCGAGTTGGGGCCAGGAGCCAGAAGTTGGTGTTTGGGACGCCTCAGATAGGGCCCCAAGTCTGGAGAGCAGTGAAGAGCGGCCCGCAGGGCTACGGGAGAGGAGGCGGCTGCTGCAGCGAGAGGGGGCGGGGCGGGCACTTCGGGACGAGCCAAGACTGGCCGCCCCTCTCCTTGGCTGCCCAGGCCCAGGACCGAGATACTTTGGGCCGTTCTTCGAAAGCAGTGCAGCCCAGAGAGCCTTTTGTACAACTAGATTGTCCGTGAGCGGCGGCAGCCAGGGCAGCCGGAGCTGGGACGCTGGGGGAGACGGCCGATTCCTTCCACTTCTTGCCTTCGGCCAGTGGCGGCGTAAATCCTGCCAAGATGAGGCTGCGGGCGACCCGGGCCACAAGGGTCCCCATGACAGATTATTCAAATAAGCCACAGACGTGATCAGCGGCCTTAGGGCGCCCTGACGGCTTGCCCAGCTCCGAAGGCCTTCCAGGAAGGTTAAATAAGGAGTGGGGGGCGTAGAGGGACAGGTTGGGAAAGAAAGACGAAGTCAGTGAACGGGACAGAGGAATCCTAATCTTGCTACAGAACACAAGGCAGCATGCTTTCCCTCTGCGTGGCAAGGAGACCTGTTTCCAAATTTCATTCTATACAGCGTTTTGAGAGTGGGAGGAAGGAGAAGGGGGACAAGAGGACAGAGTAGGAGAAAGGAAGGTCTCGGAGGGGAGGGCGAGCCAAAGTTTTACTGCGTGCAATTTTAAGTGACTGTCTGTGCGTCTGTCTGCCAGGGTTCCATTGTGTCCGAGGCCTGACTGCCTTTCCTAACCAGTTCAGCAGAGTTCTGCACTTCGGCCAGAGACCCCATGCAGGAGGCTCATTTGCCCCAGCGGGATGTGCGTCTTCTGCTCCTAAACCCAGTGTTTCTCTTCCCCGCAG
Seq C2 exon
ATAACCCAGCAGCCAACTGGCTTCATGCGCGCTCCACTCGGAAAAAGCGGTGCCCCTATACAAAACACCAGACCCTGGAACTGGAGAAAGAGTTTCTGTTCAACATGTACCTCACCAGGGACCGCAGGTACGAGGTGGCTCGACTGCTCAACCTCACCGAGAGGCAGGTCAAGATCTGGTTCCAGAACCGCAGGATGAAAATGAAGAAAATCAACAAAGACCGAGCAAAAGACGAGTGATGCCATTTGGGCTTATTTAGAAAAAAGGGTAAGCTAGAGAGAAAAAGAAAGAACTGTCCGTCCCCCTTCCGCCTTCTCCCTTCTCTCACCCCCACCCTAGCCTCCACCATCCCCGCACAAAGCGGCTCTAAACCTCAGGCCACATCTTTTCCAAGGCAAACCCTGTTCAGGCTGGCTCGTAGGCCTGCCGCTTTGATGGAGGAGGTATTGTAAGCTTTCCATTTTCTATAAGAAAAAGGAAAAGTTGAGGGGGGGGCATTAGTGCTGATAGCTGTGTGTGTTAGCTTGTATATATATTTTTAAAAATCTACCTGTTCCTGACTTAAAACAAAAGGAAAGAAACTACCTTTTTATAATGCACAACTGTTGATGGTAGGCTGTATAGTTTTTAGTCTGTGTAGTTAATTTAATTTGCAGTTTGTGCGGCAGATTGCTCTGCCAAGATACTTGAACACTGTGTTTTATTGTGGTAATTATGTTTTGTGATTCAAACTTCTGTGTACTGGGTGATGCACCCATTGTGATTGTGGAAGATAGAATTCAATTTGAACTCAGGTTGTTTATGAGGGGAAAAAAACAGTTGCATAGAGTATAGCTCTGTAGTGGAATATGTCTTCTGTATAACTAGGCTGTTAACCTATGATTGTAAAGTAGCTGTAAGAATTTCCCAGTGAAATAAAAAAAAATTTTAAGTGTTCTCGGGGATGCATAGATTCATCATTTTCTCCACCTTAAAAATGCGGGCATTTAAGTCTGTCCATTATCTATATAGTCCTGTCTTGTCTATTGTATATATAATCTATATGATTAAAGAAAATATGCATAATCAGACAAGCTTGAATATTGTTTTTGCACCAGACGAACAGTGAGGAAATTCGGAGCTATACATATGTGCAGAAGGTTACTACCTAGGGTTTATGCTTAATTTTAATTGGAGGAAATGAATGCTGATTGTAACGGAGTTAATTTTATTGATAATAAATTATACACTATGAAACCGCCATTGGGCTACTGTAGATTTGTATCCTTGATGAATCTGGGGTTTCCATCAGACTGAACTTACACTGTATATTTTGCAATAGTTACCTCAAGGCCTACTGACCAAATTGTTGTGTTGAGATGATATTTAACTTTTTGCCAAATAAAATATATTGATTCTTTTCTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000078399-HOXA9:NM_152739:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.617 A=NA C2=0.327
Domain overlap (PFAM):
C1:
PF046178=Hox9_act=WD(100=99.5)
A:
NA
C2:
PF0004624=Homeobox=WD(100=71.2)
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:
AATGCTGAGAATGAGAGCGGC
R:
AAGGGGGACGGACAGTTCTTT
Band lengths:
353-1389
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)