GgaINT0123732 @ galGal4
Intron Retention
Gene
ENSGALG00000008532 | COBRA1
Description
negative elongation factor B [Source:RefSeq peptide;Acc:NP_001006202]
Coordinates
chr17:1897631-1898081:+
Coord C1 exon
chr17:1897631-1897794
Coord A exon
chr17:1897795-1897981
Coord C2 exon
chr17:1897982-1898081
Length
187 bp
Sequences
Splice sites
5' ss Seq
AAGGTCTGT
5' ss Score
6.43
3' ss Seq
TTGGTTTTATGTGTTTTCAGGTA
3' ss Score
10
Exon sequences
Seq C1 exon
ACAGAAAATGGGGTCCTGCTGCCCTCGCTGCAGTCGGCCCTGCCCTTCCTGGACCTGCACGGCACTCCCCGGCTGGAGTTCCACCAGTCGGTGTTTGACGAGCTGAGGGAGAAGCTGCTGGAGCGGGTCTCGGCCATCGCCTTGGAAGGGAAGGTGGAGGAAAG
Seq A exon
GTCTGTAGGCTCGTTGGTTATTTGCGGTGAGCGGGGGATTTAATGTGAACATTATCTGCAGTGGGCAAGTGGCTTCTGAAAAAGACTTGAGTCTTCTGGAGGCTCAAGTTGTAGTGTTTGAGATGAGCCATTTTTGTCCTTTGCAGTTAAACGGTAGTTGGAGTCTCTTGGTTTTATGTGTTTTCAG
Seq C2 exon
GTACAAGAAGCTGGAAGATCTCCTGGAGAAAAGCTTTTCCTTGGTCAAGATGCCTTCCATACAGCCTGTGGTAATGTGTGTCATGAAGCACTTGCCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000008532:ENSGALT00000013905:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF062098=COBRA1=PU(3.4=47.1)
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:
ACAGAAAATGGGGTCCTGCTG
R:
ACACACATTACCACAGGCTGT
Band lengths:
245-432
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]