BtaINT0031283 @ bosTau6
Intron Retention
Gene
ENSBTAG00000013239 | CAPN12
Description
Bos taurus calpain 12 (CAPN12), mRNA. [Source:RefSeq mRNA;Acc:NM_001192697]
Coordinates
chr18:48748924-48749140:-
Coord C1 exon
chr18:48749098-48749140
Coord A exon
chr18:48748984-48749097
Coord C2 exon
chr18:48748924-48748983
Length
114 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGG
5' ss Score
7.61
3' ss Seq
TAAACTACCCAACCCCACAGGTC
3' ss Score
7.46
Exon sequences
Seq C1 exon
GGAGGTAGATGACGTGATCAGCGCCGACCTGCACGCCCTTATG
Seq A exon
GTGAGGCGCGGCTCTGGGAAAGGGGCGCTATGGTGTGTGTATGTGGGCGGGAGAGGCGGGGGAAGGGGACGGCGTGGAACTTCTTGGCCAGAAGTAAACTACCCAACCCCACAG
Seq C2 exon
GTCCCCTACATTCCCCTGGAGCTGGAGTTGCAGCAGCTTTTTCAGGAGCTGGCAGGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000013239:ENSBTAT00000044705:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0106717=Calpain_III=PD(0.1=0.0)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGGTAGATGACGTGATCAGC
R:
TCTCCTGCCAGCTCCTGAAAA
Band lengths:
102-216
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development