HsaINT0077284 @ hg19
Intron Retention
Gene
ENSG00000106004 | HOXA5
Description
homeobox A5 [Source:HGNC Symbol;Acc:5106]
Coordinates
chr7:27180996-27183287:-
Coord C1 exon
chr7:27182665-27183287
Coord A exon
chr7:27181705-27182664
Coord C2 exon
chr7:27180996-27181704
Length
960 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAAG
5' ss Score
5.39
3' ss Seq
CGCTGACTTTTCTATTGCAGACA
3' ss Score
10.04
Exon sequences
Seq C1 exon
GGGTGCTATAGACGCACAAACGACCGCGAGCCACAAATCAAGCACACATATCAAAAAACAAATGAGCTCTTATTTTGTAAACTCATTTTGCGGTCGCTATCCAAATGGCCCGGACTACCAGTTGCATAATTATGGAGATCATAGTTCCGTGAGCGAGCAATTCAGGGACTCGGCGAGCATGCACTCCGGCAGGTACGGCTACGGCTACAATGGCATGGATCTCAGCGTCGGCCGCTCGGGCTCCGGCCACTTTGGCTCCGGAGAGCGCGCCCGCAGCTACGCTGCCAGCGCCAGCGCGGCGCCCGCCGAGCCCAGGTACAGCCAGCCGGCCACGTCCACGCACTCTCCTCAGCCCGATCCGCTGCCCTGCTCCGCCGTGGCCCCCTCGCCCGGCAGCGACAGCCACCACGGCGGGAAAAACTCCCTAAGCAACTCCAGCGGCGCCTCGGCCGACGCCGGCAGCACCCACATCAGCAGCAGAGAGGGGGTTGGCACGGCGTCCGGAGCCGAGGAGGACGCCCCTGCCAGCAGCGAGCAGGCGAGTGCGCAGAGCGAGCCGAGCCCGGCGCCGCCCGCCCAACCCCAGATCTACCCCTGGATGCGCAAGCTGCACATAAGTCATG
Seq A exon
GTAAAGCCAGCCTTTTTCTAAATCCACGCGACCGCGGGGACGCGGCTCTCGGTCCCCCCTCTCTTCTCTGCCGCCCTCTCCCAGTCTCTCTTGGTCTCATTTCTCCCAGCCCTGCGGAGCTCTCCTTGCCGTTCTCCCTCCCCTGCCTTCCTCCTTCCTCCTCTTCTTTGCGAGCACCCTGCGCTCACAAATAGTGGGGGAAATGGGCGTTCTCTGGGACAGTTTAGACGTTGGAAGGGGGAGGAAGCAAAAAACCCCTCTGGAACCCCACGCCTTGGGACGCGCTCCCGGGTCAGGCCAGCCGAGCAAGGCGCAGAGAGGTAGAGGATGGCTGTAGCAGCCGTGAATCGGGCTTGTCACGGCGGATAATTTATGAGGAGGGCTACGCTGGGGAAACAGCGTTACTAATTACAGCCCCCGAAAAGGGGCTTGGGGGAAAGAATCGAGGCGAGAGCCTGCAGGATTCTGAATTTTGGGGGCAGGAGGGAGAGAGAAGGAAAGGGAAGAAAAAGAAAACAGGCTCCCCAACCCTGCAGGCTGGAAACGGGAGGCGGCTCTCGGGGCTGGAACTTTGAGGGAGGGTGACCCGAAGGCCACTTGGGCGCTCAGGAAAGGGCCTTGCTTCCTGGGTTTCTGTGCGGTGGGCAGCCTGGGAGGGCTGTGCCTCCCGATCGGGGCGCCCGGGGCAGGGCGGAGGGGGCAGGAGAGGGGCCAGGGAAAGCCGGAGTCCGCCGGGACACGGCCCCAGCCTCAGATGGGCAGATTGTTCCCAGGGTCCAAATCGTATTGTTTTCTTTCTAGAAAGGAAGAGAGAAGGAAATTCGGGAGGGGTGTGCGGGCTGGTAGGCAGAACTTGTTGAGCTTTTCGCCTGGGTTCCCTGCTCATGACCCAAGCTTGTCCCCCTGGCGGACTTTGGAAGACAGGAGTTGGTGGCTAAACCGCTGACTTTTCTATTGCAG
Seq C2 exon
ACAACATAGGCGGCCCGGAAGGCAAAAGGGCCCGGACGGCCTACACGCGCTACCAGACCCTGGAGCTGGAGAAGGAGTTCCACTTCAACCGTTACCTGACCCGCAGAAGGAGGATTGAAATAGCACATGCTCTTTGCCTCTCCGAGAGACAAATTAAAATCTGGTTCCAAAACCGGAGAATGAAGTGGAAAAAAGATAATAAGCTGAAAAGCATGAGCATGGCCGCGGCAGGAGGGGCCTTCCGTCCCTGAGTATCTGAGCGTTTAAAGTACTGAGCAGTATTAGCGGATCCCGCGTAGTGTCAGTACTAAGGTGACTTTCTGAAACTCCCTTGTGTTCCTTCTGTGAAGAAGCCCTGTTCTCGTTGCCCTAATTCATCTTTTAATCATGAGCCTGTTTATTGCCATTATAGCGCCTGTATAAGTAGATCTGCTTTCTGTTCATCTCTTTGTCCTGAATGGCTTTGTCTTGAAAAAAAATAGATGTTTTAACTTATTTATATGAAGCAAGCTGTGTTACTTGAAGTAACTATAACAAAAAAAGAAAAGAGAAAAAAAAACACACAAAAAGTCCCCCTTCAATCTCGTTTAGTGCCAATGTTGTGTGTTGCACTCAAGTTGTTTAACTGTGCATGTGCGTGGAAGTGTTCCTGTCTCAATAGCTCCAAGCTGTTAAAGATATTTTTATTCAAACTACCTATATTCCTTGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000106004-HOXA5:NM_019102:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.824 A=NA C2=0.253
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=67.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAACCCCAGATCTACCCCTG
R:
AGTACTGACACTACGCGGGAT
Band lengths:
356-1316
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)