BtaINT0107937 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004561 | PAX6
Description
Bos taurus paired box 6 (PAX6), mRNA. [Source:RefSeq mRNA;Acc:NM_001040645]
Coordinates
chr15:63369235-63372994:-
Coord C1 exon
chr15:63372934-63372994
Coord A exon
chr15:63369366-63372933
Coord C2 exon
chr15:63369235-63369365
Length
3568 bp
Sequences
Splice sites
5' ss Seq
ACAGTAAGT
5' ss Score
9.49
3' ss Seq
TCTCCTCTCCCTTTCTTCAGGTC
3' ss Score
13.84
Exon sequences
Seq C1 exon
AGCCCCATATTCGAGCCCCGTGGGATACCGAGGCCCCCAGCCAGCGCCAGCATGCAGAACA
Seq A exon
GTAAGTGCCTCTGGTCTTTTTGGACTTCGGGCGGGGGAGGCGCGGACTAGCGCGCGGGTCGGGGGAGGGCTTGGAGGCTCTCGGTGTCCGCGCTGGCCAGGCCCGGGGCGCGAGGGAAGAGGCCCGGGGACCTGAGGCAGCTGCTCCAAGAGGGGAGGGCGTTTGCTCTGTTCTCCCTCCTGGAAGAACAGGGGCTGGGCCCTTGGGAACAGCCCGCAAGAGTTTGCGAAGCTGCGGTAGAGAAACCCCATCCCCCCAAATCCTGTAACTCACACCCCCTCCCCGCCCCTGCCCGGGCTCTGACCCCAGAGAGGGGGGCTGGACTGAGCGGGGCGGGGCGGAGGCCTCTCGCCGTCGTAGCGCGAGAAGGAGGCCCCTTGGGCTTAGTCAAGACTGAAAGTCTCCACCGTCTGGGGCGGGTGGGGGCTCCTCTACCCCAGTCACCCTAAGAGCAGCTCCTCCCATCGCCACCCTGGCGAGGGGCCTGGAAGGCCAAGGGAGTGGGGCACCCAGGCCTGCGGTGGGGTGGAGTTGGTACTGGAACCGTGGACTGTTACAGGGCGCAGACCGGCGAGAGCAGGTTTACTAGGTCTGGGAGGAGTGGGGATCGAGCCCAGGAGTTGGAGCAGCCCTGCCCTGGTGGCTACTGTGTGGGTCCTAGTCATTCCGGGCCCGATGTGCCTTTGGTTCGCTGGCTCTTGCATCTCCCATCCTCCCTTTGCCTAGACCCCTTGGGCACCCAGCCCACCTTCCTGCTCAGTACGTGGGTGCTGCTTTGTGGCAGGACGAATCTGAGACCGGGCCTGAGAGCCTGGAGGCCCAGTGAAACTAGGCCCCGGTAGAGGGACAGAGCCCTGAGGCGGTTTAAGGGCTCCGCTGTATGGAGTGCCTGAAAGCCTAAATCTTCTAGAAACATTCCCTTGCCGAACTGCAGACTGAGAGGGGTCCCTAGCCCCTGATGCATCTGTCCTGCAGCCGCTAGCTGTCCCCTGGCCCTTTAGCGGCTGGGTGGGCGTGAAGCGCAGGAGAGGGCTCAAAGCGGGCGCCGAGCTGGAAGGCGGATTAGTTGTACAGAACGTGCCAGGCCCCGGGGACTTGGCCCGGTAGGAACCCTCCTTGGCGAGGCTCGGGCTTCTGGCCACTCTTCCTGGCTGCTGGGTCCTCCCCTCTCCAGCACAAGGGCCCCAGCCGCAGGCTCTTGGGCAGGCCGGCCCCGGGCGCGCGGCGCTGAGCATTTGCCGCTGCGGCCTGGCTGGCGGGCCCCGAGGGGCGCGGGGTCGCGGGCCGGCCTGCAGGGCTTTGTGCCGCTCGCTCCCGGGTGTGCGCGAGGCGCAGAGCATCCAAATTGACACCATATGTTTTCCTATTAGATGCTTCGCGGTCGAATTCTAGGCGCATAATCATCGCCACTGGGCGAGAGCGCCAGCCGTCCCTAGGGAAGGGACACAATGATTGAGGCTTAACCTCTGAAGGGGAACTTAGAGCGGCGCTTCCTCGCTGCCATTTCGATGCTGGCAGAGGCGACCTGGCCCTGGGCAAGCACCCGCCGGCGGTCGCCGCGGAGGTGGTGGGCAGGTTATTATTATTATTTTTTTTGCCTGTTTGGGGGAGAAAGAGGGAGGTCTAGGATTAGGCGGCTTCATACGCCTTGGCATTCCCAGATTGGGAATTGCCTCGGCTGCGCGTGAAGTTTGGAAGGTCTTTCTCGATCTTTCTCTGGGAGTGCCTTTCTTTTTCCTGGAAGGCGTCCTTTGCCCAAAGGGGAGGCTCCTGTAAGCTGGAGCAGCAGAAGTTCTTTAGAGGCAAGGGAAGGCAATAAAGGGAATTTAGGAGAAACCAGGAGCGGGCTCTAGGCCTCGCTCTGTTGGAGAAGCGGTTTCCCCGCGATGTCCCTGCTGGAGCCCGGCCCGGCGGAGCCTAGATACCCCAAACGCCTGTCACTTCTCATCGAGTTGAGGCTTCAGCACGCCCCCTCAGTCAGCGTCCCCCCCCCCCCACCCCTCTGCCCCAAGCCTTCGGCTACTCTGAAAACGCGGCTCCCCTCGAAGGGGAAACGAGTGCAGTTCAATCTCGTCTGAGTGATCTACAAATAGGGACGGAAAGGGTCGTTTTATCACGGTCCCGTTTGTCGTGACGATGCAATTTCCCGGAGCGGAGCACTGTCACAAAGTGACAAGGCTGCCACAAGCGCCCCGACTGATCTTTTCAATTAGCCTTCCATGCATGATCCGGAGCGACTTCCGCCTATTTCCAGAAATTAAGCTCAAACTTGACGTGCAGCTAGTTTTATTTTAAAGACAAATGTCAGAGAGGCTCATCATATTTTCCCCCCTCTTCTATATTTGGAGCTTATTTATTGCTAAGAAGCTCAGGCTCCTGGAGTCAATTTATCAGAGGCTCCAAGGAGAAGAGAGGAGAGGAGAGCTGAGCGGGGGAGCCACATCTCCTGGAAGGGCTACTCTCTAGAGTCGGGGCTGCAGGTTGGAGATTTTTAAGGAAGTGGAAATTGGCAATTGGCTTTATTTGTGTGCCTGTGGTTTCTGGGGAGGGGGGCTACAGGGGTGCTAACTCCTCCCTATTCTCAGTTTAGACAATAGGGTGAGGTTGTGAGATAACCAGATAAAGGAGGGAAGGGGACACTGTGGTGTGGTCTTTTCCTTTTCACTTTTTGATTTTTGCTCCTGTCTATCCTGGGCTGTGGGGAGGGCCGAATTTAGCATCGGAAGTAAAAGCGGAGCTGTAGCTGGTGCAGACAGACTCCCAGACCTCTGGCCCACTGTAGCAGCCAGACTACTTTGTGGTTGGAGCCGATATGAGGGGCTTGAGGAAGTCTGCATGGGAGGTGCTGAACCCAGGTTGCGGTTCACTGGCCACAGATTTGCTGTTCTGGTTCTTCTTTACTCTATTCACTTTTTTTCTCCTATTTTTTTTTTTTTTAAATCCTGGTGCTTCACCAGAGTTTGGAATATGACAGCAAATGTTTCTGGATCTAGCATCTGAGGGAACACTGAGGAGCTGTAGGGTTTGCCATCACAGTTCTAACAATGCAGGGAGCTTGAAGATGCAGTGGGGGTTCTATAGGACTCGTGGTTTTTCGTTACACTCAGAGGGGATCTTTGGGAGGATATTTCTGAGCTGATTATTTGCACCTTTCGGGTTCAAAGACTGGCTGGGGTGTTTCTGGAGGGCAGCAGTGGGCTGGGGGTTCTCCTGGAGTGAAAGCAGTGAGTAGTAGTGAGGTGTGTGTGTTCTTACGTGTGTCTGCACCGTGCTTCTGTTCTGCAGGCGGGTGGGCAGGAGCTCCGCTGTGTCTGGGCTGGGCTGCCCGATGCCTGGAATGGCTTCGAGGTCCGGTTGTCATTTTCCATCGAGAGCAGGGACCTGATCACTGAGGTTGGCCAGGGCTGGCAGGGAGCTGAGGATGCATTGTGGTTGTCTTTTCTTCTTTTCCTTCTTCCTTCCTCCTTTTCATCCTTCTCCTTCTTCCTCCTCCACCTCCTCCTTCCCCTTCTCTTTCTTGCCCCTTCTTCCCCTCCTCTCTGCTCTGCTCTCCTCTCCCTTTCTTCAG
Seq C2 exon
GTCACAGCGGAGTGAATCAGCTCGGTGGTGTCTTTGTCAACGGGCGGCCACTGCCGGACTCCACCCGGCAGAAGATCGTAGAGCTAGCTCACAGCGGGGCCCGGCCGTGCGACATTTCCCGAATTCTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004561:ENSBTAT00000005994:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (disopred):
C1=1.000 A=NA C2=0.739
Domain overlap (PFAM):
C1:
PF0029213=PAX=PU(0.1=0.0)
A:
NA
C2:
PF0029213=PAX=PU(34.4=97.7)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development