HsaINT0120737 @ hg38
Intron Retention
Gene
ENSG00000135903 | PAX3
Description
paired box 3 [Source:HGNC Symbol;Acc:HGNC:8617]
Coordinates
chr2:222296978-222298996:-
Coord C1 exon
chr2:222298531-222298996
Coord A exon
chr2:222297214-222298530
Coord C2 exon
chr2:222296978-222297213
Length
1317 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
TCTTTTTCACCTTCCCACAGTGT
3' ss Score
10.85
Exon sequences
Seq C1 exon
ACTCGGTGTCACCACAGGAGGAGACTCAGGCAGGCCGCGCTCCAGCCTCACCAGGCTCCCCGGCTCGCCGTGGCTCTCTGAGCCCCCTTTTCAGGGACCCCAGTCGCTGGAACATTTGCCCAGACTCGTACCAAACTTTTCCGCCCTGGGCTCGGGATCCTGGACTCCGGGGCCTCCCCGTCCTCCCCTTTCCCGGGTTCCAGCTCCGGCCTCTGGACTAGGAACCGACAGCCCCCCTCCCCGCGTCCCTCCCTCTCTCTCCAGCCGTTTTGGGGAGGGGCTCTCCACGCTCCGGATAGTTCCCGAGGGTCATCCGCGCCGCACTCGCCTTTCCGTTTCGCCTTCACCTGGATATAATTTCCGAGCGAAGCTGCCCCCAGGATGACCACGCTGGCCGGCGCTGTGCCCAGGATGATGCGGCCGGGCCCGGGGCAGAACTACCCGCGTAGCGGGTTCCCGCTGGAAG
Seq A exon
GTAAGGGAGGGCCTCAGCGCGCCGCCTGGATCCCAGGGCCTGGGACCGGCTGCCTCACCCCATCCCCAGGCTCCGCAGGCTCCTTTGGTGCTTCCAGGAAGCCCATTCCCTGGGCACCCCACACCCCAAGAAGCACCAGTCGGGGGCGAGGACCTACTCGATTTCCTTTCTGCAAATGGAGCGCGCTGCTCTCTGCAAATCCTGGCGGAGCTGGGCGGTCAGGCCTGCGGCGAGCCGGGGAGACTTGTCCCTGTTGTTTTGGAAATGCCGCGGTGGAGAAGGAGGTGAACCGGCTTCTGAGCGGCAGAAGCAACTTCTCCGCAATTTGTCCATTCGAAATTGTCTCGAAGTTGTCTCGAAATTGTCCCGGCTGCGCCCACACTTGTGAAACATATGTTAGTTCAGGAAGTATTTTTTTTTTTTTGCCCTGCAAAGTTGTGGTGGCTAACGCCGCGCCATTGTGATTGGAATTTTTAGAATAATTAAATAAATTAGAATTCTATGTATCTCAAATAGCATCTAGAAGTTTCTATAACTTGTTTAGGAATCGCCTTTCCGTCCACTTGAAGATTCTGGGAATCCCGGGGAGGCAGGAAGTCTTGCAAGCCTGAGCCGTTTTCAATGGTTTTCCAGGTTAGGGCGCCCCAGCAGAGATGCTCATCGCCCCCGCCACCCACTCCCTTCACACCCAGCCTAGAGTAGAATGTAACACCCAGAGCAAGAATGGGGGCTGGGGGCCCAGGAACAGCCCTGCCGCTGCTGTGGTCTCTGTCCCAAGATGTAACAGGTGACACAGGCACTGCTGCTTGGGCCTCCTTTCTGGACCCTCTTTGACCCTTGGCTGCTGCACTTTTGGCTAGAAACCCCAAGGGCTATCAGCTGGCCCAAGTCCCTTAGAAAGGGAGAGATCCCAATTGGACAGGGATCGGTGGGAGCAGAGTTCATCAAGGCCAGCTCCTGGGTGAACTTCTCTTCGCCAGGAGGCTGTTTCTAGAGCAAGCTAGACTCTCTACCAGCTGCAGGGTCTCCTAAGTTGCCACTCCCCGGGCCCGAAGGGGAAGACGCTTTCTCTGGGGAGAATTATTTTGCCCCATTTGCTGTCTTTACACAAGATTACATGCGCTATATTGCTGAATAATTTGAACAAATGTGATTGAAAGGAGGTCTGGGTCTGGGAGTCCGATGTCGAGCAGTTTCAGCGTCGGTGCTGTAACATGAGGATAGGACAGAAGACTGCGAAATTACGTGCTGCTGTTCTTTGCTTTTTATTTTCCTCCAGTGACTTTTCCCTTGCTTCTCTTTTTCACCTTCCCACAG
Seq C2 exon
TGTCCACTCCCCTCGGCCAGGGCCGCGTCAACCAGCTCGGCGGTGTTTTTATCAACGGCAGGCCGCTGCCCAACCACATCCGCCACAAGATCGTGGAGATGGCCCACCACGGCATCCGGCCCTGCGTCATCTCGCGCCAGCTGCGCGTGTCCCACGGCTGCGTCTCCAAGATCCTGTGCAGGTACCAGGAGACTGGCTCCATACGTCCTGGTGCCATCGGCGGCAGCAAGCCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000135903:ENST00000344493:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (disopred):
C1=0.949 A=NA C2=0.153
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0029213=PAX=PU(57.9=92.4)
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:
CTTTCCGTTTCGCCTTCACCT
R:
AGGACGTATGGAGCCAGTCTC
Band lengths:
347-1664
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