HsaINT0120768 @ hg19
Intron Retention
Gene
ENSG00000007372 | PAX6
Description
paired box 6 [Source:HGNC Symbol;Acc:8620]
Coordinates
chr11:31822239-31823324:-
Coord C1 exon
chr11:31823109-31823324
Coord A exon
chr11:31822405-31823108
Coord C2 exon
chr11:31822239-31822404
Length
704 bp
Sequences
Splice sites
5' ss Seq
AGCGTAAGT
5' ss Score
10.07
3' ss Seq
GATTTTGGTTTGATTTGCAGGTG
3' ss Score
9.04
Exon sequences
Seq C1 exon
GTGTCCAACGGATGTGTGAGTAAAATTCTGGGCAGGTATTACGAGACTGGCTCCATCAGACCCAGGGCAATCGGTGGTAGTAAACCGAGAGTAGCGACTCCAGAAGTTGTAAGCAAAATAGCCCAGTATAAGCGGGAGTGCCCGTCCATCTTTGCTTGGGAAATCCGAGACAGATTACTGTCCGAGGGGGTCTGTACCAACGATAACATACCAAGC
Seq A exon
GTAAGTTCATTGAGAACATCTGCCCTCCCTGCCCTAAGCCCAATGCTCTCTCCTCTTTACCTCCTCCCACCCTCTCTCTCCACTGTCTCTTAGTCTGTGTCCTCTCCCTGCTCCACATTTGTCTCCTTTGTACCTGGGGGAACAGAGAGGAATGCCCTGACTTTTCTTTGACTGTCTGGAAAATGGGAGTCAAGTGTGGGGAGTCATTCACTTCATTTGCATGCTGCAAAACAGAGGGCGGAGGCACCAGGGAAAGGCACTTGAATGAAGAAGGAAAATGAGAACCAGATTGTAACTTCGTCCTAATCCACCTGCCAGAACTTTCCTTCAGGTGTCACACATCCATTTCCATCCTAATATTAAACAATATAATGAAAGAAAGCTTTACAACAAGTCTAAATAGTTTTTATTTTCGGGCAGTCTTTTAACAAAGCAAAGCAACCGTGTGAGTTAGGTCACCAGAGACACCAAGCAATGGTGAAGGACCCCCTCCGCCCAATTCTCTATCCAACTAAATTTCCATGCCCAAAGTGATAGCTATCATTTTTTCCACGGTGTATCTGCAAATCCACCCACTGTCCCGGGGTGGCTGGGAGCTTTTTAACGGGTTGAGAGTTGCTTTTTAAGGTTGTGGGTGAGCTGAGATGGGTGACTGTGTCTTCAGGAGACACTACCATTTGGTTTGATTTTGGTTTGATTTGCAG
Seq C2 exon
GTGTCATCAATAAACAGAGTTCTTCGCAACCTGGCTAGCGAAAAGCAACAGATGGGCGCAGACGGCATGTATGATAAACTAAGGATGTTGAACGGGCAGACCGGAAGCTGGGGCACCCGCCCTGGTTGGTATCCGGGGACTTCGGTGCCAGGGCAACCTACGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000007372-PAX6:NM_001127612:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=0.015 A=NA C2=0.814
Domain overlap (PFAM):
C1:
PF0029213=PAX=PU(88.0=98.6)
A:
NA
C2:
PF0029213=PAX=PD(24.7=37.5)
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:
GTGTCCAACGGATGTGTGAGT
R:
AAGTCCCCGGATACCAACCAG
Band lengths:
358-1062
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)