BtaINT0032419 @ bosTau6
Intron Retention
Gene
ENSBTAG00000008723 | CCBE1
Description
collagen and calcium binding EGF domains 1 [Source:HGNC Symbol;Acc:HGNC:29426]
Coordinates
chr24:58888057-58888312:-
Coord C1 exon
chr24:58888173-58888312
Coord A exon
chr24:58888093-58888172
Coord C2 exon
chr24:58888057-58888092
Length
80 bp
Sequences
Splice sites
5' ss Seq
GTGGTCAGT
5' ss Score
4.85
3' ss Seq
GAGGTCCCTTTGCCTTGTAGGGT
3' ss Score
8.23
Exon sequences
Seq C1 exon
GCTCACCAGGACCAAAGGGGAGCCCCGGCTTCCCAGGGATCCCAGGCCCCCCAGGGCAGCCTGGCCCGCGGGGCTCGATGGGACCCGTGGGACCATCTCCCGACCTGTCCCACATTAAGCAAGGCCGGAGGGGCCCTGTG
Seq A exon
GTCAGTATTTCACCAGCGCTTCCATCCGTGGTTGGGGAACGCGTGTGCCTTCTGCTAAACGAGGTCCCTTTGCCTTGTAG
Seq C2 exon
GGTCCGCCAGGCGCCCCAGGAAGAGATGGCTCTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000008723:ENSBTAT00000011491:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(66.7=72.3),PF0139113=Collagen=PU(20.5=17.0)
A:
NA
C2:
PF0139113=Collagen=FE(28.2=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:
CTCACCAGGACCAAAGGGGAG
R:
GAGCCATCTCTTCCTGGGGC
Band lengths:
171-251
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]