GgaINT0123738 @ galGal4
Intron Retention
Gene
ENSGALG00000008532 | COBRA1
Description
negative elongation factor B [Source:RefSeq peptide;Acc:NP_001006202]
Coordinates
chr17:1903941-1904869:+
Coord C1 exon
chr17:1903941-1904036
Coord A exon
chr17:1904037-1904726
Coord C2 exon
chr17:1904727-1904869
Length
690 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGC
5' ss Score
8.27
3' ss Seq
TCTCCTTCCATCCCTCTAAGGAA
3' ss Score
8.3
Exon sequences
Seq C1 exon
GAAAGCCCAGATCTGCTGCTGCTCCTTAGGATGCTGTCTTTAGGACAGGGAGCCTGGGACATGATTGACAGTCAAGTCTTCAAGGAACCAAAAATG
Seq A exon
GTGAGCCTTCTTTAGATCTCTTTCTTATTTGATGCACATGGTGTGTCCCTGGTTTAATCTTCAAGTCAGCTTTCTGCATATTTTTCAACAAGAGCTTCCTTCAAAACAGCATGTAAATGGTCACTGTGCAGCAGCTCAAATGGGCACACTGTAAGCTTTGTGTACCTGTTTCATTTACATGGATGTCTGACCCTTACTGTTTCTAAGTTGAACTGTTCCTCTCTTAAATTCTTTAGCCTACTGTTCTGTAAATCTGATGCAGCACTGTGTTCTGTGGAGAGAAGATGCACATAAATATTTTCTCTTACTACTCTAACTATGCATTGATCTCTGTCAGTTTAGGGAATAAAGAAAATGATTTGTAATTGCTGTTAAAGGCAATGGTACCATCCTTAATGTGCAGTGCTTGCAGATCAGAAAACATCTCTTGGAAGAATTGCTACGTCATGGTCCAAAGAAATCATTTGAGCAGGACTAGGTGAAATACTGTTTTCCTCATTACCAGTGGATCTTGTGGAAGTTTCAAGAAGTTTGAAAGGAACTGGATGTCTGAAAGCTTGTTTTCATAAGCATGGGGTGGAGCTAGTAACATTGCCTCAGTATCTGTTATGGTGCTGTGGAATTATTAGATGGCGTGAACTGATTGATGAAAGCATTCTCCTTTTTCCTCTCTCCTTCCATCCCTCTAAG
Seq C2 exon
GAAGCTGAGTTGATCACGAAGTTCTTGCCTATGCTGATGTCCTTTGTGGTGGATGATCACACGTTCAATGTAGATCAGAAACTGCCCTCGGAGGAAAAGGGGCCGATTCCCTACCCCAGCACCATTCCTGAGGCTTTCACCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000008532:ENSGALT00000013905:8
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=0.042
Domain overlap (PFAM):
C1:
PF062098=COBRA1=FE(6.6=100)
A:
NA
C2:
PF062098=COBRA1=FE(10.0=100)
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:
GAAAGCCCAGATCTGCTGCTG
R:
TGGTGAAAGCCTCAGGAATGG
Band lengths:
238-928
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]