BtaINT0040557 @ 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
chr21:41957114-41958034:+
Coord C1 exon
chr21:41957114-41957340
Coord A exon
chr21:41957341-41957517
Coord C2 exon
chr21:41957518-41958034
Length
177 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAG
5' ss Score
9.06
3' ss Seq
TTATGTCTCTCTCCCATCAGGCT
3' ss Score
10.24
Exon sequences
Seq C1 exon
GAAAAGCCTTGAAGCATACCGCCCAGAAATTCTTCACAGCGGACACTGGAGCGAGGAAAGGGATTCCCAAAGTGGTGGTGGTGTTTATTGATGGCTGGCCTTCTGACGACATCGAGGAAGCAGGCATTGTGGCCAGAGAGTTTGGCGTCAATGTATTTATAGTTTCTGTGGCTAAGCCTATCCCTGAGGAACTGGGAATGGTTCAGGATGTTGCATTTGTTGACAAG
Seq A exon
GTAAAGAGTTGAGAGATGTCTTCTAATATAGTAGTGACTCAGTTTGGGACCTCAAGGGGTAGTGCTGACTGGCCCAGATCTGGATTAACTTTGAACACTCAAGATTTAACATTTTCATAATTTTAAAGAAACAACTTGTAATTCCTTTGGATATCTTTTATGTCTCTCTCCCATCAG
Seq C2 exon
GCTGTCTGTCGGAATAACGGCTTCTTCTCTTACCACATGCCCAATTGGTTTGGCACCACAAAATACGTAAAGCCTCTGGTACAGAAGCTCTGCACTCACGAGCAAATGATGTGCAGCAAGACCTGTTATAACTCAGTGAACATTGCCTTTCTGATCGATGGCTCCAGTAGTGTTGGAGAAAGTAATTTCCGCCTCATGCTTGAATTTGTTTCCAACATAGCTAAGACTTTTGAAATCTCAGACATTGGTGCCAAGATAGCAGCAGTACAGTTCACCTATGATCAGCGCACAGAGTTCAGTTTCACTGACTATAGCACCAAAGAGAATGTCCTAGCTGTTATCAGAAACATCAGCTACATGAGTGGTGGGACAGCTACTGGGGATGCCATTTCCTTTACTGTTAGAAATGTGTTTGGCCCGGTGAGAGACAGCCCCAACAAGAACTTCCTGGTAATAGTCACAGATGGGCAGTCCTATGACGACGTGCGAGGGCCTGCTGCTGCTGCACATGATGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021844:ENSBTAT00000053676:10
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:
PF0009223=VWA=FE(46.3=100)
A:
NA
C2:
PF0009223=VWA=PD(3.1=2.9),PF0009223=VWA=PU(72.8=72.8)
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:
CTGACGACATCGAGGAAGCAG
R:
GCTGCACATCATTTGCTCGTG
Band lengths:
242-419
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]