DreINT0110556 @ danRer10
Intron Retention
Gene
ENSDARG00000010192 | pax3a
Description
paired box 3a [Source:ZFIN;Acc:ZDB-GENE-980526-52]
Coordinates
chr2:47577400-47578701:-
Coord C1 exon
chr2:47578340-47578701
Coord A exon
chr2:47577636-47578339
Coord C2 exon
chr2:47577400-47577635
Length
704 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGG
5' ss Score
9.16
3' ss Seq
CTTTTCCTCTTTTGTTGCAGTCT
3' ss Score
10.28
Exon sequences
Seq C1 exon
AATCCACAACAACAAGTGTGTCAACAACAACGGAACCAAGCTTTGAGAGTGTTATCTTCCAAACCGCTTTGAGATAAACCACGATTGAAAACCTGGATATCCGTGAATAACTTCAGAGGACTGGAAGCGACGGTTTGACTTCTGAAGTTGACTTTTTGTTTTCGCCTGAAGACCTCAATACTTGGGCAGTCCACTGACACTTGACGACTAGCGCTTTCTCTTTGGATAACTTTTTCTATCAAGTGCTTCGTGCATCCTTTTTTCGTGCAGAGGAGATATGACCGCATTAGCGGGGGGCATTTCCAGGATGATGCGCCCCACGCCACCCCAAAACTACCCGAGAGGTGGCTATTCCTTGGAGG
Seq A exon
GTAAGGTGTTAGCTTGCTATAGCACAGCCTACTAGATACATCCACAAAGTTGTTTTTTAAAGACCTATTTAATCTTATGGATATTTTATTGAAATGACATTACTGAAAATGACATTAATAAAATATTTAATTGTTTATAATTTATTTAGCATTTGTATATAATTAGTAAGTATATTTTAGTCAGTAGGCTAACACTGAAAAACTACATTTAGCTAATTATTTTGAAGCGTCAAAATGACTGAATTAGTTTTTTTATTACATTGAAAGAAAATCAAGCTGAATCCAGAGAAAACTGCATAATGCAGTCGAAGTGAACCAGTTTTAGTTTAGATTTAGGAAGTCAATATTAGACGTACATTTTGTACAAAGCATTTATTATAAAATATCTTATTTCTAAAAACATTGTCAGTATTGACGTACTTAAGAAATATATTTTAAAATTAAAATATGTAGTAAGAAGTAATGACTTAGATTGCTATTATCATTATTAACCATTGACATTTTACAAGCAGACTAGCTTTTTATTATGGTTAAGTAATATTTCTGAAATACATAACTAATTGTTAATATCAATAGAAGTCGCTTTATTACTGTATACTATTTATATCAGGTCAGTCAAAGGCTGTCAAGTTTTTTTTACGATTATGCTTTCACGTTTAGCTTGCATACAATGTCATTCGCTGACTTTTCCTCTTTTGTTGCAG
Seq C2 exon
TCTCTACGCCTTTAGGTCAGGGCCGCGTGAACCAGCTCGGCGGAGTCTTCATAAACGGGCGCCCTTTGCCCAATCACATCCGCCACAAGATAGTAGAGATGGCCCATCACGGCATACGACCGTGCGTCATCTCCCGGCAGCTGCGAGTCTCACACGGATGCGTGTCCAAAATTTTATGCAGGTACCAGGAGACCGGTTCCATTCGGCCCGGGGCTATTGGTGGCAGCAAACCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000010192:ENSDART00000038828:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (disopred):
C1=0.857 A=NA C2=0.215
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0029213=PAX=PU(57.9=92.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTTCAGAGGACTGGAAGCGA
R:
TCTTGTGGCGGATGTGATTGG
Band lengths:
343-1047
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]