HsaINT1026213 @ hg38
Intron Retention
Gene
ENSG00000106331 | PAX4
Description
paired box 4 [Source:HGNC Symbol;Acc:HGNC:8618]
Coordinates
chr7:127613450-127613881:-
Coord C1 exon
chr7:127613756-127613881
Coord A exon
chr7:127613533-127613755
Coord C2 exon
chr7:127613450-127613532
Length
223 bp
Sequences
Splice sites
5' ss Seq
AAGGTGCTG
5' ss Score
4.05
3' ss Seq
GTGAGACTCGATCTCCGCAGAGT
3' ss Score
5.77
Exon sequences
Seq C1 exon
CTGTTTTGGCTCCAGCTGTCCTCACTCCCCATAGTGGCTCTGAGACTCCCCGGGGTACCCACCCAGGGACCGGCCACCGGAATCGGACTATCTTCTCCCCAAGCCAAGCAGAGGCACTGGAGAAAG
Seq A exon
GTGCTGGGCTGGGACAGATGGAGGGTCAGAGAGTCCTCAGTGTGACACAGGGACAGTGGCCCTGAGGCCTGTGGGCAAAGGCTGAGAGGTGCAGGTGTGAGTGGCCCTGCCTTGAGGAGGAAGGTAGTTTGGGGTTGTAGCAGGTGGGGAGTGTTGCCTAAGGGGAGACCCATGCCTTGCTCCTCTCCCGGTGCCCTTACTTTGTGAGACTCGATCTCCGCAG
Seq C2 exon
AGTTCCAGCGTGGGCAGTATCCTGATTCAGTGGCCCGTGGAAAGCTGGCTACTGCCACCTCTCTGCCTGAGGACACGGTGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000106331:ENST00000341640:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=0.922 A=NA C2=0.613
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(29.8=39.5)
A:
NA
C2:
PF0004624=Homeobox=FE(47.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTTTGGCTCCAGCTGTCCTC
R:
CACCGTGTCCTCAGGCAGAG
Band lengths:
204-427
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains