DreINT0110598 @ danRer10
Intron Retention
Gene
ENSDARG00000103379 | pax6a
Description
paired box 6a [Source:ZFIN;Acc:ZDB-GENE-990415-200]
Coordinates
chr25:14935653-14937625:-
Coord C1 exon
chr25:14937543-14937625
Coord A exon
chr25:14935804-14937542
Coord C2 exon
chr25:14935653-14935803
Length
1739 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
ACAAAAATATGTGCATCCAGGTC
3' ss Score
5.7
Exon sequences
Seq C1 exon
AGTTTGAAAGAACGCACTACCCTGACGTTTTTGCACGAGAAAGACTTGCTGCAAAAATAGATTTACCAGAAGCAAGAATACAG
Seq A exon
GTGAGTGAAAACAGGACAAACTAATGTACAAAAACAGGATGAATAGGCATCGTCAAATAATGCTTGTTTTTACAAGATTTTTGGCATGTAAACTATTGTTATGAAAACAACATTTTAGTTTTTAATAAATCAAGTAAATCTCTCCTTCAGAAGAAACAACAAAAATACTGATGACTCATCATTTCCATCCAGTCAGACGCTCTGTAGAATGAGAATGTCCCACACACTAAATCGATTTGTATCTGTCTAGTATCGCTATCACTATCAAGTATCTGTGATCTAAATGAATACATTTTACTTTATAAAATAAAACCAAAAAAAAAAACAAATTAGCATTCAAAGTTCCTGTTTCAACAGGAAATAAACCCCCATGTACAGTTGAAGTAAGAATTATTAGCTCCCCTTTGATTTTTTTCTTTTTTAAATATTTGCCAAATTATGATTTGAATTACTAGCCCCCCTGAATTATTAGCCAAAGTTTAATTGGCAGAGACCCCCCCTCCCACACCCATTTAATTTTTCCTCAATTCCTGTTTAACAGAGAGAAGATTTTTTTCAACACATTTCTAAACATAATAGTTTCAATAACTCATCTCTAATAACTGACTTATTTTATCTTTGCCATGATGACAGTAAATAATATTTTACTAGATATTTTTAAGACACTTCTATACAGCTTAAAGTGACATTTAAAGGCTTAACTAGGTTAATTAGGTTAACTAGGCAGGTTAGGGTAATTAGGCAAGTTATTGGATAACGATTGTTCTGTAGACTATCGAAAAAAAATTAGCTTAAAGGGGCTAATAATTTTGACCTTAAAATGTTTTTTTAAAAATGTAAAACTGCTTTTATTCTAGCCAAAATAAAACAAATAAGACTTTTTCCAGAAGAAAAAAAAATATCAGACATACTGTGAAAATTTCCTTGCTCTGTTAAACATCATTTGAGAAATATTTAAAAAAGAAAAAAAATTCAAAGTGGGGCTAATAATTCTGATGTCAAATGTACATCAGTTTACCATCAAATCCTCTGACCAATTAAATGCTCTCTAGTATCTAAGATGTCCCACCCCCTTAAAGATGCTATTACTATATGTGCTTGAGCTTGACCACTCTCACAGACAGAGCTGTTACAAAAAGGGGAGGAGTTACTATTTGCTCCACCCTGTCTTCATGTTTCAGTTGAGATTAGGTCAAACATCGAATAAAACTGCACATTTCAAAGCGCTTTAGGGACCTTTAAGCTCTATACTACTCTACAGGGTCTGTATTTCTATTACCTGCTCTATTTAATTATTGATAACCAATTAAACATAAATATGTACATTAAAATGGTTTAAAGAATGTTTATTTAATTGTTCATATTTCATAATATAAATATGTTATATTTCATGTTTCTGTAACACATTTATGCATTTGAGAAATTAAATTGCATAAAAAATCTATAAAACATTTGAAATTGAAAATAATGATATAGAAAAGTACCATATTTTCAGTAAAATAAAAATAATTTTATAAGTCTAAACCTTTCTACAATTAAGTAATTATTCTTGTTATTTTAAAATGTTATTTCATCTGTCAAAATTCAATATTTTTGTATAAAATATGTAGAGAGGTGCTCTTATTCTGCATAATATGGAAATCCTTATGGAAATCTATATGTATTTGAAAATTAAATCTGCAGCAAAATTGTCTATATATATAGATTCACACCAACTAAACAAAAATATGTGCATCCAG
Seq C2 exon
GTCTGGTTCTCAAACAGAAGAGCGAAATGGAGGAGGGAGGAAAAGTTAAGAAATCAAAGAAGACAAGCCAGTAATTCCTCAAGTCACATACCCATCAGCAGCAGCTTCAGCACAAGTGTCTATCAACCAATCCCTCAGCCCACAACGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000103379:ENSDART00000164384:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=0.697 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=FE(47.4=100)
A:
NA
C2:
PF0004624=Homeobox=PD(19.3=21.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTTTGAAAGAACGCACTACCCT
R:
CGTTGTGGGCTGAGGGATTG
Band lengths:
230-1969
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]