HsaINT0077275 @ hg19
Intron Retention
Gene
ENSG00000005073 | HOXA11
Description
homeobox A11 [Source:HGNC Symbol;Acc:5101]
Coordinates
chr7:27220776-27224835:-
Coord C1 exon
chr7:27224055-27224835
Coord A exon
chr7:27222648-27224054
Coord C2 exon
chr7:27220776-27222647
Length
1407 bp
Sequences
Splice sites
5' ss Seq
CCAGTACGT
5' ss Score
7.19
3' ss Seq
TGCCTTTTCTCCCTCCACAGGTG
3' ss Score
13.84
Exon sequences
Seq C1 exon
CTTCAAAGAGGCAGCTGCAGTGGAGAATCATGTTAAGCTCGGCTACTGCGGAGAGCCCAAGGTAGCCCAATAATGGATTTTGATGAGCGTGGTCCCTGCTCCTCTAACATGTATTTGCCAAGTTGTACTTACTACGTCTCGGGTCCAGATTTCTCCAGCCTCCCTTCTTTTCTGCCCCAGACCCCGTCTTCGCGCCCAATGACATACTCCTACTCCTCCAACCTGCCCCAGGTCCAACCCGTGCGCGAAGTGACCTTCAGAGAGTACGCCATTGAGCCCGCCACTAAATGGCACCCCCGCGGCAATCTGGCCCACTGCTACTCCGCGGAGGAGCTCGTGCACAGAGACTGCCTGCAGGCGCCCAGCGCGGCCGGCGTGCCTGGCGACGTGCTGGCCAAGAGCTCGGCCAACGTCTACCACCACCCCACCCCCGCAGTCTCGTCCAATTTCTATAGCACCGTGGGCAGGAACGGCGTCCTGCCACAGGCTTTCGACCAGTTTTTCGAGACAGCCTACGGCACCCCGGAAAACCTCGCCTCCTCCGACTACCCCGGGGACAAGAGCGCCGAGAAGGGGCCCCCGGCGGCCACGGCGACCTCCGCGGCGGCGGCGGCGGCTGCAACGGGCGCGCCGGCAACTTCAAGTTCGGACAGCGGCGGCGGCGGCGGCTGCCGGGAGACGGCGGCGGCAGCAGAGGAGAAAGAGCGGCGGCGGCGCCCCGAGAGCAGCAGCAGCCCCGAGTCGTCTTCCGGCCACACTGAGGACAAGGCCGGCGGCTCCA
Seq A exon
GTACGTATAAAGGCAGCGCCCTGCGCTTTATGAAAGGGGAGTTGGAAATCTAGCGCAGCACCGCTGTTAAATTTTTATATGCTGTTTTATAAGCATATAAGGTTTATGAAGGGCCTTTAGGTTTCCCCCAACAAAACTTTGTTATAAAAGGCGGGATCACGTGGCGAGTGCTGAAATTGGCCGTGAAATACCCACCGGCCAAGGCATGCCTGCAAAAAAAAACAACTCCCCTTTTCCCTTTTTTCCCTTCTCAGCTCCCAAGCCCAGCAGCTCGACCCCGCTCGGGGCCAGCTCCAGGCTGGGGAGCCGGAGGTGGGCGCCTGTAAATTCCCCCTGCAAGGGCTTCGGGAGCTTTTGATAGCGAGGTAATCCGGAGATTTTTATAAAAGCCATGTGTTGCGCCGGGACTCCAGTCCCGGCCGGGATTCAAAGGCGTCGCTGTTTAACGACGGCGCTAGGAGCGCGTTTAACAGATAAAGTAGCCCGCTTAGCTCTAGCAATATATTAAAAGAACAAATTAACCCAAAGTTGGCCTTTTTGTCCAAAGGAAGCCATTTTCCTCTGGCGTGGTGGCAATTACGTGCCTCCTTCTGCCCAACTGCATGTTATTCACAATTGTTATTCAATCTGTCAAAAGCGATTTTTTTTTTGTCTTGTGGGTCTTTTTTTTTTTTTTTTTTTTTTTTTTAAAGGGGGAGCAAGTAGAGCCTGCCCGCAGCTTCGGGAAGCCCCCTTTCCCTTCACCCTACCTAAGATAGAGCCGCTGCTCTGCCGTGTGCAGGATGGCCGTGTGGCCGTGGTGCTCAGCGAAGGCCTAGGGTAGGGGGCTTCCGCCGCCACCTCCCCACCTCGGCGGAGCCGGAAGGCTGGCCGGGGAGGCAGAAGCTGGTGGCCAGGACTCAGGCTGACAAAGACCCGGCAGCCGCCCCAGATGTTAAGGACTGCCCAGTCTTGGCCGCAGCCGGGAAAGACTGGGACTGGAGCCGCCTTTACTGCCTTGGGAAGGGGCAGCCCAGGTGCTGGAAGGTGAAATGTCCGCAGGCGGCTGTTTGTTTAGTCTGGCCTGCGAGAGGCAGCCGGCAACCCCCACTTGGCTGCTTTCAAAGAGGCTTAGGCAGCGCAAACTCGCCTGTTGCTGTGCGAAGCTCTCCTTTCTGTTCTGGGGGCAGCGGGAGCAGCTTCCCCGGGGGCCTATTTAGGGAGCTGGCTTTTATCTGTGGCTGAGCCTCCAACTGCGGCCGTTCCAAGCATGCAGTCGGAGCGTTAAAGGCAGGGGCCTGGGCAGACTTTGACGGGGCTTGGGCTGGACCACCAGTCCCCATGGCAGCCCTTCTCCTCAGCTATGGGCTCTGGGGTGGATTGCAGCCCCCACACCTGGCTCACCCCATGCCTTTTCTCCCTCCACAG
