BtaINT0107932 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004561 | PAX6
Description
Bos taurus paired box 6 (PAX6), mRNA. [Source:RefSeq mRNA;Acc:NM_001040645]
Coordinates
chr15:63360395-63360757:-
Coord C1 exon
chr15:63360607-63360757
Coord A exon
chr15:63360511-63360606
Coord C2 exon
chr15:63360395-63360510
Length
96 bp
Sequences
Splice sites
5' ss Seq
CTGGTAACT
5' ss Score
5.45
3' ss Seq
TTGTGTTCCTCTCCCTGCAGTTT
3' ss Score
11.06
Exon sequences
Seq C1 exon
GTATGGTTTTCTAATCGAAGGGCCAAATGGAGAAGAGAAGAAAAGCTGAGGAATCAGAGAAGACAAGCCAGCAACACACCTAGTCATATTCCCATCAGCAGCAGTTTCAGCACCAGCGTCTACCAACCCATCCCACAACCCACCACGCCTG
Seq A exon
GTAACTGGAAATATTAATTCTGCTGATCAGTGTGTTTCAGCCTTTCTGCCCTTGGCTCTGACTCTCACCACGACTGTTGTGTTCCTCTCCCTGCAG
Seq C2 exon
TTTCCTCCTTCACCTCCGGCTCCATGTTGGGCCGAACAGACACAGCCCTCACAAACACATACAGTGCTCTGCCGCCCATGCCCAGCTTCACCATGGCGAATAATCTGCCTATGCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004561:ENSBTAT00000005994:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PD(19.3=21.6)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCCATCAGCAGCAGTTTCAG
R:
GGCAGATTATTCGCCATGGTGA
Band lengths:
171-267
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development