HsaINT0120741 @ hg19
Intron Retention
Gene
ENSG00000135903 | PAX3
Description
paired box 3 [Source:HGNC Symbol;Acc:8617]
Coordinates
chr2:223064606-223066161:-
Coord C1 exon
chr2:223066131-223066161
Coord A exon
chr2:223065960-223066130
Coord C2 exon
chr2:223064606-223065959
Length
171 bp
Sequences
Splice sites
5' ss Seq
CGCGTAAGT
5' ss Score
9.93
3' ss Seq
TGATTTTCTTCCTCCAATAGTTG
3' ss Score
7.7
Exon sequences
Seq C1 exon
GTGCCTTTCATTATCTCAAGCCAGATATCGC
Seq A exon
GTAAGTGAACTGTCCACTTGGAGCTAAAACTGGCCCTGTTTCTGGTCTTCGCAGCCTAGATATGAAGAATCTGCTCTGAAAACAAAAAAAAATTACCCTTTTGTTGGGGGGGGTGGGGCAGTGGTCCCAATAGGAGACAAAGGAGAGTGATTGATTTTCTTCCTCCAATAG
Seq C2 exon
TTGGTTTCAAATCCTTTTGAACACGTTCGACAAAAGCAGTGGAGAAGAGGAAGACCTGGAGCAATAAAAGACAAATGCAACATTTTAAGGCAATGGTTTCACATGGTTACATATCAAAACATCCCAATTCTTTAGTGCTGATCATCGAGGAGCTAGAACATTCCATTTGCTTGTGTGCGTGCGTGCGTGTGTGTGTGTGTGTGTGTATTGAGATTTACCCAGACTGGTTTGGGCAAGCAGACTGTTCTAAAATATAATAGAATACCCTAAAGTATAACATGTCGATGTTCGATGCTGATACTTCTACAACTTTAAAACTGCTCATTTCATGAAGCAAGAATGGAGGAATCCTTGACTCTTACACACTGGAAATTGAAATAAAGATAAATGCAACCATTTTTAGGAAGCTAGACTAGCTGTAAAGGACCTCCTAAATAAATTATTTGTTACTGTATCCTCATTTGTAATCTAGTTGTCAATAAATGGCCCGGACATGTCTTGCTAACAGGATATGGGCTACCAGGAAGAAGGACTTGTTTCCCTTTCCTGTGTGGGGAGAGGTGTGTGACGTTTTTCCAGTTCACATTTATTTGGTAGCCCACCTGGGTTGGAGGAAGGGCACGGTGGAGAGAAAGTGACATGCATTCACATATCTGCTTATCAGTGTGCAATACTGTGTACCTCATGGATGCTTTGGCAATGCCCAAGGCGATATAAGCAAAATCAGAAGTATATTTTTGCAGGTGCTTTTATTTTCACAGCCCATAATTCATAGTGATAGAGTGCAGTGATGTTTGCCATTTGCTGGACAACCAACACCCGGGTTGCTCCTTTGATTAGAGACCAGATCAGATAATTATGCTTTTAAACTGATTACGTTTACATTCTTCTCTTTTCTATGAAAGGCAGGGCAAGAACAGAAGTGTTCACATGGCTCTCATGTACTTTTAAATTATACAATGATATCCAATATTAAAAGATTATAGGAACTGAGGTTTACATACGTTTGTGTGGTGACATTTTAGAATGTCAATAAATTTGCTTTTTGAGATGTTGAGAGGAACAAGAAGGTGGAAGGCAGTGTTATTTATTTCTTTCTATTCTTGGAACCACGAATGAGGTAGGCACAAATACATTCCTTTTAGAGTTAAGAACTATGACGTAGCGAGTTAGTGAGACTAGACATAGTACCGAATTTAGTTCATGCATTGGTCTTAGAGGGTGATGGAACAAGAGAAGTACTATCTTTGTGTTGCAGCCTCAACCAACAACAATGTGTTGTAAAAATGTCTTTCATGTAAAAAGTGCAGTAAATATTTACTATTTATAATGAATAAACAGTTATGAAAACTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000135903-PAX3:NM_181460:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (disopred):
C1=0.490 A=NA C2=0.714
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCATTATCTCAAGCCAGATATCGC
R:
GCCCAAACCAGTCTGGGTAAA
Band lengths:
258-429
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)