GgaINT0123731 @ galGal4
Intron Retention
Gene
ENSGALG00000008532 | COBRA1
Description
negative elongation factor B [Source:RefSeq peptide;Acc:NP_001006202]
Coordinates
chr17:1897293-1897794:+
Coord C1 exon
chr17:1897293-1897430
Coord A exon
chr17:1897431-1897630
Coord C2 exon
chr17:1897631-1897794
Length
200 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGG
5' ss Score
6.92
3' ss Seq
TTCCCCGTTTGTGTTGGCAGACA
3' ss Score
7.64
Exon sequences
Seq C1 exon
GCGGCGGGAGCGGGCCCGGCGGGGCGGCCGGCTGCCATGTACGCGGGGCTGCAGGAGCTGGGGGTGGCCAACGGCGAGGATCTCAAGGAGACGCTGACCAACTGCACGGAGCCGCTGAAGGCCATCGAGCAGTTCCAG
Seq A exon
GTGGGGCGGGTCGCCATGGAGACGGCGGGGCGAGAAGGCCGCGGGTGGCGCCTGTGCTTTGTTTTGGGGTGAGAAGGCCGCGGGTGGCGTCTGTGCTTTGCTCTGTGCTCTTTCGGCCCCCCTTTTTTTTTACTACTGTTTCTTTTAGCAGCCCCTACTGTCACTTGCTCACCGCCCCTGTTCCCCGTTTGTGTTGGCAG
Seq C2 exon
ACAGAAAATGGGGTCCTGCTGCCCTCGCTGCAGTCGGCCCTGCCCTTCCTGGACCTGCACGGCACTCCCCGGCTGGAGTTCCACCAGTCGGTGTTTGACGAGCTGAGGGAGAAGCTGCTGGAGCGGGTCTCGGCCATCGCCTTGGAAGGGAAGGTGGAGGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000008532:ENSGALT00000013905:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.029 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGTACGCGGGGCTGCAG
R:
TCCTCCACCTTCCCTTCCAAG
Band lengths:
263-463
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]