HsaINT0120771 @ hg19
Intron Retention
Gene
ENSG00000007372 | PAX6
Description
paired box 6 [Source:HGNC Symbol;Acc:8620]
Coordinates
chr11:31815200-31815662:-
Coord C1 exon
chr11:31815580-31815662
Coord A exon
chr11:31815351-31815579
Coord C2 exon
chr11:31815200-31815350
Length
229 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCG
5' ss Score
10.05
3' ss Seq
CTGTCCCACCTGATTTCCAGGTA
3' ss Score
8.7
Exon sequences
Seq C1 exon
AGTTTGAGAGAACCCATTATCCAGATGTGTTTGCCCGAGAAAGACTAGCAGCCAAAATAGATCTACCTGAAGCAAGAATACAG
Seq A exon
GTACCGAGAGACTGTGCAGTTTCACACTTTGTGATTCATACCATTTGTCTTTCCTAGAGACAGAGGTGCTTGTACAGAGTACTATTTATTTATAGGACTAATATAATAAAAAGGTTCAGTCTGCTAAATGCTCTGCTGCCATGGGCGTGGGGAGGGCAGCAGTGGAGGTGCCAAGGTGGGGCTGGGCTCGACGTAGACACAGTGCTAACCTGTCCCACCTGATTTCCAG
Seq C2 exon
GTATGGTTTTCTAATCGAAGGGCCAAATGGAGAAGAGAAGAAAAACTGAGGAATCAGAGAAGACAGGCCAGCAACACACCTAGTCATATTCCTATCAGCAGTAGTTTCAGCACCAGTGTCTACCAACCAATTCCACAACCCACCACACCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000007372-PAX6:NM_001127612:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=0.624 A=NA C2=0.947
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=FE(47.4=100)
A:
NA
C2:
PF0004624=Homeobox=PD(19.3=21.6)
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:
TGAGAGAACCCATTATCCAGATGTG
R:
GGTGTGGTGGGTTGTGGAATT
Band lengths:
228-457
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)