BtaINT0040553 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021861 | COBRA1
Description
Uncharacterized protein [Source:UniProtKB/TrEMBL;Acc:G5E5S2]
Coordinates
chr11:105846601-105846944:-
Coord C1 exon
chr11:105846842-105846944
Coord A exon
chr11:105846697-105846841
Coord C2 exon
chr11:105846601-105846696
Length
145 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
AGGCCTGCATTTCCCTGCAGGAC
3' ss Score
8.82
Exon sequences
Seq C1 exon
GGACCTATCCATGATCCTGTGTGACCCCTTCGCCATCAACACCCTGTCTCTGAGCACCGTCAGGCACCTGCAGGAGCTGGTGGGCCAGGAGGTGCTACCCAGG
Seq A exon
GTGAGTGCCCCCGGCCAGCCGCACGCTGCCCTTGGGGAGCGTGTAGGGGTGACCCTGGGGTGAGCCCATGCCCCCTCCAGGCAGAGGGTGCGTGCGGTCAGGGCGGGACGCTGGGTGAGCCGCCGAGGCCTGCATTTCCCTGCAG
Seq C2 exon
GACAGCCCGGACCTCCTCCTGCTGCTCCGGCTGCTGGCGCTGGGCCAGGGTGCGTGGGACATGATCGACAGCCAGGTCTTCAAGGAGCCCAAGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021861:ENSBTAT00000029144:7
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(7.2=100)
A:
NA
C2:
PF062098=COBRA1=FE(6.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTATCCATGATCCTGTGTGACC
R:
TCTTGGGCTCCTTGAAGACCT
Band lengths:
194-339
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development