BtaINT0107905 @ bosTau6
Intron Retention
Gene
ENSBTAG00000009950 | PAX3
Description
paired box 3 [Source:HGNC Symbol;Acc:HGNC:8617]
Coordinates
chr2:111227732-111229639:-
Coord C1 exon
chr2:111229275-111229639
Coord A exon
chr2:111227968-111229274
Coord C2 exon
chr2:111227732-111227967
Length
1307 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
TTCTTGACTTCTGTTCCCAGTGT
3' ss Score
7.99
Exon sequences
Seq C1 exon
GCCGCGGGGCCGCCGGCCCAGACTCGCACCAAACTTTTCCGCCCTGGGCTCGGGATCCTGGACTCCGGGGCCTCCCTGCCCACCCCCTTCCCCCGGTTCCACCTCGAGCCTCTCTTTGGACTAAGAGCGAGCAGCTCCCCTTTCCCGGGTCCCTCCTTTCTCTCCAGCCTTTTTGGGGAGGGACTCTCCACGCTCGGGGGAGCTGCCTGGGGTCACCAGCGCCTGTATCATCTATTTCGCCTTCACCTGGATATAATTTCCAAGCGAAGCTGCCCCCAGGATGACCACACTGGCCGGAGCTGTGCCCAGGATGATGCGGCCGGGCCCGGGACAGAACTACCCGCGCAGCGGGTTCCCGCTGGAAG
Seq A exon
GTAAGAAAGGGCCTCAGCGCCGCCCAGATCGTGGATCCGCGGCCAGGCTGCTCCACCCAGCCGGGGTCTCCACGGGCTCCTTCGGCGCGTCCAGGAGCGCATTCCCGGGGTACCCCCATATCAGGAGGGAACAGTTGGGCGAGGTCCCCTCTCGAGTTTCTCTGGGTAAACGAAGCGTCCTTTTTCTCTGTAACTCCTGCCGGAGCTTGGTGGCCAGGCCTGCTCCTGGGCGGGTATGCTTTCCCCTGTTGTTTTGGAAATGCCTTGGTGGGGCAGGGATCAACCGGCTTTTGAGCACCAGCAAGCAACTTCTCAGCACTTTGTGCCCCCGAAGGCATCTCAAAACTACCCCGGCTGTTCCTGTATTCGCTAAACTCTTGTTAATTCTGGAAGGATTTTCTTAGGGGGTGCAAAGTTGTGGTGGCGCATGCCCGTGCAGAATCGTGCTGGGGAATTTTTAGTATTTATTGATTCCTTAATTAGGGCCCCATTTATCTCCAGCTTCATCTGGAAGTTTCCACAATCCATTTGGGGGACTGTCTTTCAGTTAGAGTGAAGGTTCTGGACTCCAGGGAGGCAGGAGACCTTGCAAATCATTTTTCGGATTTTCTAGACAGTTTGCCAGGTTCGGTCGCCCGAGCCGGGTTGCTGACCCTGCCGGTGCCTGGGCTTGGCCCTCAGTCTGAAATAGTATGTATTATTAATAATAATCAGAGCACCAGCGGAGGCGAGGGGCCTGTGAGCAGACTGGACTGTTGTCTCTGGCCCGAGGTGTAACAGGTGACTCACGATGACACCTGCGGCTTGCTTTCAGTACCCTCTTTGACCTTTGGCTGCAGTACTCCTAGCCCAAAACCCAAAGGGTTATCAACTCTTCCAAGTTTCTTAGAAAGAAAGCCCCCCAGTTAGACAGGGTTTAATGCCAGCCGCAGAAGGCCTGGGTGAACTTCTCTCTGCAGGGAGGCTGTTCTTTCACCAGCCTCTAGGTCTCCCCACCCCACCCCTTGCCCCTGCAAATTGTCCCCTTTCTTGGGTCCAAAGGGAAGACAGGTTCACTATAGCGAGTTTATTTTGCCCTGGTTGCTCCTTTCACACAAGATTATGTGCCCTTGAATTGCTTAATAGTTTGAACAAGTGTGGTTAAAGCAGGGTCTCAGGTTGGGAGCCCGAATGGAGCAATTTCAGTGCTAAGGCTGTAACATACCGATTGGCCAGAAGAGTGTGAAATTGGGGTTCATCTTTTGGGCTGCTCTCCTCTCTCCCCAAATGATCTTCCATTTGTCTCTCTTCTTGACTTCTGTTCCCAG
Seq C2 exon
TGTCCACTCCCCTCGGCCAGGGCCGGGTCAACCAGCTTGGAGGTGTTTTTATCAACGGCAGGCCACTACCCAACCACATCCGCCACAAGATCGTGGAGATGGCCCACCATGGCATCCGGCCCTGCGTCATCTCCCGCCAGCTGCGTGTGTCCCATGGCTGCGTCTCTAAGATCCTTTGCAGGTATCAGGAGACTGGCTCCATCCGCCCTGGTGCCATTGGTGGCAGCAAGCCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000009950:ENSBTAT00000013131:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (disopred):
C1=0.897 A=NA C2=0.228
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0029213=PAX=PU(57.9=92.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTCGAGCCTCTCTTTGGACT
R:
GATCTTGTGGCGGATGTGGTT
Band lengths:
356-1663
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]