BtaINT0107941 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004561 | PAX6
Description
Bos taurus paired box 6 (PAX6), mRNA. [Source:RefSeq mRNA;Acc:NM_001040645]
Coordinates
chr15:63360987-63361691:-
Coord C1 exon
chr15:63361533-63361691
Coord A exon
chr15:63361070-63361532
Coord C2 exon
chr15:63360987-63361069
Length
463 bp
Sequences
Splice sites
5' ss Seq
AAGGTGATG
5' ss Score
5.22
3' ss Seq
AATGCAACTTACTCTTTCAGAGT
3' ss Score
7.66
Exon sequences
Seq C1 exon
ATGGCTGCCAGCAGCAGGAAGGAGGGGGAGAGAATACCAACTCCATCAGTTCCAATGGAGAAGATTCAGATGAGGCCCAAATGCGACTTCAGCTGAAGCGGAAGCTGCAAAGAAATAGAACATCCTTTACCCAAGAGCAAATTGAGGCCCTGGAGAAAG
Seq A exon
GTGATGGAGTTTTTCAAAGTAGGGAAGCAGTAAATCAAAGTAAATGCCACATCTTCAGTACAAAGAGCTAAATTTAGCCAGGGCCCTTGCACAGAGGCCTGAAAAGGTTCCCTTTTTCTGTCTTTTCTGGGTATCTCTTTTAGTGTATGTGTTTTCTTTCTTCTTTCCACGTACCAGGAATTCAAAGATGAGAAATCTGACTTCTCATAAAGAAAGAGTCATGATTTGGCTAATTCAGGCCACAGAAGAGACCTTGAATGAATGTCATTAAACAAAAAAATAGAACACGGTTCTGATGGGATAGTTCTTCCAAGTACAGTCAATGCTAATAGTAGTAGCATTTTAAAGGGAATTGGTTGAAAGTGATGGAAGTCAGGAGGTGAAAATCAGCTTGATCCAGGCTTTGGTTGACACATTTTGTATAGTTCTGGTGCAACATAGAAAATGCAACTTACTCTTTCAG
Seq C2 exon
AGTTTGAGAGAACCCATTATCCAGATGTGTTTGCCCGAGAAAGACTAGCGGCCAAAATAGATCTACCTGAAGCGAGAATACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004561:ENSBTAT00000005994:8
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=0.982
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(29.8=31.5)
A:
NA
C2:
PF0004624=Homeobox=FE(47.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGCAGGAAGGAGGGGGAG
R:
CTGTATTCTCGCTTCAGGTAGA
Band lengths:
231-694
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development