GgaINT0123736 @ galGal4
Intron Retention
Gene
ENSGALG00000008532 | COBRA1
Description
negative elongation factor B [Source:RefSeq peptide;Acc:NP_001006202]
Coordinates
chr17:1902106-1902973:+
Coord C1 exon
chr17:1902106-1902218
Coord A exon
chr17:1902219-1902870
Coord C2 exon
chr17:1902871-1902973
Length
652 bp
Sequences
Splice sites
5' ss Seq
GGGGTAAGG
5' ss Score
8.05
3' ss Seq
ACTTTTACCTCTTCTCTCAGGGA
3' ss Score
9.83
Exon sequences
Seq C1 exon
TTCACGTGGTGCCTTGATGCCTGCATTCGGGAGAAGTTTGTGGACAACAAGAGAGCTCGGGAATTGCAAGGCTTTCTGGATGGAGTGAAGAAAGGACAAGAGCAAGTTTTGGG
Seq A exon
GTAAGGTGCTTAGGGTCTTTATTGAGAGACTGCAAATTGGGTTCCAGTTGTCACAATATGTGACATACTTCAGGTGTTAATTCTTCCCTAAAACCAGCTAATTCTACATGGTCAAGTGCAGTAGGTTCAGCAACATTATTGCACTAGGGCATATTCAGGCACCTTCAGGTGAGATCTTGGTAGTGCTTCAGTTACCTTGAGTAATTGTTGCAGGTTTCTCTGGGACCTCATAACTGTGTGAGCTTTCCTATTTCATTTCAGCTCTAAAGACCTTTGGTAATTATTTTATTTGACTCGATAGAGCAGGTTATCTGAAATAACATTCATGATGTTTTGACAAAGGCAGGAGAAGGTTTGTGGAATGAAAACCTATAGGTAACAAAAGACAGAAATTTGAGTTTTATGTTACAATAGTTAAGGTATTGTTGCCCTTTAACACAGCAGTTTCTGGGTTTTTTGTTGATTTATTGCATGTACTACTTTGGCATTACATCTCATAGTTGACAGGATTACAGGATTACAACAGCGTGCTCTGTTCTGTGTTCAGTGAGACACATCTTAAGAAGCTAGTGTCCTACAGCTGGGTATGAAACTAGTCTGCTGCATTGTTTGTTAGGTGTGACATGTATTTGACTTTTACCTCTTCTCTCAG
Seq C2 exon
GGACTTATCGATGATCTTGTGTGATCCCTTTGCCATTAACACCTTAGCCCTGAGTACCATAAGGCACCTGCAGGACCTAGTTGGGCAGGACACCTTACCCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000008532:ENSGALT00000013905:6
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:
PF062098=COBRA1=FE(10.7=100)
A:
NA
C2:
PF062098=COBRA1=FE(7.2=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:
TTCACGTGGTGCCTTGATGC
R:
CTGGGTAAGGTGTCCTGCCC
Band lengths:
215-867
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]