BtaINT0040549 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021861 | COBRA1
Description
Uncharacterized protein [Source:UniProtKB/TrEMBL;Acc:G5E5S2]
Coordinates
chr11:105849014-105849677:-
Coord C1 exon
chr11:105849578-105849677
Coord A exon
chr11:105849245-105849577
Coord C2 exon
chr11:105849014-105849244
Length
333 bp
Sequences
Splice sites
5' ss Seq
AAGGTAACA
5' ss Score
8.92
3' ss Seq
GTGGCCTGTGGGTTATGTAGGTT
3' ss Score
4.94
Exon sequences
Seq C1 exon
GTATAAGAAACTGGAGGACCTCCTGGAGAAGAGCTTTTCTCTGGTGAAGATGCCATCTCTGCAGCCGGTGGTGATGTGTGTCATGAAACACCTGCCCAAG
Seq A exon
GTAACAGCTGCCTGGCTGGCTCTCTCTGGGGAGGGTTCCTGGGCTGCCTGTTCCAGTAAAGACGGCTTCGGAGCACGGTTCCCTGCCCTGGCTTCTCCCTGAGCCAAGCAGACACTGAAGCTTGGCATGTGCTCCGGGGTGTGGAGCCCTTTCTGGGAAAAAGCTGTCTGTGGTTCCTGTCCATGCCACGGCCTGAGGGACTGGTCCCAGGTGTCCCCGTCAGTTGGGCTGGGCTGGATGTGGTCTCTGCTGTGGGGAAGCTGAGGCCTGCCAGTTGTCTGAGGGAGACCGTCGGGGCAGGGTGCTGCTGACGGTGGCCTGTGGGTTATGTAG
Seq C2 exon
GTTCCTGAGAAGAAGCTGAAGCTGGTGATGGCTGACAAGGAGCTGTACCGGGCCTGCGCAGTGGAGGTGAAGCGGCAGATTTGGCAGGACAACCAGGCGCTCTTTGGCGATGAGGTCTCCCCGCTGCTGAAGCAGTACATCGTGGAGAAGGAGAGCGCGCTCTTCAGCACGGAGCTCTCAGTCCTGCACAACTTTTTCAGCCCTTCCCCCAAGACCAGGCGCCAGGGTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021861:ENSBTAT00000029144:3
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=PU(3.4=47.1)
A:
NA
C2:
PF062098=COBRA1=FE(16.0=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:
GGACCTCCTGGAGAAGAGCTT
R:
CCTGGTCTTGGGGGAAGGG
Band lengths:
304-637
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development