Seq C2 exon
GTGGCCAACGCACCCGCAAAAAGCGCTGCCCCTATACCAAGTACCAGATCCGAGAGCTGGAACGGGAGTTCTTCTTCAGCGTCTACATTAACAAAGAGAAGCGCCTGCAACTGTCCCGCATGCTCAACCTCACTGATCGTCAAGTCAAAATCTGGTTTCAGAACAGGAGAATGAAGGAAAAAAAAATTAACAGAGACCGTTTACAGTACTACTCAGCAAATCCACTCCTCTAAGACTCCAGCGGCTGGAATTGGGTGGGGGGCTTCATACACATGAGATAATATGCAGATTTTGCCCTTGACAAAGTCAAGCCACATGGTGACTTTTGAAAAGAGGTGTGCAAGAGAGGGATGCATGGAGATAGCCCCACAGGAGGTGGTCTGGGACTCTCTTGATTAAGATCTCAGTGGTTAAGATTCCTAATAATCATTGGATTCTGAGAGCTGTGCATCAGCTAGAATGACAGGTTTGGGACCCCTGGTGGTTCACTCTTGGAGCCTGCAGAGCTGCGGGCTGGGTGTGGTCTCCACTGGGGATTGGGCCCCTGCCAGACCCCCTGGAGACTAACCCCACCACACCCTCCCTCTACTGGGAGCCTACCCACCCCCAGGACCCCTGAGTAAAAAAGCTGTGTGCTCTCCAAGCCCAGTTCAGCTTGGGGACAGGGGCAGGAGGAAGGGGTAGGATTACTAGGTGCCCAGAATGAGGCTGCTTTCCAAAGCCAATGTGAACAGCGGCTGGACTTGGAGGTAGCTTTGAGGTGGAAGAGGGCTGCAAATCCTTGTGGGAAAAGAAATCTATGATTCCAGGTGGCATCAGTGTCTTTCCACTCCTCCTAGCCACCCACCACACTGATCCAGCCCTGAGTTCCTAGCCACCGCCTCCTACAGCCCACCTGGCTTTTCTTTCTACCAAATGAGGGTCTTGGTTCCAGCCTGCCACTCAGGCCCAAAGCCTCGACACAGAGTGGACTGTTCCCTGAGGTGGGAGATGTGGAAAAGCCAAGAGGCTGCAGCCAGGCCACTGGCCCCTGAGATCTCTGCAGGAAATGGCTGTGGAGTGTGGCAGTTTGGCAAACTCTCCACCACACGTAATGAAACTTGGATTTGCTCAGTGTCTGGCTGCAGAGCAGTGGGCCTGGCCAGCAGGTCCCCAGCTTTGGCTATGAGGGCCTTGAGTCCCCCAAAACACCGGGTTCCAGCACCACACTCAGCCCTCATTGGCTCTTGAACTGAGCTTGGAAGCTTCTGGTGACCTTCCAAGAGCCTGAGAGTGAGGTGGAATTATTTTAAAAGATAAATATTATATTATATATATATATATTTCCCTGAAGGAACCAAAGCGAATTTTAAAAGATGCAATGTAGAGGGGAAAAGAGATGATGAAAATATTTAAAGGCCCTATCTGTTTACAGTGTTCCGTGGTTAAACTCGCTCACTGCTAAGAATATTTGAATGTATGCTTCATACAGGGATGGTGTTCAAAAAACTTGTAAATAAAGGAACCATAATCAATTTTCTTTTCTTTCTTTCTCTTTTTCTTTTTTCTTTTGCCATTAGTTGATTTCCTTTAGGGTGTTGGAGGGGGTGGAAAAGGTATTGAGAATGGTCTTTTTAATCTCTTGCAACATTTGGAAAGAGTTAGGGAAATGCTCAGAGGCAGTCGGCCTGGCCGGCCTGGGGATCTCATCTGGGAAAGCCAGGCACCCTCCCATTGAATCTCCTTTGCCTCCCTGTGTTAAGAAATGTCTGTTGGCTCCATTTGTACTGGGAGTGTTGGCCTGTCCTCAATTCTGGTTCTTACCCACCGTGTGTGTTGCAGCACTTATACAGGCAACTGGGCACAAGGAAAATAAAGACGGTGGAAATTTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000005073-HOXA11:NM_005523:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.456 A=NA C2=0.234
Domain overlap (PFAM):
C1:
PF120453=DUF3528=PD(89.6=65.8),PF146721=LCE=PU(90.5=41.3)
A:
NA
C2:
PF146721=LCE=PD(7.1=7.7),PF0004624=Homeobox=WD(100=73.1)
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:
CCACAGGCTTTCGACCAGTTT
R:
GTACTTGGTATAGGGGCAGCG
Band lengths:
345-1752
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)