BtaINT0107916 @ bosTau6
Intron Retention
Gene
ENSBTAG00000000410 | PAX4
Description
paired box 4 [Source:HGNC Symbol;Acc:HGNC:8618]
Coordinates
chr4:92643395-92643818:-
Coord C1 exon
chr4:92643693-92643818
Coord A exon
chr4:92643478-92643692
Coord C2 exon
chr4:92643395-92643477
Length
215 bp
Sequences
Splice sites
5' ss Seq
AAGGTGCCG
5' ss Score
5.74
3' ss Seq
GTGAGCCTCCATCTCTGCAGAAT
3' ss Score
7.84
Exon sequences
Seq C1 exon
CTGGTCTGGGTCCAATTCCTCGAACTCCCCCCTGTGACTCTGAGGCTCCCCGGGGTCCCCACCCAGGAACTGGCCACCGGAATCGGACAATCTTTTCCCCAGGCCAAGCCGAGGCGCTGGAGAAAG
Seq A exon
GTGCCGGGGCTGGGTGGATGGGGGCCACAGAGGTGAGGACCTAGAGGCCTATAGGCCATGGCTGAGCGCTGGAGGCTGCAGGTGGCCCTGCCTCCAGGAGGAGGGCAGTTCAGGGTTGTCCTAGGAAGGGTGGGAGTTGGGGGGCTGCTGCTGACGGGGAAGCAGGCCTTGTTCCTCTCCCTGTGCCCTTGCCGTGTGAGCCTCCATCTCTGCAG
Seq C2 exon
AATTCCAGCGTGGGCAGTATCCTGATTCAGTGGCCCGTGGGAAACTGGCTGCAGCCACCTCTCTGCCCGAGGACACGGTGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000000410:ENSBTAT00000045264:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=0.953 A=NA C2=0.071
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:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGGTCTGGGTCCAATTCCTC
R:
CCGTGTCCTCGGGCAGAG
Band lengths:
204-419
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]