HsaINT0077285 @ hg19
Intron Retention
Gene
ENSG00000106006 | HOXA6
Description
homeobox A6 [Source:HGNC Symbol;Acc:5107]
Coordinates
chr7:27185116-27187368:-
Coord C1 exon
chr7:27186927-27187368
Coord A exon
chr7:27185537-27186926
Coord C2 exon
chr7:27185116-27185536
Length
1390 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGA
5' ss Score
9.84
3' ss Seq
CCGGCCGTTTCTGCTCGTAGGTG
3' ss Score
9.24
Exon sequences
Seq C1 exon
ATGAGTTCCTATTTTGTGAATCCCACTTTCCCCGGGAGCCTTCCCAGCGGCCAGGACTCCTTCTTGGGCCAGCTGCCCCTCTACCAGGCTGGCTATGACGCGCTGAGGCCCTTCCCGGCCTCGTACGGGGCGTCGAGTCTCCCGGACAAGACGTACACCTCACCTTGTTTCTACCAACAGTCCAACTCGGTCCTGGCCTGCAACCGGGCGTCCTACGAGTACGGGGCCTCGTGTTTCTATTCTGATAAGGACCTCAGTGGCGCCTCGCCCTCGGGCAGTGGCAAGCAGAGGGGCCCCGGGGACTACCTGCACTTTTCTCCCGAGCAGCAGTACAAACCCGACAGCAGCAGCGGGCAGGGCAAAGCACTCCATGACGAAGGCGCCGACCGGAAGTACACGAGCCCGGTTTACCCTTGGATGCAGCGGATGAACTCCTGCGCGG
Seq A exon
GTAAGACATATCCCAAGACAGTGGAGGGAGAGGGGAAAGGAGGCAGGAAAAGAAAGAAAGAAGGAGGAAACAGAGTAGAAAGAGGAATAGAGAGAAAGAAAGGATGAAAGAACCAGCAAAGTTTCTTTGGCTTCTTAAAAGAGAAGAAAAAATCAGTTCCCAATGGGGCTATCAGGCCATGGCAGAGGAAGGGCAAGGCCCCAGTGTCCATGTAAGCTGACACCTTAGGGGAGGATGGGGGCACTGGCACGTATATGAGACCTGTGACAGGGACAGCCTGAAGAGAGAGAGAGGCTGGTGGGGAGGGACAGCCTGTCCATGCACCCTGAGTACCCTGCTCAGCTTCCCAAGCCAGAGGGCCTTTTGCACTGCGTCACTGATAAATACCCTTTGCTTCCCAACCCCCTCTCCTTTCTGCCCTTCAGAAACCCGTACAGAGAGGTGGCCATTTGGCCTCTTCCAGTGTCTCCCCAAAGCCTTGGAGGGCCACAGCCCCAGACTCAGGATTTTTTTCTCTCTCCTCCCTCATCTCCCCCGGCTTCTACTCAACTGCCCACTCTTAGCCAACTTCTGCCCTCTTCTGAGCCCATGCCTGAGCTTCATACACCTGTCTTGGAGGGACCCCCCACCACCCTTGGGGAACTTTGGCACCAGATCAGACAGCCCAACACAATCCTACATTGCCAGAAATCCTAGACTACCTATAGCTCCATCTCTTAGCCTCTGGTTTCCAAGGACTCCACAGGGAATCCCAAAGACTCCTAGGAATTCCCTAGGACAGAGCCTAATGCGGATTGTTAAAATTATAATGTTTTCCATTAACATCCACTTTATCCTTGGGGGAGTTCTGCATTTCTCAGAAGGGTCATATAATTTGGGAGAATGTGTAAAGATTCAAGAGGGCTGACCATTTTTAACTCTTCAAAAAATGTGTTGAGTTCCGACATGGCTGGTCACAGTAGCATCCTCAGAGAGACCACTATGAATTCAGAGTGTGTACACTACTTACATGGTTCCACACCACCCACCCCAGACACACACACACACACACACACAAACACACACACACACCCTGCATCCCCACAAAAACACGACCTGGGCATCCCAAATTAAGAATGCTCATTCTGTTATTTTGCTTGTAATGGTTTTCCTATGAGGCAGATTTTTCAAAAACGATAATGTCCACCCCAAGTCGTTATAGGTGGAAAACATCTCGCTTGGTATGAAATAATCTCCCATTCAGTATGCTTTGGGCCCCAGACATAGTGGGAGAGGCTGGAGTGGAGGCGGGGTGGTTTCTAGTCTGGGTGCCTCTTGTGGGAGGCACTGGGCTGACTGGGTCAACCCTCCAGGCCCTGGCTTACCGGCGCCCGGCCGTTTCTGCTCGTAG
Seq C2 exon
GTGCTGTGTATGGGAGCCATGGGCGCCGAGGCCGCCAGACCTACACGCGCTACCAGACACTGGAGCTGGAGAAGGAGTTCCACTTCAACCGCTACCTGACACGGCGCCGCCGCATCGAGATCGCCAACGCGCTCTGCCTCACCGAGCGCCAGATCAAGATCTGGTTCCAGAACCGCCGCATGAAGTGGAAAAAGGAAAACAAGCTCATCAATTCCACGCAGCCCAGCGGGGAGGACTCAGAGGCAAAGGCGGGCGAGTAGATGCCTGGGCAGGGACCAGGCCAGCGCTGCAACCTCCTTCGGCTTTGCCCCCTTGCCCTCGCCTGTTCCCCAACTTTTCTCCCCGCCTGCTCCCATCTGGGGGCTTCCGCAGCTTCAGGGGAGCCCGGAGCTTTGCAAGCGTCTGTGCATTTATTTCTTAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000106006-HOXA6:NM_024014:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.264 A=NA C2=0.279
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=65.5)
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:
CAACAGTCCAACTCGGTCCTG
R:
TCCTTCTCCAGCTCCAGTGTC
Band lengths:
344-1734
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)