BtaINT0107931 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004561 | PAX6
Description
Bos taurus paired box 6 (PAX6), mRNA. [Source:RefSeq mRNA;Acc:NM_001040645]
Coordinates
chr15:63377213-63384294:-
Coord C1 exon
chr15:63384186-63384294
Coord A exon
chr15:63377394-63384185
Coord C2 exon
chr15:63377213-63377393
Length
6792 bp
Sequences
Splice sites
5' ss Seq
CAGGTAACC
5' ss Score
8.66
3' ss Seq
AATCTCTGTCTCCTTCCCAGGGA
3' ss Score
9.15
Exon sequences
Seq C1 exon
CGCGTAGAACGCGGCTGTCAGATCTGCCACTTCCCCCTGCGGAGCGGCGGTGAGAAGTGTGGGAACCCGCGCCGCCAAGCTCACCTGCCTCCCCGCCCTCGGTTCCCAG
Seq A exon
GTAACCGCCGGGTCTCCGGCCCCGGCTCCGCTCGGACCCGTGCCGTCCCTCTGCTGCCCACGACGGTGTCCCCAAACCAAGCCGGCCGGCCCCAAGTAGCCCAGGGGCTTGATTTTTGCTTTTAAAAGGAGATAAAGGTGGAAGGGAATTGCCGAGGGCAGGATAAAATGGGAGGTTGGGGGGGGGGGGTATCTTGTTCTTGCCGAGCGTGCTTTTCTGCAATAGTGGCAAAACGTCCCAGTGTTTTGAGTGGACTTCCAGTTGAGTGCTGAGCTGCGGGGAGGGGTTGAGAGGGAAGTGGGAAAAGGGAGACAGGGATCTGCTGGTACTGTCTGCTGCAGCCTCTTGCGATCGTGAGACATGCTGGGGGTGGGGGTGATGCAGTTTGTACCTGGAACTCCCTTGACTAGCAGTTCGCGACATTCACGCGTGCAGAGGTCCCCACCCGAGCCAGGAGTGCGTAGGAACGCCCCGCCGCGCGGGTCGGGCGAAGTGCAGCAAAAGTTTCCGGCGGCTGCAAAGTGTAGATAGTTGCGCCGAAACAAAGTCTTAGAGATAGGAGTTCGTTTCTCGGAAAGGAGAGGAGGACGAAAGAATGCTGCCCACAGAGCTGGGCAGCGCATAAAGCACGCAGCGTGCGATTTGAGCTTCACTTAGGAAGACCTAATAATTAGCGATTCTCACTGAGCTAGAACGCGGGCTCGGGTTACCGCGGGCGCTGCGCTAGCTGCCCGGGTGGGAAGATCGTGGGCGCCAGGGTAGTCGGGCCTCTGAGTGCCGGGGAGAGCAGCGCCCAGCTAGCTACTCTCACGTCCCAGGACAACCCAAGCCGACCGCCGGAAGTTTCTCCAAAGTGAGTCAGGTTAGAGACGACCCCAAACTACCTCTTGGTTCAGGAGTCTAGCCCCACGCAGCCGGAGATGCCAGAAAGGCTTACGCCAGGCACTGGAGCACCCGCCTGAGAGGTTGGGGGGCCTCTAGGTGAGGCCTGGGTTCTCCCCACTGCTGCTGACATCCCCTCTCTAGACTTTCTGGGGACACCTTCGGTGTCATTTCTATTTCAGGCACCTGTGACAGGTGCTCAGGACCACCGCCCAACTCTGAGCAATGGCCGCCCTCTGCCCACCTTGTCCAGGAAGCCCGGGAAGGAGAGAAGTGGCCACGCAGCCGAGCGCCTTACCTGGGCCTGGGGTCCTCTCCTCCGCGGGTTCCGTTCTCCAGAGCCGGGCGGCTAGCAGGTTACCCGCTTCGCAGTGGGAAGTGAACCTTCTCCTCCAGTCATAAATCAAACCCAGCCATCCTCGGGCCTCCTCCCTCATTAGAGATGTTTATTGGAGATTGTGTTTATTCGGCTGTCACGGCGAGAAAACGCACTGACATAATTACCTCTGACCAGAGTCCTCGCCCCGCGCCCAGGGCGAGCCGGGGACCTCCTCTGTCGCCTTCTCCGTCCCCTGTCTTTGAGTAGAGGGCACATGCAGTTGGCTTGTTTATTTTTTCTCTCAGATCCACTCATATAATTTGGATTATTGAATCAGTTACTATTCAAATTTCCCCAAGGTCTGGACGTTTATTTATTTTAGAATTTTAAAGGAAAGCCGAAGGGTACCAAACACCCCTCCGAGGCAGAAGGGGGCAGCGCTGGAGAGACGGAAGGAGAGTCCTTCTCGCTGCGCAAACTTTCCGGCCCGCCCCGCTGCGGCGCGCTGGGGGCCAGACGCCACCGTGCGCTGGAGCCCGGCCGGAGCAGTGGGGAGTTGCCCTGAGGAATGGGTGTCGATATCGGTGGCGATATTTATTGTTTTATTCATCATTCTCTCTGCTCTCGGGAGGAATGAATCTGAGGCTTCAGGGCCCCGGGCTGAGTATTCTTAAAACTCTCGAGGGCCGAACTCGGTGGAGCCAACCCGCAGCTCCTCCCCCGCGCCTCTCGCCCCGGGTCGCTCCTCGGCTTTGGTTTTCCCTGCTAGTCAGGTTTGTAAGTCACTATCTGTGAAACTGAGTTAGGAAGTGATGAAAAGCGTCGAATTGTTTCCTAATTGATAATACTTTTTTTTTTTGGTGACGGGGCTGACCAGTATCTGGGATCTCCGCTTTTGATCCCTCGCTGCCGCCTCTGTTCTCCAATCGCTAATAAAACTCGCATTGAGCCCCTTAGTGCCTTGATTAACAGGCAGATTAACTCTTACCAGGGTGGGGAACAGCTTGTCCCAATCAATGTCATTTTAAAAGCCCGTCAGGATACGCTCAGCTCCGGTTCCCTGGCTGCTCGAGCGAGCCAGCCATGACATTTGCTCCCTCCTCCTTCCCCTGCCGCAAACCCCACAGCAAAGCCCTCAGTTTCCAGCCCGCGTGTTCCCTGCGCCAATCCAGGACAAATTGCAGGACTCGGTCCCTCGCCTTTAAATACAGGCAGCTGTTTAGAGAGGGAATCTCCAGGGAGAAGGGACTGAGGTGGCCTTGGCTTGCTTTTCATTTGAAGCAGAACTCTGGCCTCTGAAGGGCGGAGGTTACAGGGAAAGGAGCGATGGAGAGCCTGGGTAATGAAATGAACAGCAAACTTTCCTAGAAACCGTATTTGTAAAAATCGGAGAGTGCTGTTACTTGCAAGTATGTGCATGTGTCCTGCACATCAGGAGTTTTAAACCTGGTCCCTATCTAGACAACAGCATGTAGGGTCCAGAAAGCAAAGGCTTGAGAGTCCAACCTGCGGGGCAGCAGGGATCTCACAGTTAGGATTTTTTTTTTTTTTCTTTTTTTTTCTGAGTATTGGAGGGGGAGGTGTGAGAAAGAGACGCTTGCCGCCTAATGTGAATGGAAGAGAATCGAACCCAGAGGGTGCTGAGACACACTTGCCATTTGGCAGGAGGCGAGGAAGGGCGAGGGCACCGCGGCTTTCCCCAGCCTAGCGTGGCCACAGCCCGGAGGCGCCACCCGTCCGGCTTCTGCTCTCCTCCGCTTCCCGGCGCTCTGGGCTCGGCGAGGCTGCCGAGTGAGCTGGAAACCCGCAGGTTGCTGGAGAAAAGAGAGAGGCCCGAGGGGAGAAGGCGCCCCTGGCTGGGCGGCAGGATGGTCGCCTTTGCGTTTGGTGCTCGTTGGACCCGTTTCGTCAGCTCCACGAGGCTGGGAACCCACTTTCCCAGGGCCTGCAGAGAGAGGGAGAGCCGTTTCAGGCTCTGCAAAGTGACGCAGGTGTTGGCGGAGACTTTCCTCCTCCAAAGAAAAGCTCTCCTCCGCCCTGACCAGCACGCCAGCCCCGCTCCTCTGCTAGGCGGTGGAAAGCTGCAGTTCAGAGGTGTCACAGCACCGGGTGGGAGACTCTTGGTTCCGAAGCCGCGAAGCAAGCGAACATTCTTCACGAGCCGGGCATGGCTTTGCCTCGCCAGAGGCCGCCCTCCGGGCGGGAAACCTGAAGATCGGGCAGGGGGCGAATGCCAGGGACCGCTAGGGGTGAGATGCTGCCCGACCTCACACTTACGCACCAATACTGACCAGAGACTCCGGGCACTCAGGCGAGCGGCGATCCCCCAGCGCGACTCCTTCGGCAAAGACAGCCTCCCCCTACCGGGTGGGATGACCCGGGCAGCCCCTGCGGGAACAGGCCAGAGAAAAGTCCTCCTCCGACGCCAAAGGGTGAGGGCGGGGGCGGGGGGGGGGGGTACCTAGGGAGAGGCGGGAAAAGGCGTGAAAGAAATGGAAGACGCGACTCCCTCCCTCCAACCCCGACTCGGAGGGCAGCAAGTGGGCCTCGGTCTTGTTGGAAGCCGCAATTAAAATGGCGACCTAGGAATTGTCTCAATTTTGCGCACACCTCTGGCCCTGGCGCGCTGCAGCTCCGTCCCAGTCCCCCAACCTGCCCTGTCGCACCGCCCCCCCCCCCCTGCCCCCGGAACAGGTACTTGGCAGAGGGCGCCAGGCGGCCCGAGGCAGAACGGCACCCCCGCCCTCCTTGAGGCTAGCCCAGAGAGGACAGGAACTCAAGCTCTCCTCCCTGCTCTCCTCCAACTTTGAAAACTCTGCCTCTCGGCGGGCTGAGCTCCCCCCTCCCCCAAATATTGACACATTGGAAGCTGCCAAGTCCTTTTTTTGTTTCTTGTTTGTGCAGAGTGGTTTCCAAGAGTCCTTCTTTGAGCCCCCACCTTCACCCAATGACGTCAGTGGCATTCACTCCCGCTCCTCGCCTCTTATGATTTTTTGTTGTTGTTTAAAACTTTTCTCCGAGGTGAGGTGGGGGTGGGAGGGTGGGAGAAGGAGCTGATTCAAAGAGCTAGTGCCCAGGGGGGAAATAGCAACAAGATTACGGCTGCTTCTCTCTAAGGCAAAGCTTAAGAAGGTGCTAATCCACTCGGTCGCTAATTGAGAGGTTGTAAAAATGATATTCGCCTCCAATTCGGACAGTCTCTGGGATTCCTCCCCCCGCCGCTTATGCTCAGTGGACTTGAGTTGGAGCTTCTTTACTGATTGTTACGAAGTAAAGGGAGAGAGAGAAAGAATGCAGGCTTTCGCTGGTCTGGGATGGGCCCGCTGCCTCGCTGCCTGGGATCCTCTGAAAGTCGCGGTCCTACGAAGTCTCGCACAGAAGGCGCCGACCGGGGCGCCCATCGCCACCTCCTTAGCTTCTTTGGTCTGGGTTTTCTCCCGGCGCTGTATGGCTCCTGGGCCGCTGGAAGGGCCTTCCGCAGGCCGAGATGGTGATCGGGTTGTGCTACCCCAACTCTGGCCCAGATAGGGGAGACCTCCCAGCTCACCCCGCAGCTCTGTCCGGCCTCTCCGCTGCGGCGTTAGTGGGCGCAGGTAGGGGAGGAGAACGTGAGACCCACGTTAGGCCCGGAGCCGGCCCAAGGCAGCCTGCAGCCTCCTCGGGGTCCCAGCTCCCGGGGCAGCCGTCGCGCCGCGTGTCAGCGGTGAGTTCAGGTGGCAGAGACTTTATTGATGAGCTCTGACTTTTTGCACTTTGCACAAGTGGAGAGGAATCAAGTCTACCTGGCGACGGCTTCCTCTCAGCCTCCCTACCTCAGCTCTTCCAAACCCATCCTCTTTTGTCGGATCCTGGGGTGTGTGCCCCATCCCAAACCTTCCCCTTTCCTTGCCTCGCGACCTGCAAGTTCCAAGAGAGCCCGGAATTTTGCCGGAAGGGGCAGCCGCTCCCTCCCCTGTCACCTTAACTGCGGGCACCGAGGGGAGCCTTTGGAGTGTACTGAGGTGTGTCCTAATCGTCCGGCATTCAACAAATGGACTTGTGGTGTGTGGTCAGAAGAGAAAAGCCATTTACTTACTTTCCTCCCCGGTTTTCTGGCAACAGCTGAAGGGGAATTGCCTCCGTGAACTGAGCAGACCCAGGAGAGGGAACCGTCGTGCGAAAGACTCACACACCACAGAAGATAACTGGTGGCACACACGGATACACGCTGACACGCCGACATCGCGAGCGAGCGAGAACGCGCGCGCGCGCGCAACACACACACACACACACACACACACACACACACACTCTCCCAGCATTGGTCGTTTCCCTCCACTCCAGGCCTCCACCCCCCTTCTTATCTCCCCCTTGCGTCCCCTCCTCTCGGGCGCCTGGAAAAACAGCCGCACTTAGTCAACAAATGGCACGTGGGAGAAGTTGGTGAGTGTTTGGTGAGGACTCTTCAGGCTTTTCACAAGAACCCTCTGTACACAAAGTAAGTGGCGTGTTTGCTCGGGCCTCTCCAGCCCCGGCTGTGCCTCCGCTCCACTGCGCACCGCGCCTTCCGAAAGGAGAACGAACAGAAGAAAGGGCCGGGGGAGCGAGGGTCGGGGAATGGGCAGGCCCCAAAGGCCTGCACTGGGAAGGCCGCCTGGCCTCGCCAAGTGCCCGGCCGGGCGGCCTCCTCTCGGCCTAAGCTTCGCCTTAGCCTCAGCGCGAGTGTGGCTGCCGGGACCCAGTGACGCTAACGCCCTTTTCTCGTCGTCTTCTCCTCGGCCAGGTGGGCTAGGGCGCGGCCACTGCGGTGTTCGCGTCCCAGGGTCCAGACGGAGATGGGGTAGGGACGCGGGGGGGGGGGGGGGGAGGCGGGCGGAGACGGGGCAGCAGGCCACGCTGCACGGGAGTTGGCAAGAAAGAGAAGCGCGCAGCTACAGAAACTTGCTCCATCCATGAGCTGTGAGTCCCGCGCCCAGCTGAAGTGTGTGGGAGGCGCGACCCCCAGCTCAGCGGCCTTCACTCCACCTCTCAAGTTCGGGGCCACAGAGCTGGCCGCGCTGATTCCCGGAGTGCTCTGAGCCTTAGAGATGTCGCGAGCGCCAGCCCCAGAGCCCAGGCGCGGGGGGCCCAGCGCCGGGGAGAGCAGCGGGGACACACCGGCGGGGCCGAAAACAAGTGTATTCATATTCAAACAAACGGACCAATTGCACCAGGCGGGGAGAGGGAGCATCCAATCGGCTGGCGCGAGGCCCCGGCGCTGCTTTGCATAAAGCAATATTTTGTGTGGGAGCGATCCGTGCATTTGCATGTTGCGGAGTGATTAGTGGGTTTGAAAAGCGAACCGTGGCTCGGCCTCATTTCCCGCTCTGGTTCAGGCGCAGGAGGAAGTGTTTTGCTGGAGGATGATGACAGAGGTCAGGCTTCGCTAATGGGCCAGTGAGGAGCGGTGGAGGCGAGGCCGGGCGCCCGGCACACACACATTAACACACTTGAGCCATCACCAATCAGCATAGGTGTGCTGGCTGCAGCCACTTCCCTCACCCACACTCTTTATCTCTCACTCTCCAGCCGCTGACAGCCCATTTTATTGTCAATCTCTGTCTCCTTCCCAG
Seq C2 exon
GGATCTGAGATTTGCTCTCACACACCAAACCAGCAGCGTCCGTGGAGAAAACTCTCGCCAGCAACTCCTTTAAAACACCGTCATTTCAAACCGTTGTGGTCTTTAAGCAACGACAACAGAAAAAAAAAAATCAAACAAAACTCTTGACAGGAGCTTTGACTAGAGAGGATGCCTCAGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004561:ENSBTAT00000005994:1
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
Rat
(rn6)
No conservation detected
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