BtaINT0107935 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004561 | PAX6
Description
Bos taurus paired box 6 (PAX6), mRNA. [Source:RefSeq mRNA;Acc:NM_001040645]
Coordinates
chr15:63373345-63377393:-
Coord C1 exon
chr15:63377213-63377393
Coord A exon
chr15:63373422-63377212
Coord C2 exon
chr15:63373345-63373421
Length
3791 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
TCTCCCCTGTTTTGTCTTAGGGG
3' ss Score
10.79
Exon sequences
Seq C1 exon
GGATCTGAGATTTGCTCTCACACACCAAACCAGCAGCGTCCGTGGAGAAAACTCTCGCCAGCAACTCCTTTAAAACACCGTCATTTCAAACCGTTGTGGTCTTTAAGCAACGACAACAGAAAAAAAAAAATCAAACAAAACTCTTGACAGGAGCTTTGACTAGAGAGGATGCCTCAGAAAG
Seq A exon
GTGAGTCCGCTTCTTTCTTCTTGCTTCATTTTTATTGCAATATTCAGGCAGGTCTCCCCCTTCCTCCCCCCTTCCTTCCTCCCTCTCGCCCGTCCCCTCCCCCACTGCTACGCCGGGAGAGTTGGACCGGAGAAGTTTCCACGCAGGAGCCCAAACTTTCTACTTCCAGCGAAAGCCGGCGTCAGAGGGCGACCGCCAGCGAGCGGGAGCAGCGCAGGGCTCGGGGCGGCCGGCCCGCTCAACCCCAGCGCCAGCGCCAGCGCCAGCGCGGGTTGATCTCGCAGGAAGGACCAAGGCTCTGGGCGCCGCAGCCTCCGCGGCTCCCGGCCACAGCGTTGCCAAATGCTCCCGGCCGGCCGGAGAGGACGAAGAGGCTCTGCGGTGCCACAGGCCCAGGAACGGCTGCAGCGATCGGCCGCCGCCGGCCGCTTTGTCCAGTCTCGGGCCCAGCGAGCGCGCAGAGAGCCGCGCGCCGAGGGAGCGCCGAGGGAGCCGGCTCGCCTCGCCGCCGCCCTCCCGCCCTCCGGCTTTGTGCGGCGCTCTCCCGGGCTCCGAGGAATCCGCTGGCACCCGAGCGCTCAGGACAGCCGCGCCCGCCGCCAGCTCGAGCAGTCAGTCGGCACTGCAGCCCCACGCCGGAGGCCGAAGGAAAGAGCGAGGGAGCGGGAGCCGGGAAGGAAGCTGCCAGGCCCGGGCGGTGGAACGCGCGCTCCGAGGGAGCTCGGAGACGAACGGGAGGATTGTCAGCTTCCATCAAGCCCCCAGGCTCTGGCCCCCAACTTGGGCGCAGAGCTCGGAACTTGAAAACTCTCTGCGCCCCGGGTTTTCCCCAACCTTCGCCCTCACCCTGCGAAAGCTGGGGTCCTCCCTGTCCCAGCGTTCGGTGGGTATTTTTCCTTGTCTTCCTCTGACAAAGCTGCCCCGATGTTGCCATTTCAACAAGTTTCGAGGTGGAAAGGTTGTTTGTTTATTTTAATCCAAAGCTCCTGATTTTTTTCTTTGTGAGGCCTTTAGAAAAATCAATATGAAAGCAGTGGCTTTCCGTTGGTCTGATCACATCCTCTCCCTGCTAATTAGTCTGAGTAATTCGAGAGCTTTTCGATTCTAAGGCCCCAGGAGAAAAAGTGTCTTTTCAAAGTTCATAAAGTTGTTGCCTCTTTCCTTGTGCAGATTTTCTCAGTCTCCCTGCACCATAATAGCCCTGAATTTTAGCAAGTGTAATTTGGGGGAAATGGAGTTGAATTTCAAGTGGAAATGCTTTCTTTTTCGAGTGCTAAAACGCGGCCCTCCAGTCACGAGTGATTTCTAGAAAGTTTAAAAACAAAGTGAACGGTGGTTTCTCTCTCTCTCTCTCTTTTTTTCTCATTTTATCCAAAGCTCCCTAAGCCATACTGGACGTTTAACTAGAACTTGGGAAGATTTGAGGAGGGGGTGGGAGCAGAAAATGAAAAGCAAAGACCTTGAAAGCCTGGCGAGTTTACCGAGGAGAAATAATAGTTTGTGGCCATTGACATTACATTTTTTATAGCTGGTGACCTTTGCAAACGTCTGAAGGTAATTTGATTAGTTGTTGTCTTATTTGGCCCTAGAGAGTAAAACTTTGTCATCTTAATTGGTAATTACTCTTTGGCTGGGGGCGGGGAGGGCCAAAAGTGAGCTCTCCCCTTCACCCTAGCTAAGAAGTTTGGAGACGGTTTTGAGAATGAAGTAATTAAAACAACAGCAGCAAAACTGAGGCTTGGATCTGGGATAGGGAGGCAGTGGCCCAGTGGCCTAGTGGACCACGGCAAGGCGACTCCGAGGTGTTTGGAGACTCCCTTCCTTTCCCAAATGGGTCTCTGACTGGGCTAGGGCTATAGGAAGCCCCGAGGTTGAGCTGGGGGGCTGAAGCTGTGGCTGAGGTGGGGGGAGTCTAGTCTCCGCGAGAGTGCTTCCGGGTGTGATGCCTGGCTTCCCGGGTTGCTTTTGCACTGTGTTAACGATTACTTAAGTAATGAGATAGCTTCTTAGTTGAGAGGAGGGTGGGAAAGGAGCAAAACCAGGATTTGAAATGCTTCCACCTTCCCAGCTGCTTGGAAAATTAATCGGTTAGGCCTCTCTGGAATCAGCTAGTGATTTTTTAAAAATGGCTCCAAGAATGTACCAACCTGGACTGGGGGCATTCGGTTGTGGTTAAGTATAGGTATAGGTTACAGTAGGAAGTTTTACCCTTCTAGGGGAATTTCAGTCCCCCTTCTCCCCACCAGCTACTATTTGCAGTTTCAGAATCCGACTTGGTGTGTGTGGGGAGTTGGGCATTCTGCAGAAAGTTGGGTTTTTCTGCGTCTCCTGGACTTGACTTGGTCTCGGGGATGGAGAGACAGGAGAGAGGCTTTGGGAAACTGCCTTGGGAAGCTGGGGGAAAGTCCTCTAAGTTTATTTTTATGGATTTAAGCTGCCTCCCAGCTAGTTAATAAATTAGACCATGAATAGCCTTGAAGAAAAAAAAATTTTGCTTCTTAGAATTCTTTACTTGCAGACAGGCAAAATTAATAATCATAATAAGCAAAACAGAAAAAAGAATGAATATTTTAATTTTTTAAGCAGGGAAAGTGATGCTGTGACTATTTAATTATTTTACATTTTTTTTTTTTTGGCAAACCTTTTGAATGGGTTCTTTATTGTAACTCTCTCTTCCCAATTGAGCTCCCCACGGTGCCGTTGTATCTTTTTACAGCCCCTAACAACTCACACCAGTAACACAATTACGTCCAGATATTTATAACAAGAAATTACTTTTCTATTTTCTCCCCCACCCAGAACCTACTTCTTAAGAGAAGACAGGGAGGGGTAGTGGTGGAGGAGGTGTTAACCTTGGGGGACTAGCACTGGGTCAGGACTTACAAATCGAGAAGTGTCCCTCTGTTCCCTTTAAGAGTTGGTGAGTTGTTGGTACCTTTGGTTGGAAGCTGTGTTGCTAGTTAGGGAGATTCGGTTTTGCTCTTTGGGTTTGGGGAGAGCTGGAGAATAGAAGCCATTGTTCGCTCTCTGTAGGCTTTGTCGGCCACGCTCACCCCCTCCTGTTTGTACTTTTTAAAGCAGTGAGGCGAGGTAGACAGCGTGTGTCACAGTACAGTAAAAGGGGGGAAGATCTAAACACCAAAAGAGAAGTTAATCACAATAAGTGAGGTTTTGGGGGGAAAAAGTTGGGCTTGCCACTTTCAAAGTCCCAGAAAGAATGGAAGTGAATGGCGATCAAGCCGACTGGGAAGCTTTGAGGGGAAGAGTGAAGGATAAAGAGGTAACCAAAGACTTGGGTTGGGGCGAGGGGCTTGGGGCAACTGGGGTAGTGAAATTCTTGAAAGGAGTAATGGTTCTGACATCCTCCCAAGCAGCCCCAGCCTGCACCCTCAAGCACTCTGAAGTTCCAGGGTCCTCTGTGCTTCACCTCTAAACTTCAGGTATAAGCCCCCCTTCTCCCAGCTCTTGGCTTCTTCTCCTAACCCCACTGTTTCTCTTGTTCTCTCCTTTTCTTTCCCTAGTTCTTGGTATTTTTGCAAAATGGGGCCCTAAATTGTCAGGCTCTGCAAATTGCCCAAAGCCGGGTCAGAGCAGCCACTATCAAAACCTGGAGACCTTTGCAGGACAGGCTGCTGGAAATGTGGGTGTAGCTCTGGGATTTAGAGTTTAATGGCAGTTTGAGCCCAAGATGGGTTTCTTTTCTTTTCTTTCTGAGAGTGTGGATCAGAGAGTCCATGATCTATGCTTTTGAGTCATAGTTTGACATACCTTTCTCCCCTGTTTTGTCTTAG
Seq C2 exon
GGGGAAGACTTTAACTAGGAGCGCGCAGATGTGTGAGACCTTTTATTGTGAGAGTGGACAGACTTCCCAGATTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004561:ENSBTAT00000005994:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (disopred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
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