DreINT0129959 @ danRer10
Intron Retention
Gene
ENSDARG00000057737 | rxraa
Description
retinoid X receptor, alpha a [Source:ZFIN;Acc:ZDB-GENE-070314-2]
Coordinates
chr21:17896007-17898987:+
Coord C1 exon
chr21:17896007-17896136
Coord A exon
chr21:17896137-17898854
Coord C2 exon
chr21:17898855-17898987
Length
2718 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
ATTTTGTCCGTCTCTTTCAGGAT
3' ss Score
12.35
Exon sequences
Seq C1 exon
CCCAACGATCCAGTCACCAACATTTGTCAGGCTGCAGACAAGCAGCTCTTTACTCTGGTGGAGTGGGCGAAGAGGATTCCACACTTTTCTGAGCTCCCGCTTGACGACCAGGTCATTCTACTACGAGCAG
Seq A exon
GTGAGTTTAAGAGCACAAACAGACAGATGCACTCCTATAAGACAGCCTGCTCAGCTAGAAACAGGACCAGTTCATTTATATGTAAAACTCGGAAGCAGGAGTGTTGATATTAAAGTAATGCAGCTATTATTATTATTTAAGGTATTTCAAAACCTAGAAAATGCTAAGTTTCACATTAGGGCTGCACATTATATGGTTTCAGTATCTGTATCAAAGTATGTGTGTCTGAAATAGTCACATCACAGGATATGCATTGTTGAGTTGGGTTTAAAGTTGATCAACAATTTAGAATAGTATAACCATAACAGAGGGAAACTTTATCATTTGTATGCATTTTAAACACATTTCAAGAGCGTTTAAAGCATTTGTGCTCAAAAATATACAACATTTGTAACGTCAATGAAGAATCATTTTGCTGAATTACTTCGATAAATTCTATACAGTTTTATTTTACACTTCATTCAATTTTTGTACTCCCCGGAAACCATTTATTTTTGTTGCTAGATTGTAATTAGTCTTGCTTGCAATCTGTTGAAATTGTATTCATACAATATATATATCGCAAAAAAACTAAATATTGCAATGTCAGATTTTTCCAACATTGTTCAGCTCTAATTCACATGTATATTTGAACTCTATAATGCACAAATCTCCCTATTTAATGTCACTCCGAAATAAATTTATAATTGCAAGAAAATAAAGATTGTCCTTACAAAGAGCTTCTAGGTTCTAAAAGTGTATATGAACAAAATGTAGTTACTGTATGCACTGCAATAAATATTTTGGGCCAAAACCTAAATCAGAAATTGTTGATGCACTTGGCAAAAACCAAAACTGCAAATACTTTGTAATAATTATTTATTATTTTATTAAATATTATAAAGTAATTTTAAAGGACTTTCCATTAAAACTACTTAAATGTGCTAATTTAAAATACAGTTAATATAATAATAACCATTTTTTATTACCTGTAGCATTTTATCGACAGTGAGTCAAGATGTGCCATTTTACCAGCAAATGGGTTGATGGATTGTTGAGCAATTTTGAACTGTGACTGTGGCACACTTGCCAGCTAGTTGACAGTGAACTTTTCACATCCAGTGCGAAAGCCACTTGAGACTATGTAGTGACTAGCGCTGGAGTAAAACCAGCGCACTGAACACTGTAGCATTGCGTAGTGGTGTAGCATAGCCCTTTGTTTGGCTAATTATTATTAATAACTCATTTTCCACTTTCGAACGAAAACAGAAATACAATTTTGGGGCATCCTTACCTAAATTATTTACTTATAAAAACAGATATGTCACAAGTTCTGAGCTTCTGAAGATTTATGTTTTTGCATTTATTTAACTTATTTGCTAATATAACCTTATTTGTTAATCAAATGGTGCGTAATACACACAAACAGTTTTATGGCTTCTTATGGTGCTTTCACACTTGGTTCAGTTGCCTGGACCGTACATAAGTTCGAATGCCCACCAGACCACCTCTTTCAGGCAGACTTGGGTACAGTTCACGGATGCGCACCCGAGTTCAGAAGACAACTTTCACACTAGCTTAACGTACAGAACCTGATGTCTAACAAACTCAGGTGCCGGCCAAAAGTGCTAGTGTGAAAGCACCCTTAATGTTTTGCCTGTGAATACAGTTATCCCTAAAACCCCAGCTCACTTATTGGAAATTTATATGGTTTTGACATATTGTTTGTTTAAGTGATTAACATGACTGCTGTAGACATGGGACAATAATCATTTTCAAGGTATACTGTGGTTCGGAAAAGTCAAGATTTTAAAACCACCAACATTTATTGTTTATTATTATTATTATTATTTATTTTTTTATTTTTATTATTTTTAGTTTTTTTAGGACAACAGTATCTCCATCAGAAAAGGTATCAAAAGATGCCGTTTTAAATTGTAAAGAAATCTTTTTTTAAACTAATGAAGACAGCAGAAGTCAGTGATTGATTTGAATCATTTAGTCTGACATGTTTACTGCTCCAAAATATTTAAAATGTTTCTCAAAATAAAATATATTGTGTTCAAAAGGGAAAAAGTTTTAGTTTTTTTTACCCAGACATTTAAAAAGAACTTATTTTAGAGCAGTAATCACAATATCGTGAAACTGTGATATTTCTATCCAAGCCTATCCTACCGTCAGAATCAAATACCGGCCCATGCCCACACTGGTGTGGGATGAGGATGTGGACTTAAGAATGTAAAATATAGTGTCCATGCATGGTCACTATTATAAGGAGCGTTGTGTCCTTACTAGTTACAGAAACACACTAGAAAAGAAAGTTCTGACACAACAGTTTATATTTACAAGGTCAGATTTATAAGTGAGTTTCTTAGAAGTTGACCAAGTATGACTCAGAAAGAAAGATGCTCTGTAGACCAGCATTTTACAAACAAACAATTTTGCTTTTAATTTCCTGCATGGCTCATTGTATTAGCGAATCGTTCTGATGTTCTCAGAAGAAGCTGAAGAGCATTTGGAGAGGGCCTTCTCGGCGAGCTCTCAGGTTTTCTATAAATAACCACTTTAGTTCTGCTGTCTCACAGATGAAAGCATCTCAGTTTTTCTCAAGCTCAACTCTGGGGAAATGAGGGGTAGTTGCTAGGCAGACTAGTTAAAGGAGCCCTGTCACTCACATGCTTGCTTAATTCCCCCTCACTGTGTGCAATGAGGTATGGTGATTTTGTCCGTCTCTTTCAG
Seq C2 exon
GATGGAATGAGCTCCTCATTGCGTCATTTTCGCACCGATCCATAGCAGTGAAAGATGGAATACTGTTGGCCACAGGATTACATGTGCACCGAAACAGCGCCCACAGTGCCGGAGTAGGAGCCATATTTGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000057737:ENSDART00000080481:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.136 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0010425=Hormone_recep=FE(22.1=100)
A:
NA
C2:
PF0010425=Hormone_recep=FE(22.6=100)
Main Inclusion Isoform:
NA
Other Inclusion 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]