DreINT0110563 @ danRer10
Intron Retention
Gene
ENSDARG00000028348 | pax3b
Description
paired box 3b [Source:ZFIN;Acc:ZDB-GENE-080917-53]
Coordinates
chr15:42248212-42250798:-
Coord C1 exon
chr15:42250454-42250798
Coord A exon
chr15:42248448-42250453
Coord C2 exon
chr15:42248212-42248447
Length
2006 bp
Sequences
Splice sites
5' ss Seq
AGGGTAGGC
5' ss Score
7.26
3' ss Seq
CTGGATTTGCTTCGATGCAGTGT
3' ss Score
4.58
Exon sequences
Seq C1 exon
CTCGAGTTCAACCTAAACGCCTTTTAATAACAAAAAACGCGGCGATTATAATTCTCCTCACATAATGAGAACAACGAGCAGGAACCACACAAGGGGAGATTCTACATCTGATTACTAACTTTTCATCCTAGACTACATTTCTTTTCCTCGAGGGATAGTTACAAGATCATCGGAAATTAATTATTTGTTTTTGTTTATTGATCGTGGAATATTACATGCATTTTAAGTCCTAAGATTTTGGTCAACGCTTTCCCGGAGCAATGACCGCTTTCCCAGGGACCATTCCCAGGATGATGCGCCCATCACTCTCTCCAAACTATCCCCGCAGTGGATTCCCCATGGAGG
Seq A exon
GTAGGCTATGTTACTTTTTAAAGCGTAAAAACATCGTTGTATTTATTAGTAGCAATTTAGACTAATACTTAATCATTTTTTAAAAACTTAACTGTGTTATTTAATACTTTCTAAGGTATTTTTAATCGTAATTAATGGTAATTTAGGCCAAATGCAGACTTTTTTTTAACTGTTAGCCTATATTATTTTATTATGTAAGTTTTTTTAAGTTATCTTTTGCTAACATAAAAATAAATCATGCATTGCAGTCAACATTATGTTGATTTTTATTATAAAAATATGAAATAAATGTTCTTTAGGTGTTCTTTGTATAACTTTTAACTTAAGTTTTAAATGTGTTCGTGTTAAATTATTACATTACGTTCTTTACATTACTGTATTTGTTTTGGTTTTCCAAAAATAATAAAAAGATTATTTAAAAACTAATGGTCGGATTATGATTGTTACGTGATATAACTTATCAACAACAACAACAACAACAACAACAACAACAACAACAACAACAGGTTGATTTAACTTTCCTTCCCAATATTCACATAAATTGTACTCGGTTTTTTATATGCTAACTTCCGAAGTTGGTTGATTAAATTAAAATATGAATAAATATAGGAGATTTGACCTTTATAACCACTTCCATTTAAAGCAAAGATCGCATCATGATTTTTTGTTGTTTTATTTATTTTTAGAGTTTTTTTAGCCCTAGATATAAAGAAATAAACTCATATGGAGCCTATAAAAAACTTAAAGAATCGTCTTACCTCTTCATTGAAAGCACACTTCAGAGATACATCTGCTTTTCAACAACAACAAAAAAAGTTTTTCATGCATTTAACTCTCCTTCCCAATAATTCCCAAGATTTCCATTCAGTTATAGGCTATTTAGTTTAATTTCCAAAGCCATCTGATTACATTTAATTATGTATAAAAGTAGGGGATTCTAACATTGCAACCACTTTTTAATAGATCTAAGGTAAATATCTATGACCACTTTCATTTAAAGCAAATACGTTTTTCTGAAGCTGGTTTATTTTTAGAATTTTTAGCGCTACATTTAGGGAAATAACTTCAAAGGAAGCCTAAAGACTAAAATAATGATTATCTCTTCACTTCTTAGATGCATCTGCAATAACAAAAGGTTGGTTTTCATGCATTTCTACCCAGTGGCATTTCGCCTATATTATAATTGCCATAGCTGACTGATTGCATTTAAATATACGTAAATAGGAGATTCAAACTTTACAATCACTTTCATTTAAAGCAAATGGACTTTTTTTGTTTTATTTTTTATATAATCTTTAGCGCTACATTTATGAAAATAACTTAGGGAGCCTAAAGAATAATAAAAAAACCCTCTTTAATACAAAGCACGATTCAAATATGCATCTGCAATACCGAAAGGTTGGTTTCCATGCATTTCTACCCAGTTCTAGAGTATTTTCTATTTCAGTATTCATAGCTTATTGATTACATTTCAATATGAATAAATATTGGACATTCAAACTACACAACCACTATCCTTTAAAGCAAATGGACATGTTCCTGTTAATAGCTGTTATTTAATAATAATTATTAATCGTTGTGTTTTTGTTAATTGATGTTTTTTATTCTTTTAGCGCTACACATAGGGAAATAACTTATAAGGAGCCTTAAGAGTAAAATAATTTACACCTCTTCATTAAAAGCACACTTCAAAGATAGATTTCTACGCAGTTCTATCCATTTTATATTAATTTCCTTAGCTGATTGATTACATGTAAGTAGTACAATAGTAAGTTGAGAAGATTTTAACTTTAGAACCACTTTCATTTGTGATATACACAATTTGCACTACATGTTCATATGGAGCCTATAAAGACTAAAATAATTGTCTTACATCTTCATTAAAAGCACACTTCAAAGATGCCTCTGCCATGCATGCACAAATTCTCTTATTTCTTCCATGTTTCTGCAACTTTTCCTTTGATTATTTCACCACCGTCACATCATCTGGATTTGCTTCGATGCAG
Seq C2 exon
TGTCAACTCCGATGGGTCAGGGTCGAGTCAACCAGCTCGGGGGAGTTTTCATCAACGGTCGGCCTCTGCCCAACCACATTCGCCATAAGATAGTAGAGATGGCCCATCACGGAATCCGGCCCTGCGTGATATCCCGCCAGCTCAGAGTCTCTCACGGCTGCGTCTCCAAAATCCTGTGCCGGTATCAGGAGACTGGATCCATCCGGCCTGGAGCCATCGGCGGGACTAAATCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000028348:ENSDART00000015843:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (disopred):
C1=0.862 A=NA C2=0.241
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0029213=PAX=PU(58.4=92.4)
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]