BtaINT0107939 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004561 | PAX6
Description
Bos taurus paired box 6 (PAX6), mRNA. [Source:RefSeq mRNA;Acc:NM_001040645]
Coordinates
chr15:63367163-63368302:-
Coord C1 exon
chr15:63368087-63368302
Coord A exon
chr15:63367329-63368086
Coord C2 exon
chr15:63367163-63367328
Length
758 bp
Sequences
Splice sites
5' ss Seq
AGTGTAAGT
5' ss Score
8.46
3' ss Seq
GATCTTGATTTGATTTGCAGGTG
3' ss Score
8.08
Exon sequences
Seq C1 exon
GTGTCCAACGGATGTGTGAGTAAAATTCTGGGCAGGTATTACGAGACTGGCTCCATCAGACCCAGGGCAATCGGTGGTAGTAAACCGAGAGTAGCGACTCCAGAAGTTGTAAGCAAAATAGCCCAGTATAAGCGGGAGTGCCCGTCCATCTTTGCTTGGGAAATCCGAGACAGATTACTGTCCGAGGGGGTCTGTACCAACGATAACATACCAAGT
Seq A exon
GTAAGTTCACTGAGAACATTCCCTCTCCCTGCCCTAAGCCCCATGCTCTTCCCTCTTTACCATCACTTTCTCTGCGTCCCCCTGCTCTCCTTTCTGCCAGTGTCTTTCTCTTTCTCTCCTCCCTGCTCCACCTCTGTTTGTCACCTCTGTACCTGGGGGTCTTGAGAGGAGCACTTTGACCTTTTTATTGACCTTCTGGAAATGGGAGTCAAGTGTGGGAGGGTTAGTCACCATATTTGCATGTGGCAAGGTAGAGAGTGGAGAAAGTCACTGGAATCTAGAAGGAAAGTGAAAATGAAAACCAGATTCAAGCAAGCTTCCTCCACATCTTGCTGTTTGAACCTTCTTTCAGAAATCAAACATCCATTTCTGTCCTAATATAAAAAACAAATAACAGTGAAAGAAATCTCTAAGCCAGGTCTTAATATTGGAGACAGGGAATCTTTGTAACAACAACAATAATAAAAAAGCAGCCATGTGAGTTAGGTCACCAAAGACACTGAGCGACAGTGAAGGACCCCTCCCTAGTGTTCCAGCTCTCTACCCAACTCAGTTTCCATGCCCAGAGTGATAGCTGACATTCTTTCCACGATGTCTCTGCAAGTCCACCCACTGTCCCAGGATGGCTGGGGATTTTTTTTTTTTAATGTATTAGGGGTCATTCTTTAAAGGGGTGGCATGCTGAGATGGAGACTTAAGAGGGCAACTGTGTCTTCAGGAGACTCTGCCATTTGGTTTGATCTTGATTTGATTTGCAG
Seq C2 exon
GTGTCATCAATAAACAGAGTTCTTCGCAACCTGGCTAGCGAAAAGCAACAGATGGGCGCAGACGGCATGTATGATAAACTAAGGATGTTGAACGGGCAGACCGGAAGCTGGGGCACCCGCCCGGGTTGGTATCCGGGAACATCAGTGCCAGGGCAACCTACGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004561:ENSBTAT00000005994:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=0.000 A=NA C2=0.786
Domain overlap (PFAM):
C1:
PF0029213=PAX=FE(56.8=100)
A:
NA
C2:
PF0029213=PAX=PD(6.4=14.3)
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:
GTGTCCAACGGATGTGTGAGT
R:
ATGTTCCCGGATACCAACCCG
Band lengths:
358-1116
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development