HsaINT0120770 @ hg19
Intron Retention
Gene
ENSG00000007372 | PAX6
Description
paired box 6 [Source:HGNC Symbol;Acc:8620]
Coordinates
chr11:31815580-31816336:-
Coord C1 exon
chr11:31816178-31816336
Coord A exon
chr11:31815663-31816177
Coord C2 exon
chr11:31815580-31815662
Length
515 bp
Sequences
Splice sites
5' ss Seq
AAGGTGATA
5' ss Score
4.18
3' ss Seq
AAATCAACTTACTCTTTCAGAGT
3' ss Score
7.31
Exon sequences
Seq C1 exon
ATGGCTGCCAGCAACAGGAAGGAGGGGGAGAGAATACCAACTCCATCAGTTCCAACGGAGAAGATTCAGATGAGGCTCAAATGCGACTTCAGCTGAAGCGGAAGCTGCAAAGAAATAGAACATCCTTTACCCAAGAGCAAATTGAGGCCCTGGAGAAAG
Seq A exon
GTGATAGAGTTTTTCAAAGTAGAGAAGCAGTAAATCAAAGTAAATGCCACATCTTCAGTACAAAGAGCTAAATTTAGCCAGGGCCCTTTGCATAGAAGAATGAAAAGATTTCCTTTTTTCTGTCTTTTTATTTCTCTGGGCATCTTTTCAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGGTGTGTGTGTGTGTGTTTCTTCTTTTCATCTACCAGTAATTCAAAGACTAAATGTCTGACTTATAAGGAAAAATGATGATTTGGCTATTTCAGGCCACAGAAAGGTCACTGAATGCCATTCCAAAGAAAATTTAACTTGGTTCTGGTGGGAAAGTTCTTCCAAGTACAGTCAACACTAGAAGCATTTTAAAGGGAATTGGTTGGAGGTAATGGGAGTGGGGAGGTGGGAACCAGTTTGATGCACAGTTTGGTCAACATATTTTGTGTAGTTCTGGCACAATATGGAAAATCAACTTACTCTTTCAG
Seq C2 exon
AGTTTGAGAGAACCCATTATCCAGATGTGTTTGCCCGAGAAAGACTAGCAGCCAAAATAGATCTACCTGAAGCAAGAATACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000007372-PAX6:NM_001127612:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=0.902 A=NA C2=0.624
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(29.8=31.5)
A:
NA
C2:
PF0004624=Homeobox=FE(47.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGCCAGCAACAGGAAGGAG
R:
CTGTATTCTTGCTTCAGGTAGATCT
Band lengths:
238-753
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)