Special

HsaINT0120761 @ hg19

Intron Retention

Gene
Description
paired box 6 [Source:HGNC Symbol;Acc:8620]
Coordinates
chr11:31814986-31815350:-
Coord C1 exon
chr11:31815200-31815350
Coord A exon
chr11:31815102-31815199
Coord C2 exon
chr11:31814986-31815101
Length
98 bp
Sequences
Splice sites
5' ss Seq
CGGGTAATT
5' ss Score
6.79
3' ss Seq
GTCATTTCTCTTGCCCTCAGTTT
3' ss Score
9.26
Exon sequences
Seq C1 exon
GTATGGTTTTCTAATCGAAGGGCCAAATGGAGAAGAGAAGAAAAACTGAGGAATCAGAGAAGACAGGCCAGCAACACACCTAGTCATATTCCTATCAGCAGTAGTTTCAGCACCAGTGTCTACCAACCAATTCCACAACCCACCACACCGG
Seq A exon
GTAATTTGAAATACTAATACTACGAATCAATGTCTTTAAACCTGTTTGCTCCGGGCTCTGACTCTCACTCTGACTACTGTCATTTCTCTTGCCCTCAG
Seq C2 exon
TTTCCTCCTTCACATCTGGCTCCATGTTGGGCCGAACAGACACAGCCCTCACAAACACCTACAGCGCTCTGCCGCCTATGCCCAGCTTCACCATGGCAAATAACCTGCCTATGCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000007372-PAX6:NM_001127612:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact

ORF disruption upon sequence inclusion

No structure available
Features
Disorder rate (disopred):
  C1=0.947 A=NA C2=1.000
Domain overlap (PFAM):

C1:
PF0004624=Homeobox=PD(19.3=21.6)
A:
NA
C2:
NO


Main Inclusion Isoform:
NA


Main Skipping Isoform:


Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
ALTERNATIVE
Zebrafish
(danRer10)
LOW PSI
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATCAGAGAAGACAGGCCAGCA
R:
AGCGCTGTAGGTGTTTGTGAG
Band lengths:
167-265
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