HsaINT0120745 @ hg19
Intron Retention
Gene
ENSG00000106331 | PAX4
Description
paired box 4 [Source:HGNC Symbol;Acc:8618]
Coordinates
chr7:127253504-127253935:-
Coord C1 exon
chr7:127253810-127253935
Coord A exon
chr7:127253587-127253809
Coord C2 exon
chr7:127253504-127253586
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-PAX4:NM_006193:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (disopred):
C1=0.994 A=NA C2=0.750
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
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]
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)