GgaINT0096706 @ galGal3
Intron Retention
Gene
ENSGALG00000012799 | RREB1
Description
NA
Coordinates
chr2:65890464-65892050:-
Coord C1 exon
chr2:65891961-65892050
Coord A exon
chr2:65890628-65891960
Coord C2 exon
chr2:65890464-65890627
Length
1333 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAT
5' ss Score
7.79
3' ss Seq
CAAATCATTGCTTTCTCTAGCAT
3' ss Score
5
Exon sequences
Seq C1 exon
GAAACAAAAGAAGAGAAGTCTTCCTATACCTGTCCTCTGTGTGAAAAGATTTGCACTACACAGCACCAGCTAACTATGCACATTCGTCAG
Seq A exon
GTACATAAAGTACAAGCTCTAGATTCCCTATTTTATTAAGAGCGTCTCCATTGCCAGTATGCATTTTGTAGTGGTGAATAACAGTTCCACGTGCAAATCAGAAATGCTTGGATATAACCTTTCATAATTGTTTTGCTTTTATTTAAGCTCTCCCCTGGTATTAATAATAAAAAAAAAATCATCACCAACCAGGAGGTGGATAATTCTCCTCTCTTTCTCTCCTTTCCTTCCCCTCCCTGCTCCCCCAGTGGCTCAAACAAGGATGTGCGTCCTGTTCTGCACAGCTTAAGGTATCCTAAGGATCCGGAAAACCACTTCCATCATGAGGCATAAGTCCTGTTTTGTTATCCTGTTTGAATACAGTTCCCTTTACTGTTCATGCAAATAAGAAGCAGGAAGAAACAACTTTAAAATCATCTCGGTGTTAAAGAGCCTCTCTGTCCTTTGCAGGGTACGGCGATTTTGGGAGGCAGAATTTAAAATACCCATTTCAAATGTATGATGCTCTTCATTTTTGTCAGATAGAGGCCTCATCTTGCTCCTCTTGAAATATGTATATGTGTGCTACGAGGAGCTTTGGCTTTTTTTGTGTCAGAAAGTTCTCCTTGGGATCATAAAGTTGTGGTTCACCTCTGTGAGTCCACTGGATACTCATTACTTCAGTTTTCCCTTCTGTACTGTAACTGTTACTTAATTTTTTTCCTTGCTCTCCATTCGATTTTGTTTTGGTTTTTTGTTTTTTGGGTTTTTTTTTTTTGGTATGTGAAGAAATGTTCACTTCTCTAAATGCAAGCAAGAAAGAGTGCTACATATAACACAGTAGCTGATAGCCATGTTTTCCCTGTAAAACAGAAACATTTGCTTCTGTTTTCTTACTACACGGTCACTTTGAAATTAATATCTTTAAAGAGTATTTTTAAGTGTCTTCTGAAGTCAAGTTTATAATTACATTCTCTTTCCTTTTCCCCCCGTACCATTTACCCTACCCCAAACTGCTACATAGCTTAACATATTCCAGGGTACCTCTTGTTGGATTGGTTGTTGCTGGATCCCTTTCTATCCTCTTCTGCTGCACACGCAGTGAAAATGCAGCATGTGGTGGGCATTCCAGGCTGCACAAAGCAGCTGCATTAAGGAGTTAAAAGCAAAGGGAGGGGGTGGAGTTAAGGGGGAGGGCTACGGAAAAGAATTGGATATGGGGCACACCTTAATATAAGGTATTGTGTCAAGTGACTTTCTGAAGCTGCTTTTAAAATGTTTACAGTTCTCTCTGATATTTTACTCACGCTTCGTAAGAGTCATTCAGTGAAAAACAAATCATTGCTTTCTCTAG
Seq C2 exon
CATAACACTGACACTGGAGGGACAGACCATTCCTGCAGCATCTGTGGAAAGTCTCTGAGCTCAGCGAGCTCCCTTGATCGCCACATGCTGGTGCACTCAGGTGAAAGGCCTTATAAATGTTCAGTGTGTGGACAGTCCTTCACCACCAATGGAAACATGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012799:ENSGALT00000037239:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.400 A=NA C2=0.425
Domain overlap (PFAM):
C1:
PF0009621=zf-C2H2=PU(91.3=70.0)
A:
NA
C2:
PF0009621=zf-C2H2=PD(0.1=0.0),PF134651=zf-H2C2_2=WD(100=47.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGTCTTCCTATACCTGTCCTCTGT
R:
TGTGCATGTTTCCATTGGTGGT
Band lengths:
238-1571
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]