BtaINT0031298 @ bosTau6
Intron Retention
Gene
ENSBTAG00000013239 | CAPN12
Description
Bos taurus calpain 12 (CAPN12), mRNA. [Source:RefSeq mRNA;Acc:NM_001192697]
Coordinates
chr18:48750281-48750757:-
Coord C1 exon
chr18:48750594-48750757
Coord A exon
chr18:48750511-48750593
Coord C2 exon
chr18:48750281-48750510
Length
83 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGG
5' ss Score
9.35
3' ss Seq
GTCTCTTTGTCCTTTCCTAGAAA
3' ss Score
9.45
Exon sequences
Seq C1 exon
GATGGAGCTGCTGGACTTCTTCCGCCACTTCGACACCATCCAGATCTGCTCGCTGAGCCCCGAGGTGCTAGGCCCCAGCCCGGCTGGAGGCGGCTGGCACATCCACACCTTCCAAGGCCGCTGGGTGCGCGGCTTCAACTCTGGCGGGAGCCAGCCTGGTGCCG
Seq A exon
GTGAGGCCTGAAGGGGGCCCCAAAGGCAAGGAGGGGTGGGGCTGTGGCAGGCTGGGTAACCCTGTCTCTTTGTCCTTTCCTAG
Seq C2 exon
AAACCTTCTGGACTAACCCCCAGTTCCGGCTGACGCTGCTGGAGCCTGATGAAGAGGATGAGGAAGAGGATGGGTCCTTGGGGTGCTGGGGGGCAGCAGGGGCACGGGGCCCCGCACGGGGTGCTCGCACCCCCAAATGCACTGTTCTCCTGTCACTCATCCAGCGCAACCAGCGGCGCCTGAGGGCCCAGGGCCTCAGATACCTGACCGTGGGCTTCCACGTGTTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000013239:ENSBTAT00000044705:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.018 A=NA C2=0.078
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=PD(6.3=33.9),PF0106717=Calpain_III=PU(13.7=42.9)
A:
NA
C2:
PF0106717=Calpain_III=FE(43.4=100)
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
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACTTCTTCCGCCACTTCGAC
R:
TGGGGGTTAGTCCAGAAGGTT
Band lengths:
173-256
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development