GgaINT0031231 @ galGal4
Intron Retention
Gene
ENSGALG00000005246 | PAX3
Description
paired box 3 [Source:HGNC Symbol;Acc:HGNC:8617]
Coordinates
chr9:7357518-7361752:-
Coord C1 exon
chr9:7361506-7361752
Coord A exon
chr9:7360981-7361505
Coord C2 exon
chr9:7357518-7360980
Length
525 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGT
5' ss Score
8.4
3' ss Seq
TCTTTTGTTTTTTTTTGCAGGTG
3' ss Score
13.04
Exon sequences
Seq C1 exon
GTAATGGGACTCTTGACTAACCATGGTGGTGTGCCTCACCAGCCCCAAACTGATTATGCCCTGTCCCCTTTGACTGGAGGTCTGGAGCCCACCACCACTGTCTCAGCCAGCTGCAGTCAGCGGCTAGATCACATGAAGAGTTTAGACAGCCTGCCTACATCACAGTCCTACTGCCCACCGACCTATAGCACCACCGGCTACAGCATGGACCCTGTCACAGGCTACCAGTATGGACAGTATGGACAAA
Seq A exon
GTGAGTGCTGTGACACAATAATCATTTATCAATTGTATGTTTTTTTTTTTTTTTTTTTTGTCTGTAACAAAGAAAATTACAGGAATTAGACCCTAATGGCTGACTGCTACTACTCTCCAAAATCGAGTGGAGTGCACTGGTGAGATAGCTGATTGTTTGAGCAAGATTTCTGCTGCATAATTATTTTCTTAAGTGATGTCAACAACATCTTGATGTTATTAATTGTTGAGACATGAAACCTGATTGCCATTAGGTAAAACATAAGGGTTGTCCAAATCGAAATAACCACTGGCATTCCATTATTAGAAACACATGTTCTTAATGAGGTCAGCTCAAGAATCATTACAGTATATAATCCCAGATACACAGAGTTTTGTCAAACTTGTCCCAGGAATAAAAATATTAGTCCCTTTCCTTTGATATATCAATATTAAATATGACAATGTCAACCTATAGTTGGCGTGGCCCCATGCTGTGAGGTTGTCACAGCATGACTTAAAAAGCTTCTTTTGTTTTTTTTTGCAG
Seq C2 exon
GTGCCTTTCATTATCTGAAGCCAGATATCGCATAAATGAACTGTCCACTTCAAGTTAAAGCTGGTGTTGTTTTCCAGTCTTGCTCCAGAGCTTGGATACCAGGGATCTTCTCAACACACTGCAGTCTAAACTGGGGCAATCCCAATGAGAGAAGCAGGCTTGTTCTGTACTCTCCAGTCATAGCTTTTAGTAGACTTTTGAAGACTGAACAAAGCTATACAGAAGACAAAGGCCAAAAGCAATAATGAATAAATAAATGCGACATGGTTCATTATGAGTGGGTATAAAAAACAGAGCAGAATTTAATATTGCTGCCTGGCAAAACATTCCGTTTTTTTTTTTTTTGTTGTTGTTGTTGTTGTTGAAATTAATGTGCATTGATTGGGACAAATGGAACATTTGGAAATTTAGCAGTTGAGCTCTGCATACTCTGACTCATCTGGCGTCCAGTGCTGACTTTAGTCTAACGTTAAAGCTGCCCAGTTTCTGAAGCATGCGCAGCAGAACCTCTTTCGTTACACACTGGAAATTGTCATCAAGAGGAAATGTCACAGCCCATAGGAAGCTAGGATAAATGCAAAAGACTTCCAGAGCAACTTACTGGTTATCTTACCATGCTTCTGTAATCACGTTGTCAATAAATGTCACTTACAAGTTTTGCTTTACCAAGAGACAAAATCTCATGTAACATGAACAATACGTTTTATCTTTTCATGTGGAGTTTTCCTGGTCCATTGTACCTTTTTGAACAAACATGGAGGAAAAAAATCAACATGACTGATTTTTTTTCACAACTGCCTAGCAATGTGTGCAATACTGTGTACCTCACACAAACTTTGGAATCATCCAAAGTCATATAGATAGAATCAGAACTATATTTTTGCAGGTACTTTTATTTTTGCAGTGCATAATTTCTAATGATCAAATGCAGAAATGTTGCAGTGTGCTGGACAGCTAAAATCCAGCTTGCTAATCATGATTTAAAGGTCATTTTCAGGAAACAGTAAGAAAAAATGATTACGTTTACATTTTTTAGTGATGTACAGGACACGAACAGAGATGGACCTGTATATAACACAGTTGTTTAAATTATACAGTGATATCCAACATAGGAAATAATTATAGGAACCAAGGTTTACAAGAAGTTTGCATTGTGACATTTTAGAATGTCAATAAATTTGTGTTTTGTGATGTTGAGAGGAACAGGAAGATGGAAGGCGGTGTTATTTATTTCTCTCTATTCTTTGAACAAGGAGAGAGGCAGAACACAAATACATTCCTTTTAGTGTTAAGGACAATGAAGTAGTGCATTAGACTAGATCCAGTACAGAGGTTAGTTCGCACATTGGTCTTAAGGGAGAGGGGAAAATGAAATCTCTTTGTGTTGCAGCCTCTACCAACAACATGTTGTAAAACAAACAAACAAACAAAACAAAAACAAAAAACAAACGTCTTTCATGTAAAAAGTTCAGTAAATATTTACTATTTATAATGAATAAACAGTTACGAAGCCTTGCAAAGCACTGATGATTTTGTCCTAAAATGTAGTATTGTGCTAAATACATTGATACATTTTAATCTGAATATCATGAAGAAATAAACCATGTTATCTTCAACTCAAGGTGTATTCCTTATCTTAGTGTCTTCTGCACACGTTCTAGAGCAGCAGTAGCCTTGGGCAGCCCCTGTGCACAGGTATTGCTTGTATGCTGCTCAGAGGTCTGGGTTCGTCTTTCTTCAAGCACTGTTTGCACTGTATGTCTTCCCAACAACAAAAGCCTCGTGCATTTACTGTGCATTTGAAGGGCTTAAACTCAGCACAAGTAGGTCAGCTACAATGGTTTCACACAGTGCTAGAGCTCTAATGAGTAGTGGGTTATGGGCAGTTTCTGTACTGATTACTTTTTCATCCTTAAAAGCCTCAGGAATTTGTTAACAGGGTTAAGGAAAAAGCATCTGAAACACGGGGAAAGACCCTTCCAGACAATTGGAATATGTTTCAGTGGCTCACCAGTGTCAGAGGGTTGGTGGGCATTTAATTTGCCCACCCTTTTGTGAGGGAATTAGCCACCTTGAAATTTTCAGCTCTTATGTACTCGTTTAGTTTTTATTTTTATTTCATTGTTTGGGAAACAAAAATAGCTATCTTATCAGTTGGAAAATGAAAGAATGACATTTTTGAGAGGAAGGCACTTAAAAATGCTGAAATATGGGGAGAGGGCATTTCTTTTTCCCCTTCTAGGTTATGTTTCTCTGGTATGCTTTTAATTTCTGTGACAATTAAAACTTCAGGCTCTTATTAATAACAATTTCCTGCTCTAAGCTTCTCATTTTTTCTGATTTTTTGTTTTCCATTGTCTTTCCCTTTCTGAGGGCTTAACAACTGGCATTTGTGCACTGTCCTAGGCTTGCTACAAAGGTCTAATGAGCCTTTTCCCCCTATTTGCAATACATAAGCTGTGAAGTACAGAATAAAAGCTGCTTGCACAGTTAGGAACTAGATGGTGTGACTGCTTCTTCCCCAAAGGGCTGCAGCTTTGTTGCAGGTGGAATGATTCTAACTCCACCTTTGCCACCAGTCTTCTTCCATTCCAGCAGCAGGGGTGGAACAGAGCCGGCATTTCTCCATCCCTGCAGCGCTGCTGAAGAGCTGCTTTCTGGACACAGAGCTCGACAGCAGGCATTTTTGCTGCTTTGATCCTCTGTTTTCAAGGTGTCTCCCAAGATTTTCCTTGCATGAGAGACTAATACAGAGCTGGTGAGCCTGGAAACGAGACAGATGTGGAGAAAATCATCCTGTTCTCTTGCAGACAAGCCATGCAGTCAGGGAGCTGGGATGAGCTCTTGGAAGAAGTGAGGATCTGGGGCAGAGGGACTAAGCAGGTTCCTGATTTATGATGTGTCATAGGAATTGTTGACAGAGCTGTAAGGATTACTTGGGGTACTCTGATCCCTCCTTGTTATCACTGCCAAGGCTGAAGAGCTTCTTGGGAGTCACATGTGTTTCTGGAATACAAATGCTAAGTGCTCCAAAAGTCAAAGGGGCATGAGACTGCCGTGGATATTTCATTTTACATAAATGCCATGGAATAGCTTAGTGATATTATGGTACAGTCCTGATTTTCAATTTATACACTGATTTTAAATCTCCCTTTTATAAAAAACAATCTGTACTCTCTAAAAAAAAACCAAAATCAAACAAACAGAAAAAACAGGGTGATGTTGGTTACTGCTAATGTATAAAGCAAACATTTTTCCTGCATCAGTAACCATGAAAGTTTTCAATGCTTTCTATCCATAAACTCTTCTGACCTTAAAGTCTGTGAAGTGGATTGCTTAAAAGACATGTCTGTATAAAATAAGAAATAAATTTTAGGCAATATCAATGAGACCATCAGGAACCAGGAACAGCTTGAATTCATAATGCTCTTTGTATTGTTCATTGCAGTATTCTTATACTTGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005246:ENSGALT00000008428:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (disopred):
C1=0.952 A=NA C2=0.364
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCTTTGACTGGAGGTCTGGA
R:
AGCCTGCTTCTCTCATTGGGA
Band lengths:
342-867
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]