BtaINT0040564 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021844 | COCH
Description
Bos taurus coagulation factor C homolog, cochlin (Limulus polyphemus) (COCH), mRNA. [Source:RefSeq mRNA;Acc:NM_001077842]
Coordinates
chr21:41953334-41953624:+
Coord C1 exon
chr21:41953334-41953378
Coord A exon
chr21:41953379-41953476
Coord C2 exon
chr21:41953477-41953624
Length
98 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGT
5' ss Score
10.45
3' ss Seq
ATTTGTTTTGGTGTTCACAGACT
3' ss Score
8.13
Exon sequences
Seq C1 exon
GCAAACGACTAAAGAAAACACCAGAGAAGAAAACTGGCAATAAGG
Seq A exon
GTAAGTATCTGGATATCCACTTGGGAATATAACATTTTTTCTCTCTCTTTTCTTCTTCTTGAAACTGCTAATGGAAAGATTTGTTTTGGTGTTCACAG
Seq C2 exon
ACTGTAAAGCAGACATTGCATTTCTGATCGATGGAAGTTTTAATATTGGGCAACGCCGATTTAATCTACAGAAGAATTTTGTTGGGAAAGTGGCTCTAATGTTGGGAATTGGAACCGAAGGACCACACGTGGGCCTTGTTCAAGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021844:ENSBTAT00000053676:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.750 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0009223=VWA=PU(27.8=90.0)
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:
GCAAACGACTAAAGAAAACACCAGA
R:
GGTCCTTCGGTTCCAATTCCC
Band lengths:
169-267
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]